Microbiology and molecular biology reviews : MMBR最新文献

Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. 关于RNA结构在SARS-CoV-2复制中的重要性的经验教训和有待吸取的教训。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2022-09-21 Epub Date: 2022-07-07 DOI: 10.1128/mmbr.00057-21

Maclean Bassett, Marco Salemi, Brittany Rife Magalis

{"title":"Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.","authors":"Maclean Bassett, Marco Salemi, Brittany Rife Magalis","doi":"10.1128/mmbr.00057-21","DOIUrl":"https://doi.org/10.1128/mmbr.00057-21","url":null,"abstract":"SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in \"long COVID\" patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"e0005721"},"PeriodicalIF":12.9,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40542591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis. 担子菌性子实体的进化形态发生：一种新的进化- devo合成。

Microbiology and molecular biology reviews : MMBR Pub Date : 2022-03-16 Epub Date: 2021-11-24 DOI: 10.1128/MMBR.00019-21

Máté Virágh, Zsolt Merényi, Árpád Csernetics, Csenge Földi, Neha Sahu, Xiao-Bin Liu, David S Hibbett, László G Nagy

{"title":"Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis.","authors":"Máté Virágh, Zsolt Merényi, Árpád Csernetics, Csenge Földi, Neha Sahu, Xiao-Bin Liu, David S Hibbett, László G Nagy","doi":"10.1128/MMBR.00019-21","DOIUrl":"10.1128/MMBR.00019-21","url":null,"abstract":"The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"e0001921"},"PeriodicalIF":0.0,"publicationDate":"2022-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8612260/pdf/mmbr.00019-21.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39907356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Regulation of Bacterial Gene Expression by Transcription Attenuation. 转录衰减对细菌基因表达的调控。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2019-07-03 Print Date: 2019-08-21 DOI: 10.1128/MMBR.00019-19

Charles L Turnbough

引用次数: 35

What a difference a Dalton makes: bacterial virulence factors modulate eukaryotic host cell signaling systems via deamidation. 道尔顿带来了多么大的不同：细菌毒力因子通过脱酰胺调节真核宿主细胞信号系统。

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00013-13

Erica J Washington, Mark J Banfield, Jeffery L Dangl

{"title":"What a difference a Dalton makes: bacterial virulence factors modulate eukaryotic host cell signaling systems via deamidation.","authors":"Erica J Washington, Mark J Banfield, Jeffery L Dangl","doi":"10.1128/MMBR.00013-13","DOIUrl":"10.1128/MMBR.00013-13","url":null,"abstract":"Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"527-39"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811613/pdf/zmr527.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31708771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pathogenesis of human enterovirulent bacteria: lessons from cultured, fully differentiated human colon cancer cell lines. 人类肠道毒力细菌的发病机制:来自培养的、完全分化的人类结肠癌细胞系的教训。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00064-12

Vanessa Liévin-Le Moal, Alain L Servin

{"title":"Pathogenesis of human enterovirulent bacteria: lessons from cultured, fully differentiated human colon cancer cell lines.","authors":"Vanessa Liévin-Le Moal, Alain L Servin","doi":"10.1128/MMBR.00064-12","DOIUrl":"https://doi.org/10.1128/MMBR.00064-12","url":null,"abstract":"Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"380-439"},"PeriodicalIF":12.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.00064-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31709209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 60

Type IV pili in Gram-positive bacteria. 革兰氏阳性菌中的IV型菌毛。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00063-12

Stephen Melville, Lisa Craig

{"title":"Type IV pili in Gram-positive bacteria.","authors":"Stephen Melville, Lisa Craig","doi":"10.1128/MMBR.00063-12","DOIUrl":"https://doi.org/10.1128/MMBR.00063-12","url":null,"abstract":"Type IV pili (T4P) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, DNA uptake (competence), and protein secretion and that can act as nanowires carrying electric current. T4P are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type II secretion systems in eubacteria and the flagella of archaea. T4P are found throughout Gram-negative bacterial families and have been studied most extensively in certain model Gram-negative species. Recently, it was discovered that T4P systems are also widespread among Gram-positive species, in particular the clostridia. Since Gram-positive and Gram-negative bacteria have many differences in cell wall architecture and other features, it is remarkable how similar the T4P core proteins are between these organisms, yet there are many key and interesting differences to be found as well. In this review, we compare the two T4P systems and identify and discuss the features they have in common and where they differ to provide a very broad-based view of T4P systems across all eubacterial species.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"323-41"},"PeriodicalIF":12.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.00063-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31709348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 173

Ecology, diversity, and evolution of magnetotactic bacteria. 趋磁细菌的生态学、多样性和进化。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00021-13

Christopher T Lefèvre, Dennis A Bazylinski

{"title":"Ecology, diversity, and evolution of magnetotactic bacteria.","authors":"Christopher T Lefèvre, Dennis A Bazylinski","doi":"10.1128/MMBR.00021-13","DOIUrl":"https://doi.org/10.1128/MMBR.00021-13","url":null,"abstract":"Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"497-526"},"PeriodicalIF":12.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.00021-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31708770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 313

Patterns and processes of microbial community assembly. 微生物群落组装的模式和过程。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00051-12

Diana R Nemergut, Steven K Schmidt, Tadashi Fukami, Sean P O'Neill, Teresa M Bilinski, Lee F Stanish, Joseph E Knelman, John L Darcy, Ryan C Lynch, Phillip Wickey, Scott Ferrenberg

{"title":"Patterns and processes of microbial community assembly.","authors":"Diana R Nemergut, Steven K Schmidt, Tadashi Fukami, Sean P O'Neill, Teresa M Bilinski, Lee F Stanish, Joseph E Knelman, John L Darcy, Ryan C Lynch, Phillip Wickey, Scott Ferrenberg","doi":"10.1128/MMBR.00051-12","DOIUrl":"https://doi.org/10.1128/MMBR.00051-12","url":null,"abstract":"Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183-206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"342-56"},"PeriodicalIF":12.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.00051-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31709349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1101

The TetR family of regulators. TetR家族监管机构。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2013-09-01 DOI: 10.1128/MMBR.00018-13

Leslie Cuthbertson, Justin R Nodwell

{"title":"The TetR family of regulators.","authors":"Leslie Cuthbertson, Justin R Nodwell","doi":"10.1128/MMBR.00018-13","DOIUrl":"https://doi.org/10.1128/MMBR.00018-13","url":null,"abstract":"The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"440-75"},"PeriodicalIF":12.9,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.00018-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31709351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 372

The multiple signaling systems regulating virulence in Pseudomonas aeruginosa. 铜绿假单胞菌毒力调控的多重信号系统。

IF 12.9

Microbiology and molecular biology reviews : MMBR Pub Date : 2012-03-01 DOI: 10.1128/MMBR.05007-11

Pol Nadal Jimenez, Gudrun Koch, Jessica A Thompson, Karina B Xavier, Robbert H Cool, Wim J Quax

{"title":"The multiple signaling systems regulating virulence in Pseudomonas aeruginosa.","authors":"Pol Nadal Jimenez, Gudrun Koch, Jessica A Thompson, Karina B Xavier, Robbert H Cool, Wim J Quax","doi":"10.1128/MMBR.05007-11","DOIUrl":"https://doi.org/10.1128/MMBR.05007-11","url":null,"abstract":"Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.","PeriodicalId":333299,"journal":{"name":"Microbiology and molecular biology reviews : MMBR","volume":" ","pages":"46-65"},"PeriodicalIF":12.9,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1128/MMBR.05007-11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40140156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 622