Advances in microbial physiology最新文献

Vitamins are indispensable cofactors that expand the chemical capabilities of enzymes beyond the inherent limitations of amino acid side chains. Among them, vitamin B₁₂ is particularly remarkable due to its exceptional structural complexity, the presence of a cobalt-centered corrin ring, and its exclusive biosynthetic origin in prokaryotes. This review explores the biosynthesis, transport, and biological significance of B₁₂, with an emphasis on the growing toolbox of synthetic analogues designed for research and therapeutic use. Recent advances in synthetic biology have enabled the complete heterologous expression of the aerobic B₁₂ biosynthesis pathway in Escherichia coli, facilitating the high-yield production of biosynthetic intermediates and cobalt-free B₁₂-precursors. These intermediates serve as platforms for the generation of metbalamins, metal-substituted cobalamin analogues incorporating rhodium, nickel, zinc, and other transition metals. In parallel, novel organo-antimetabolites and fluorescently labelled derivatives have been developed to probe B₁₂-dependent enzymes, trace vitamin transport in living systems, and selectively disrupt microbial or disease-linked metabolism. These synthetic analogues function as versatile tools for imaging, mechanistic dissection, and metabolic inhibition and more specifically in the case of molecules that counteract the physiological effects of vitamin B₁₂ in animal systems hold potential as antivitamins B₁₂. Collectively, they offer powerful new approaches to study nutrient trafficking, engineer cofactor interactions, and develop targeted antimicrobial or anticancer strategies. The review concludes by discussing future directions in applying engineering biology and chemical synthesis to further diversify and exploit the functional potential of the cobalamin scaffold.

Our research group studies copper (Cu) homeostasis in Streptococcus and Neisseria, with a current focus on species that colonise the human oral cavity. Our early ventures into this field very quickly revealed major differences between well-characterised Cu homeostasis systems in species with well-known pathogenic potential and the uncharacterised systems in species that are considered as components of the normal healthy human microflora. In this article, we summarise the known and predicted mechanisms of Cu homeostasis in Streptococcus and Neisseria. We focus exclusively on proteins that directly sense and change (increase or decrease) cellular Cu availability. Where relevant, we make comparisons with examples from species isolated from outside the human oral cavity and from animal hosts. The emerging picture depicts diverse cellular strategies for handling Cu, even among closely related bacterial species.

This review focuses on some of the persisting misconceptions and even errors in the literature of bacterial denitrification and the respiratory reduction of nitrate to ammonia. Both processes were traditionally investigated using pure culture laboratory techniques and substrate concentrations in the high micromolar or millimolar range. These concentrations are 1000-fold higher than those found in the nanomolar natural environments in which bacterial metabolism continues to evolve. Many of the enzymes involved in anaerobic nitrate reduction are metalloproteins that are easily inactivated by exposure to reactive oxygen and reactive nitrogen species. However, the metal centers of some of these proteins retain the ability to catalyze chemical reactions irrelevant to their physiological function. The review highlights some of the errors and misconceptions persisting in the literature, especially in the context of sensing, production and reduction of nitric oxide. It challenges many statements about physiological relevance. It demonstrates how knowledge of mechanisms that regulate gene transcription and mRNA translation provide clues to enzyme function. Four criteria are proposed to judge whether a protein-dependent reaction is physiologically relevant. They include whether (i) the protein is present in the correct cellular location; (ii) its synthesis is regulated in response to, or in preparation for, its proposed role; (iii) the catalytic efficiency is adequate to fulfil the need; and (iv) alternative enzymes are available that better meet the first three criteria. How errors become embedded in the literature, perpetuated and reinforced by annotation errors in genome databases are highlighted.

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.

Bacterial oxygen sensing embodies a fascinating interplay between evolutionary pressures and physiological adaptations to varying oxygen levels. Throughout Earth's history, the composition of the atmosphere has undergone significant changes, from anoxic conditions to the gradual accumulation of oxygen. In response, microbial life has evolved diverse strategies to cope with these shifting oxygen levels, ranging from anaerobic metabolism to oxygen-dependent pathways crucial for energy production and cellular processes typical for eukaryotic, multicellular organisms. Of particular interest is the role of iron in bacterial oxygen sensing systems, which play pivotal roles in adaptation to changing oxygen levels. Only free iron, heme-iron, and non-heme iron directly sense oxygen. These iron-containing proteins, such as heme-containing sensors and iron-sulfur cluster proteins, regulate the expression of genes and activity of enzymes involved in oxidative stress defence, virulence, and biofilm formation, highlighting their significance in bacterial pathogenesis and environmental adaptation. Special attention in the review is paid to the mechanisms of oxygen detection and signal transduction from heme-containing sensing to functional domains in the case of bacterial heme-based oxygen sensors.

The human gut flora comprises a dynamic network of bacterial species that coexist in a finely tuned equilibrium. The interaction with intestinal bacteria profoundly influences the host's development, metabolism, immunity, and overall health. Furthermore, dysbiosis, a disruption of the gut microbiota, can induce a variety of diseases, not exclusively associated with the intestinal tract. The increased consumption of animal protein, high-fat and high-sugar diets in Western countries has been implicated in the rise of chronic and inflammatory illnesses associated with dysbiosis. In particular, this diet leads to the overgrowth of sulfide-producing bacteria, known as sulfidogenic bacteria, which has been linked to inflammatory bowel diseases and colorectal cancer, among other disorders. Sulfidogenic bacteria include sulfate-reducing bacteria (Desulfovibrio spp.) and Bilophila wadsworthia among others, which convert organic and inorganic sulfur compounds to sulfide through the dissimilatory sulfite reduction pathway. At high concentrations, sulfide is cytotoxic and disrupts the integrity of the intestinal epithelium and mucus barrier, triggering inflammation. Besides producing sulfide, B. wadsworthia has revealed significant pathogenic potential, demonstrated in the ability to cause infection, adhere to intestinal cells, promote inflammation, and compromise the integrity of the colonic mucus layer. This review delves into the mechanisms by which taurine and sulfide-driven gut dysbiosis contribute to the pathogenesis of sulfidogenic bacteria, and discusses the role of these gut microbes, particularly B. wadsworthia, in human diseases.

The globin superfamily of proteins is ancient and diverse. Regular assessments based on the increasing number of available genome sequences have elaborated on a complex evolutionary history. In this review, we present a summary of a decade of advances in characterising the globins of cyanobacteria and green algae. The focus is on haem-containing globins with an emphasis on recent experimental developments, which reinforce links to nitrogen metabolism and nitrosative stress response in addition to dioxygen management. Mention is made of globins that do not bind haem to provide an encompassing view of the superfamily and perspective on the field. It is reiterated that an effort toward phenotypical and in-vivo characterisation is needed to elucidate the many roles that these versatile proteins fulfil in oxygenic photosynthetic microbes. It is also proposed that globins from oxygenic organisms are promising proteins for applications in the biotechnology arena.

Antibiotic resistance is an increasing challenge for the human pathogen Staphylococcus aureus. Methicillin-resistant S. aureus (MRSA) clones have spread globally, and a growing number display decreased susceptibility to vancomycin, the favoured antibiotic for treatment of MRSA infections. These vancomycin-intermediate S. aureus (VISA) or heterogeneous vancomycin-intermediate S. aureus (hVISA) strains arise from accumulation of a variety of point mutations, leading to cell wall thickening and reduced vancomycin binding to the cell wall building block, Lipid II, at the septum. They display only minor changes in vancomycin susceptibility, with varying tolerance between cells in a population, and therefore, they can be difficult to detect. In this review, we summarize current knowledge of VISA and hVISA. We discuss the role of genetic strain background or epistasis for VISA development and the possibility of strains being 'transient' VISA with gene expression changes mediated by, for example, VraTSR, GraXSR, or WalRK signal transduction systems, leading to temporary vancomycin tolerance. Additionally, we address collateral susceptibility to other antibiotics than vancomycin. Specifically, we estimate how mutations in rpoB, encoding the β-subunit of the RNA polymerase, affect overall protein structure and compare changes with rifampicin resistance. Ultimately, such in-depth analysis of VISA and hVISA strains in terms of genetic and transcriptional changes, as well as changes in protein structures, may pave the way for improved detection and guide antibiotic therapy by revealing strains at risk of VISA development. Such tools will be valuable for keeping vancomycin an asset also in the future.

Organelles are membrane bound structures that compartmentalize biochemical and molecular functions. With improved molecular, biochemical and microscopy tools the diversity and function of protistan organelles has increased in recent years, providing a complex panoply of structure/function relationships. This is particularly noticeable with the description of hydrogenosomes, and the diverse array of structures that followed, having hybrid hydrogenosome/mitochondria attributes. These diverse organelles have lost the major, at one time, definitive components of the mitochondrion (tricarboxylic cycle enzymes and cytochromes), however they all contain the machinery for the assembly of Fe-S clusters, which is the single unifying feature they share. The plasticity of organelles, like the mitochondrion, is therefore evident from its ability to lose its identity as an aerobic energy generating powerhouse while retaining key ancestral functions common to both aerobes and anaerobes. It is interesting to note that the apicoplast, a non-photosynthetic plastid that is present in all apicomplexan protozoa, apart from Cryptosporidium and possibly the gregarines, is also the site of Fe-S cluster assembly proteins. It turns out that in Cryptosporidium proteins involved in Fe-S cluster biosynthesis are localized in the mitochondrial remnant organelle termed the mitosome. Hence, different organisms have solved the same problem of packaging a life-requiring set of reactions in different ways, using different ancestral organelles, discarding what is not needed and keeping what is essential. Don't judge an organelle by its cover, more by the things it does, and always be prepared for surprises.