Advances in microbial physiology最新文献_第2页

Regulation of methylotrophy in Paracoccus denitrificans. 反硝化副球菌甲基化的调控。

Advances in microbial physiology Pub Date : 2025-01-01 Epub Date: 2025-08-05 DOI: 10.1016/bs.ampbs.2025.04.002

Trusha Parekh, Stephen Spiro

{"title":"Regulation of methylotrophy in Paracoccus denitrificans.","authors":"Trusha Parekh, Stephen Spiro","doi":"10.1016/bs.ampbs.2025.04.002","DOIUrl":"https://doi.org/10.1016/bs.ampbs.2025.04.002","url":null,"abstract":"Paracoccus denitrificans is a long-established model organism for studies of methylotrophy, the use of one-carbon compounds as sources of energy and carbon. P. denitrificans can use methanol and methylamine as growth substrates, oxidizing both to formaldehyde in the periplasm. Formaldehyde is oxidized to formate and then to carbon dioxide, which is assimilated into biomass via the Calvin cycle. Genes required for the oxidation of methanol, methylamine, formaldehyde and formate are typically expressed only under methylotrophic conditions or during growth on multi-carbon substrates (such as choline) the catabolism of which generates formaldehyde as a product of demethylation reactions. In this article, we review the pathways of methylotrophic metabolism and the proteins involved, before focusing on mechanisms of gene regulation. P. denitrificans has genes encoding calcium- and lanthanide-dependent methanol dehydrogenases. In other methylotrophs, expression of these enzymes is subject to reciprocal regulation according to the presence or absence of lanthanide ions in growth media. This regulatory phenomenon is referred to as the 'lanthanide switch'. We propose a model for the mechanism of the lanthanide switch in P. denitrificans, which extrapolates from relevant information in other methylotrophs and is consistent with prior literature.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"87 ","pages":"163-208"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Copper homeostasis in Streptococcus and Neisseria: Known knowns and unknown knowns. 铜在链球菌和奈瑟菌体内的稳态：已知的和未知的。

Advances in microbial physiology Pub Date : 2025-01-01 Epub Date: 2025-01-30 DOI: 10.1016/bs.ampbs.2024.11.001

Archie Howell, Safa Chogule, Karrera Y Djoko

引用次数: 0

A lysis less ordinary: The bacterial Type 10 Secretion System. 一个不太普通的酵解：细菌的10型分泌系统。

Advances in microbial physiology Pub Date : 2025-01-01 Epub Date: 2025-02-27 DOI: 10.1016/bs.ampbs.2025.02.002

Mechna Chowdhury, Phillip J Stansfeld, Frank Sargent

引用次数: 0

Multiple roles for iron in microbial physiology: Bacterial oxygen sensing by heme-based sensors. 铁在微生物生理学中的多重作用：基于血红素传感器的细菌氧传感。

Advances in microbial physiology Pub Date : 2025-01-01 Epub Date: 2024-12-14 DOI: 10.1016/bs.ampbs.2024.10.001

Artur Sergunin, Jakub Vávra, Dominik Pašek, Toru Shimizu, Markéta Martínková

{"title":"Multiple roles for iron in microbial physiology: Bacterial oxygen sensing by heme-based sensors.","authors":"Artur Sergunin, Jakub Vávra, Dominik Pašek, Toru Shimizu, Markéta Martínková","doi":"10.1016/bs.ampbs.2024.10.001","DOIUrl":"https://doi.org/10.1016/bs.ampbs.2024.10.001","url":null,"abstract":"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.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"86 ","pages":"257-329"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Nitrate reduction for survival in a nanomolar world, not the millimolar world of a laboratory. 硝酸还原是为了在纳摩尔环境中生存，而不是在实验室的毫摩尔环境中。

Advances in microbial physiology Pub Date : 2025-01-01 Epub Date: 2025-08-13 DOI: 10.1016/bs.ampbs.2025.07.005

J A Cole

{"title":"Nitrate reduction for survival in a nanomolar world, not the millimolar world of a laboratory.","authors":"J A Cole","doi":"10.1016/bs.ampbs.2025.07.005","DOIUrl":"https://doi.org/10.1016/bs.ampbs.2025.07.005","url":null,"abstract":"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.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"87 ","pages":"79-117"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of sulfidogenic members of the gut microbiota in human disease. 肠道微生物群中的硫化物生成成员在人类疾病中的作用。

Advances in microbial physiology Pub Date : 2024-01-01 Epub Date: 2024-05-28 DOI: 10.1016/bs.ampbs.2024.04.003

Andreia I Pimenta, Raquel M Bernardino, Inês A C Pereira

{"title":"Role of sulfidogenic members of the gut microbiota in human disease.","authors":"Andreia I Pimenta, Raquel M Bernardino, Inês A C Pereira","doi":"10.1016/bs.ampbs.2024.04.003","DOIUrl":"10.1016/bs.ampbs.2024.04.003","url":null,"abstract":"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.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"85 ","pages":"145-200"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The globins of cyanobacteria and green algae: An update. 蓝藻和绿藻的球蛋白：最新进展。

Advances in microbial physiology Pub Date : 2024-01-01 Epub Date: 2024-05-24 DOI: 10.1016/bs.ampbs.2024.04.004

Juliette T J Lecomte, Eric A Johnson

引用次数: 0

Preface. 序言

Advances in microbial physiology Pub Date : 2024-01-01 DOI: 10.1016/S0065-2911(24)00029-8

Robert K Poole, David J Kelly

引用次数: 0

Staphylococcus aureus response and adaptation to vancomycin. 金黄色葡萄球菌对万古霉素的反应和适应。

Advances in microbial physiology Pub Date : 2024-01-01 Epub Date: 2024-06-01 DOI: 10.1016/bs.ampbs.2024.04.006

Anaëlle Fait, Stephanie Fulaz Silva, Jack Åke Harry Abrahamsson, Hanne Ingmer

{"title":"Staphylococcus aureus response and adaptation to vancomycin.","authors":"Anaëlle Fait, Stephanie Fulaz Silva, Jack Åke Harry Abrahamsson, Hanne Ingmer","doi":"10.1016/bs.ampbs.2024.04.006","DOIUrl":"10.1016/bs.ampbs.2024.04.006","url":null,"abstract":"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.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"85 ","pages":"201-258"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protists: Eukaryotic single-celled organisms and the functioning of their organelles. 原生生物真核单细胞生物及其细胞器的功能。

Advances in microbial physiology Pub Date : 2024-01-01 Epub Date: 2024-03-16 DOI: 10.1016/bs.ampbs.2024.02.001

Nigel Yarlett, Edward L Jarroll, Mary Morada, David Lloyd

{"title":"Protists: Eukaryotic single-celled organisms and the functioning of their organelles.","authors":"Nigel Yarlett, Edward L Jarroll, Mary Morada, David Lloyd","doi":"10.1016/bs.ampbs.2024.02.001","DOIUrl":"10.1016/bs.ampbs.2024.02.001","url":null,"abstract":"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.","PeriodicalId":519928,"journal":{"name":"Advances in microbial physiology","volume":"84 ","pages":"243-307"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141185095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0