Microbial PhysiologyPub Date : 2023-01-01Epub Date: 2023-06-15DOI: 10.1159/000531468
Kevin J Hendargo, Ashay O Patel, Onyeka S Chukwudozie, Gabriel Moreno-Hagelsieb, J Andres Christen, Arturo Medrano-Soto, Milton H Saier
{"title":"Sequence Similarity among Structural Repeats in the Piezo Family of Mechanosensitive Ion Channels.","authors":"Kevin J Hendargo, Ashay O Patel, Onyeka S Chukwudozie, Gabriel Moreno-Hagelsieb, J Andres Christen, Arturo Medrano-Soto, Milton H Saier","doi":"10.1159/000531468","DOIUrl":"10.1159/000531468","url":null,"abstract":"<p><p>Members of the Piezo family of mechanically activated cation channels are involved in multiple physiological processes in higher eukaryotes, including vascular development, cell differentiation, touch perception, hearing, and more, but they are also common in single-celled eukaryotic microorganisms. Mutations in these proteins in humans are associated with a variety of diseases, such as colorectal adenomatous polyposis, dehydrated hereditary stomatocytosis, and hereditary xerocytosis. Available 3D structures for Piezo proteins show nine regions of four transmembrane segments each that have the same fold. Despite the remarkable similarity among the nine characteristic structural repeats in the family, no significant sequence similarity among them has been reported. Using bioinformatics approaches and the Transporter Classification Database (TCDB) as reference, we reliably identified sequence similarity among repeats based on four lines of evidence: (1) hidden Markov model-profile similarities across repeats at the family level, (2) pairwise sequence similarities between different repeats across Piezo homologs, (3) Piezo-specific conserved sequence signatures that consistently identify the same regions across repeats, and (4) conserved residues that maintain the same orientation and location in 3D space.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"49-62"},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9639934","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}
Microbial PhysiologyPub Date : 2023-01-01Epub Date: 2023-03-21DOI: 10.1159/000530228
Aristide Laurel Mokale Kognou, Chonlong Chio, Janak Raj Khatiwada, Sarita Shrestha, Xuantong Chen, Yuen Zhu, Rosalie Anne Ngono Ngane, Gabriel Agbor Agbor, Zi-Hua Jiang, Chunbao Charles Xu, Wensheng Qin
{"title":"Characterization of Potential Virulence, Resistance to Antibiotics and Heavy Metals, and Biofilm-Forming Capabilities of Soil Lignocellulolytic Bacteria.","authors":"Aristide Laurel Mokale Kognou, Chonlong Chio, Janak Raj Khatiwada, Sarita Shrestha, Xuantong Chen, Yuen Zhu, Rosalie Anne Ngono Ngane, Gabriel Agbor Agbor, Zi-Hua Jiang, Chunbao Charles Xu, Wensheng Qin","doi":"10.1159/000530228","DOIUrl":"10.1159/000530228","url":null,"abstract":"<p><p>Soil bacteria participate in self-immobilization processes for survival, persistence, and production of virulence factors in some niches or hosts through their capacities for autoaggregation, cell surface hydrophobicity, biofilm formation, and antibiotic and heavy metal resistance. This study investigated potential virulence, antibiotic and heavy metal resistance, solvent adhesion, and biofilm-forming capabilities of six cellulolytic bacteria isolated from soil samples: Paenarthrobacter sp. MKAL1, Hymenobacter sp. MKAL2, Mycobacterium sp. MKAL3, Stenotrophomonas sp. MKAL4, Chryseobacterium sp. MKAL5, and Bacillus sp. MKAL6. Strains were subjected to phenotypic methods, including heavy metal and antibiotic susceptibility and virulence factors (protease, lipase, capsule production, autoaggregation, hydrophobicity, and biofilm formation). The effect of ciprofloxacin was also investigated on bacterial susceptibility over time, cell membrane, and biofilm formation. Strains MKAL2, MKAL5, and MKAL6 exhibited protease and lipase activities, while only MKAL6 produced capsules. All strains were capable of aggregating, forming biofilm, and adhering to solvents. Strains tolerated high amounts of chromium, lead, zinc, nickel, and manganese and were resistant to lincomycin. Ciprofloxacin exhibited bactericidal activity against these strains. Although the phenotypic evaluation of virulence factors of bacteria can indicate their pathogenic nature, an in-depth genetic study of virulence, antibiotic and heavy metal resistance genes is required.</p>","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":" ","pages":"36-48"},"PeriodicalIF":1.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156717","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}
Zhaoyang Liu, Bingcong Ji, Yaqing Zhang, Xunli Liu
{"title":"Bacterial Diversity and Community Structure of the Jujube Rhizosphere in Southern Xinjiang Uygur Autonomous Region, China","authors":"Zhaoyang Liu, Bingcong Ji, Yaqing Zhang, Xunli Liu","doi":"10.1159/000525000","DOIUrl":"https://doi.org/10.1159/000525000","url":null,"abstract":"Jujube is an important economic crop in the Xinjiang Uygur Autonomous Region. Microbial diversity in the rhizosphere is essential for plant quality; however, soil bacterial diversity and community structure in the jujube rhizosphere have not been characterized in this region. In this study, we used pyrosequencing to analyze bacterial diversity and community structure at different growth stages in the jujube rhizosphere in Hetian, Kashi, and Aksu prefectures. These results revealed a greater bacterial diversity in the 8-year jujube rhizosphere as compared with the 3-year-old rhizosphere taken from the same sampling area. Moreover, samples obtained from Kashi prefecture showed the largest diversity among the different areas. The most abundant phyla across all soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Firmicutes. Dominant phyla in the 8-year jujube rhizosphere accounted for the increased observed diversity. Furthermore, comparative analysis of the bacterial communities with respect to rhizosphere age and sampling areas revealed a significant correlation between soil properties and phyla diversity. To the best of our knowledge, this is the first study of jujube rhizosphere bacterial diversity and community structure in the southern Xinjiang Uygur Autonomous Region, and we hope that our research provides a reference for future studies.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"135 - 145"},"PeriodicalIF":3.9,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42646204","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}
Arne Weiten, K. Kalvelage, Meina Neumann-Schaal, Ramona Buschen, Sabine Scheve, M. Winklhofer, R. Rabus
{"title":"Nanomolar Responsiveness of Marine Phaeobacter inhibens DSM 17395 toward Carbohydrates and Amino Acids","authors":"Arne Weiten, K. Kalvelage, Meina Neumann-Schaal, Ramona Buschen, Sabine Scheve, M. Winklhofer, R. Rabus","doi":"10.1159/000524702","DOIUrl":"https://doi.org/10.1159/000524702","url":null,"abstract":"Phaeobacter inhibens DSM 17395 is a heterotrophic member of the ubiquitous, marine Roseobacter group and specializes in the aerobic utilization of carbohydrates and amino acids via pathways widespread among roseobacters. The in vivo responsiveness of P. inhibens DSM 17395 was studied with nonadapted cells (succinate-grown), which were exposed to a single pulse (100–0.01 µM) each of N-acetylglucosamine, mannitol, xylose, leucine, phenylalanine, or tryptophan (effectors). Responsiveness was then determined by time-resolved transcript analyses (quantitative reverse transcription-PCR) of “degradation” and “uptake” genes selected based on previously reported substrate-specific proteome profiles. The transcriptional response thresholds were: 50–100 nM for nagK (N-acetylglucosamine kinase), paaA (ring 1,2-phenylacetyl-CoA epoxidase), and kynA (tryptophan 2,3-dioxygenase), 10–50 nM for xylA (xylose isomerase), and around 10 nM for mtlK (mannitol 2-dehydrogenase). A threshold for leucine could not be determined due to the elevated intrinsic presence of leucine in the exometabolome of succinate-grown cells (no effector addition). Notably, the response thresholds for presumptive carbohydrate-binding proteins of ABC-transporters were in the same range or even lower: 0.1–1 µM for c27930 (N-acetylglucosamine) and even below 10 nM for c13210 (mannitol) and xylF (xylose). These results shed new light on the sensory/regulatory sensitivity of a well-studied roseobacter for recognizing potential substrates at low ambient concentrations and on the concentration threshold below which these might escape biodegradation (“emergent recalcitrance” concept of dissolved organic matter persistence).","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"108 - 121"},"PeriodicalIF":3.9,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49384769","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}
Daniel Wünsch, Sabine Scheve, Arne Weiten, K. Kalvelage, R. Rabus
{"title":"Luciferase-Based Determination of ATP/NAD(H) Pools in a Marine (Environmental) Bacterium","authors":"Daniel Wünsch, Sabine Scheve, Arne Weiten, K. Kalvelage, R. Rabus","doi":"10.1159/000522414","DOIUrl":"https://doi.org/10.1159/000522414","url":null,"abstract":"In all living organisms, adenosine triphosphate (ATP) and NAD(H) represent universal molecular currencies for energy and redox state, respectively, and are thus widely applicable molecular proxies for an organism’s viability and activity. To this end, corresponding luciferase-based assays in combination with a microplate reader were established with the marine model bacterium Phaeobacter inhibens DSM 17395 (Escherichia coli K12 served as reference). Grey multiwell plates best balanced sensitivity and crosstalk, and optimal incubation times were 5 min and 30 min for the ATP and NAD(H) assay, respectively, together allowing limits of detection of 0.042, 0.470 and 0.710 nM for ATP, NAD+, and NADH, respectively. Quenching of bacterial cell samples involved Tris-EDTA-DTAB and bicarbonate base-DTAB for ATP and NAD(H) assays, respectively. The ATP and NAD(H) yields determined for P. inhibens DSM 17395 at ¼ ODmax were found to reside well within the range previously reported for E. coli and other bacteria, e.g., 3.28 µmol ATP (g cellsdry)−1. Thus, the here described methods for luciferase-based determination of ATP/NAD(H) pools open a promising approach to investigate energy and redox states in marine (environmental) bacteria.","PeriodicalId":18457,"journal":{"name":"Microbial Physiology","volume":"32 1","pages":"122 - 134"},"PeriodicalIF":3.9,"publicationDate":"2022-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48395045","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}
{"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}
{"title":"Heterogeneity of Subcellular Diffusion in Bacteria Based on Spatial Segregation of Ribosomes and Nucleoids.","authors":"Simon Dersch, Daniel A O Rotter, 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}
Microbial PhysiologyPub Date : 2022-01-01Epub Date: 2021-06-30DOI: 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, Anca Farkas, Rahela Carpa, 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'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}
Daniel Tyler, Kevin J Hendargo, Arturo Medrano-Soto, Milton H Saier
{"title":"Discovery and Characterization of the Phospholemman/SIMP/Viroporin Superfamily.","authors":"Daniel Tyler, Kevin J Hendargo, Arturo Medrano-Soto, 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}