Microbial Physiology最新文献

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Assembly of Bacillus subtilis Dynamin into Membrane-Protective Structures in Response to Environmental Stress Is Mediated by Moderate Changes in Dynamics at a Single Molecule Level 枯草芽孢杆菌Dynamin在环境胁迫下组装成膜保护结构是由单分子水平上的适度动力学变化介导的
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-03-10 DOI: 10.1159/000521585
Laura Sattler, P. Graumann
{"title":"Assembly of Bacillus subtilis Dynamin into Membrane-Protective Structures in Response to Environmental Stress Is Mediated by Moderate Changes in Dynamics at a Single Molecule Level","authors":"Laura Sattler, P. Graumann","doi":"10.1159/000521585","DOIUrl":"https://doi.org/10.1159/000521585","url":null,"abstract":"Dynamin-like proteins are membrane-associated GTPases, conserved in bacteria and in eukaryotes, that can mediate nucleotide-driven membrane deformation or membrane fusion reactions. Bacillus subtilis’ DynA has been shown to play an important role in protecting cells against chemicals that induce membrane leakage, and to form an increased number of membrane-associated structures after induction of membrane stress. We have studied the dynamics of DynA at a single molecule level in real time, to investigate how assembly of stress-induced structures is accompanied by changes in molecule dynamics. We show that DynA molecule displacements are best described by the existence of three distinct populations, a static mode, a low-mobility, and a fast-mobile state. Thus, DynA is most likely freely diffusive within the cytosol, moves along the cell membrane with a low mobility, and arrests at division sites or at stress-induced lesions at the membrane. In response to stress-inducing membrane leakage, but not to general stress, DynA molecules become slightly more static, but largely retain their mobility, suggesting that only few molecules are involved in the repair of membrane lesions, while most molecules remain in a dynamic mode scanning for lesions. Our data suggest that even moderate changes in single molecule dynamics can lead to visible changes in protein localization patterns.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"57 - 70"},"PeriodicalIF":3.9,"publicationDate":"2022-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43465794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Heterogeneity of Subcellular Diffusion in Bacteria Based on Spatial Segregation of Ribosomes and Nucleoids. 基于核糖体和类核空间分离的细菌亚细胞扩散异质性。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 DOI: 10.1159/000526846
Simon Dersch, Daniel A O Rotter, Peter L Graumann
{"title":"Heterogeneity of Subcellular Diffusion in Bacteria Based on Spatial Segregation of Ribosomes and Nucleoids.","authors":"Simon Dersch,&nbsp;Daniel A O Rotter,&nbsp;Peter L Graumann","doi":"10.1159/000526846","DOIUrl":"https://doi.org/10.1159/000526846","url":null,"abstract":"<p><p>It has long become clear that in spite of generally lacking internal membrane systems, bacteria contain well-structured subcellular structures of usually filamentous proteins, and a preferred 3D arrangement of their chromosome(s). Some of these systems are set up by so-called cytoskeletal elements, or by polar landmark proteins, but the mechanism of specific localization is still unclear in most cases. Intriguingly, apart from such spatially organizing systems, the bacterial cytoplasm has unusual properties in terms of the diffusion of molecules, which varies between different sites within the cell. In many bacteria, chromosomes are compacted into centrally located nucleoids, being orderly folded as opposed to consisting of random coils of DNA. In these bacteria, there is a separation of transcription and translation, such that transcription by RNA polymerase occurs on the nucleoids, and translation takes place mostly at the cell poles and directly underneath the cell membrane, because 70S ribosomes accumulate at sites surrounding the nucleoids. Interestingly, accumulation of ribosomes appears to slow down diffusion of enzymes, noticeable for larger enzyme complexes, while nucleoids provide areas of confined motion for DNA-binding proteins, yet acceleration zones for non-DNA-binding proteins. Crowded regions at the cell poles set up zones of higher concentration of the translation machinery, shortening diffusion distances for rate-limiting translation factor/ribosome interactions, and of metabolic enzymes, possibly speeding up pathways containing low concentrations of metabolites. Thus, heterogeneous diffusion adds another layer of subcellular organization on top of cytoskeletal elements.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 5-6","pages":"177-186"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9827431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10516041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes. CRISPR-Cas系统:原核生物辅助基因组的强大调节剂。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 Epub Date: 2021-06-30 DOI: 10.1159/000516643
Anca Butiuc-Keul, Anca Farkas, Rahela Carpa, Dumitrana Iordache
{"title":"CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes.","authors":"Anca Butiuc-Keul,&nbsp;Anca Farkas,&nbsp;Rahela Carpa,&nbsp;Dumitrana Iordache","doi":"10.1159/000516643","DOIUrl":"https://doi.org/10.1159/000516643","url":null,"abstract":"<p><p>Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system&apos;s impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"2-17"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000516643","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39124540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily. 磷蛋白/SIMP/病毒蛋白超家族的发现与表征。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 DOI: 10.1159/000521947
Daniel Tyler, Kevin J Hendargo, Arturo Medrano-Soto, Milton H Saier
{"title":"Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily.","authors":"Daniel Tyler,&nbsp;Kevin J Hendargo,&nbsp;Arturo Medrano-Soto,&nbsp;Milton H Saier","doi":"10.1159/000521947","DOIUrl":"https://doi.org/10.1159/000521947","url":null,"abstract":"Using bioinformatic approaches, we present evidence of distant relatedness among the Ephemerovirus Viroporin family, the Rhabdoviridae Putative Viroporin U5 family, the Phospholemman family, and the Small Integral Membrane Protein family. Our approach is based on the transitivity property of homology complemented with five validation criteria: (1) significant sequence similarity and alignment coverage, (2) compatibility of topology of transmembrane segments, (3) overlap of hydropathy profiles, (4) conservation of protein domains, and (5) conservation of sequence motifs. Our results indicate that Pfam protein domains PF02038 and PF15831 can be found in or projected onto members of all four families. In addition, we identified a 26-residue motif conserved across the superfamily. This motif is characterized by hydrophobic residues that help anchor the protein to the membrane and charged residues that constitute phosphorylation sites. In addition, all members of the four families with annotated function are either responsible for or affect the transport of ions into and/or out of the cell. Taken together, these results justify the creation of the novel Phospholemman/SIMP/Viroporin superfamily. Given that transport proteins can be found not just in cells, but also in viruses, the ability to relate viroporin protein families with their eukaryotic and bacterial counterparts is an important development in this superfamily.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 3-4","pages":"83-94"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355910/pdf/nihms-1773163.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10748046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Genome Reduction Excludes the Ribosomal Rescue System in Acholeplasmataceae. 麦草科植物基因组还原不包括核糖体拯救系统。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 Epub Date: 2022-01-31 DOI: 10.1159/000520450
Christina Zübert, Anna-Marie Ilic, Bojan Duduk, Michael Kube
{"title":"The Genome Reduction Excludes the Ribosomal Rescue System in Acholeplasmataceae.","authors":"Christina Zübert,&nbsp;Anna-Marie Ilic,&nbsp;Bojan Duduk,&nbsp;Michael Kube","doi":"10.1159/000520450","DOIUrl":"https://doi.org/10.1159/000520450","url":null,"abstract":"<p><p>The trans-translation process is a ribosomal rescue system for stalled ribosomes processing truncated mRNA. The genes ssrA and smpB fulfil the key functions in most bacteria, but some species have either lost these genes or the function of the ribosomal rescue system is taken over by other genes. To date, the ribosomal rescue system has not been analysed in detail for the Acholeplasmataceae. This family, in the Mollicutes class, comprises the genus Acholeplasma and the provisional taxon \"Candidatus Phytoplasma\". Despite their monophyletic origin, the two clades can be separated by traits such as not representing primary pathogens for acholeplasmas versus being phytopathogenic for the majority of phytoplasmas. Both taxa share reduced genomes, but only phytoplasma genomes are characterised by a remarkable level of instability and reduction. Despite the general relevance of the ribosomal rescue system, information is lacking on coding, the genomic context and pseudogenisation of smpB and ssrA and their possible application as a phylogenetic marker. Herein, we provide a comprehensive analysis of the ribosomal rescue system in members of Acholeplasmataceae. The examined Acholeplasmataceae genomes encode a ribosomal rescue system, which depends on tmRNA encoded by ssrA acting in combination with its binding protein SmpB. Conserved gene synteny is evident for smpB, while ssrA shows a less conserved genomic context. Analysis of the tmRNA sequences highlights the variability of proteolysis tag sequences and short conserved sites at the 5'- and 3'-ends. Analyses of smpB provided no hints regarding the coding of pseudogenes, but they did suggest its application as a phylogenetic marker of Acholeplasmataceae - in accordance with 16S rDNA topology. Sequence variability of smpB provides sufficient information for species assignment and phylogenetic analysis.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"45-56"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39737617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Migration of Polyphosphate Granules in Agrobacterium tumefaciens. 农杆菌中多磷酸盐颗粒的迁移。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 Epub Date: 2022-02-15 DOI: 10.1159/000521970
Celina Frank, Daniel Pfeiffer, Meriyem Aktas, Dieter Jendrossek
{"title":"Migration of Polyphosphate Granules in Agrobacterium tumefaciens.","authors":"Celina Frank,&nbsp;Daniel Pfeiffer,&nbsp;Meriyem Aktas,&nbsp;Dieter Jendrossek","doi":"10.1159/000521970","DOIUrl":"https://doi.org/10.1159/000521970","url":null,"abstract":"<p><p>Agrobacterium tumefaciens has two polyphosphate (polyP) kinases, one of which (PPK1AT) is responsible for the formation of polyP granules, while the other (PPK2AT) is used for replenishing the NTP pools by using polyP as a phosphate donor to phosphorylate nucleoside diphosphates. Fusions of eYFP with PPK2AT or of the polyP granule-associated phosin PptA from Ralstonia eutropha always co-localized with polyP granules in A. tumefaciens and allowed the tracking of polyP granules in time-lapse microscopy experiments without the necessity to label the cells with the toxic dye DAPI. Fusions of PPK1AT with mCherry formed fluorescent signals often attached to, but not completely co-localizing with, polyP granules in wild-type cells. Time-lapse microscopy revealed that polyP granules in about one-third of a cell population migrated from the old pole to the new cell pole shortly before or during cell division. Many cells de novo formed a second (nonmigrating) polyP granule at the opposite cell pole before cell division was completed, resulting in two daughter cells each having a polyP granule at the old pole after septum formation. Migration of polyP granules was disordered in mitomycin C-treated or in PopZ-depleted cells, suggesting that polyP granules can associate with DNA or with other molecules that are segregated during the cell cycle.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"71-82"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39926448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring. 模型革兰氏阴性菌对基因组重组反应的生理稳健性。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 Epub Date: 2022-08-30 DOI: 10.1159/000526651
Charles J Dorman, Matthew J Dorman
{"title":"Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring.","authors":"Charles J Dorman,&nbsp;Matthew J Dorman","doi":"10.1159/000526651","DOIUrl":"https://doi.org/10.1159/000526651","url":null,"abstract":"<p><p>DNA supercoiling and nucleoid-associated proteins (NAPs) are two of the factors that govern the architecture of the bacterial genome, influencing the expression of the genetic information that it contains. Alterations to DNA topology, and to the numbers and types of NAPs, have pleiotropic effects on gene expression, suggesting that modifications to the production patterns of DNA topoisomerases and/or NAPs are likely to result in marked impacts on bacterial physiology. Knockout mutations in the genes encoding these proteins (where the mutants remain viable) result in clear physiological effects. However, genetic modifications that involve rewiring, or repositioning, of topoisomerase or NAP genes produce much more subtle outcomes. These findings demonstrate that the high-level regulatory circuitry of bacteria is robust in the face of genomic rearrangements that, a priori, might be expected to produce significant changes in bacterial lifestyle. Examples from genomic rewiring experiments, performed chiefly with the Gram-negative model bacteria Escherichia coli K-12 and Salmonella enterica serovar Typhimurium, will be used to illustrate these features. The results show not only the ability of naturally occurring bacteria to tolerate regulatory rewiring but also indicate the limits within which experiments in synthetic biology may be designed.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"158-176"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40331489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. 9种双歧杆菌基因组中转运蛋白编码的比较分析。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 DOI: 10.1159/000518954
Hassan Zafar, Milton H Saier
{"title":"Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species.","authors":"Hassan Zafar,&nbsp;Milton H Saier","doi":"10.1159/000518954","DOIUrl":"https://doi.org/10.1159/000518954","url":null,"abstract":"<p><p>The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1-2","pages":"30-44"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8940750/pdf/nihms-1740931.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10804740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene. 利用16S rRNA基因测序研究华南虎幼崽粪便微生物区系的定植与发育
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2022-01-01 Epub Date: 2021-09-14 DOI: 10.1159/000518395
Yanfa Sun, Jie Yao, Min Zhang, Tengteng Chen, Weihua Xu, Wenyuan Fu, Qiong Wu, Yan Li, Xingxing Chen, Yuting Zhu, Xuemei Zhang, Lingyu Liu, Donghong Chen, Zhenyuan Wang, Zhangjing You, Xuebing Zhang, Yi Liu, Kaixiong Lin, Weiming Lin
{"title":"Colonization and Development of the Fecal Microflora of South China Tiger Cubs (Panthera tigris amoyensis) by Sequencing of the 16S rRNA Gene.","authors":"Yanfa Sun,&nbsp;Jie Yao,&nbsp;Min Zhang,&nbsp;Tengteng Chen,&nbsp;Weihua Xu,&nbsp;Wenyuan Fu,&nbsp;Qiong Wu,&nbsp;Yan Li,&nbsp;Xingxing Chen,&nbsp;Yuting Zhu,&nbsp;Xuemei Zhang,&nbsp;Lingyu Liu,&nbsp;Donghong Chen,&nbsp;Zhenyuan Wang,&nbsp;Zhangjing You,&nbsp;Xuebing Zhang,&nbsp;Yi Liu,&nbsp;Kaixiong Lin,&nbsp;Weiming Lin","doi":"10.1159/000518395","DOIUrl":"https://doi.org/10.1159/000518395","url":null,"abstract":"<p><p>Postnatal colonization and development of the gut microbiota is linked to health and growth. A comprehensive understanding of the postnatal compositional changes and development of the microbial community is helpful to understand the gut health and improve the survival rate of South China tiger cubs (Panthera tigris amoyensis). Fecal samples from three tiger cubs were collected on the day of birth in 2018 (June 17-21 [G0], July 18 [G1], July 31 [G2], and August 7 [G3]). The 16S rRNA genes of the fecal microflora were sequenced. Results showed that 38 phyla, 58 classes, 134 orders, 272 families, and 636 genera of bacteria from 3,059 operational taxonomic units were identified from 12 fecal samples. The diversity and abundance of species of group G0 were significantly higher (p < 0.05 or 0.01) than those of groups G2 and G3. The predominant phylum was Proteobacteria in groups G0 and G1 (38.85% and 48%, respectively) and Firmicutes in groups G2 and G3 (71.42% and 75.29%, respectively). At the phylum level, the abundance of Deinococcus-Thermus was significantly decreased in groups G1, G2, and G3 as compared to group G0 (p < 0.05), while that of Firmicutes was significantly increased in groups G2 and G3 (p < 0.05). At the genus level, the abundance of Faecalibacterium, Ralstonia, and unidentified Rickettsiales was significantly decreased in groups G1, G2, and G3 as compared with group G0 (p < 0.05), while that of Pseudomonas was significantly decreased in groups G2 and G3 (p < 0.05). The composition and structure of fecal microbiota of South China tiger cubs changed after birth.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"18-29"},"PeriodicalIF":3.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39427267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. 对海洋硫酸盐还原丝状脱硫浮游动物(Desulfonema limicola)和脱硫浮游动物(Desulfonema magnum)生理学的蛋白质基因组学见解。
IF 3.9 4区 生物学
Microbial Physiology Pub Date : 2021-02-19 DOI: 10.1159/000513383
Vanessa Schnaars, Lars Wöhlbrand, Sabine Scheve, Christina Hinrichs, Richard Reinhardt, Ralf Rabus
{"title":"Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum.","authors":"Vanessa Schnaars, Lars Wöhlbrand, Sabine Scheve, Christina Hinrichs, Richard Reinhardt, Ralf Rabus","doi":"10.1159/000513383","DOIUrl":"10.1159/000513383","url":null,"abstract":"<p><p>The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"1-20"},"PeriodicalIF":3.9,"publicationDate":"2021-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25388770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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