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Rehmani MS, Aziz U, Xian B, Shu K. Seed Dormancy and Longevity: A Mutual Dependence or a Trade-Off? PLANT & CELL PHYSIOLOGY 2022; 63:1029-1037. [PMID: 35594901 DOI: 10.1093/pcp/pcac069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy is an important agronomic trait in cereals and leguminous crops as low levels of seed dormancy during harvest season, coupled with high humidity, can cause preharvest sprouting. Seed longevity is another critical trait for commercial crop propagation and production, directly influencing seed germination and early seedling establishment. Both traits are precisely regulated by the integration of genetic and environmental cues. Despite the significance of these two traits in crop production, the relationship between them at the molecular level is still elusive, even with contradictory conclusions being reported. Some studies have proposed a positive correlation between seed dormancy and longevity in association with differences in seed coat permeability or seed reserve accumulation, whereas an increasing number of studies have highlighted a negative relationship, largely with respect to phytohormone-dependent pathways. In this review paper, we try to provide some insights into the interactions between regulatory mechanisms of genetic and environmental cues, which result in positive or negative relationships between seed dormancy and longevity. Finally, we conclude that further dissection of the molecular mechanism responsible for this apparently contradictory relationship between them is needed.
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Affiliation(s)
- Muhammad Saad Rehmani
- School of Environment and Ecology, Northwestern Polytechnical University, No. 1, Dongxiang Road, Xi'an 710129, China
| | - Usman Aziz
- School of Environment and Ecology, Northwestern Polytechnical University, No. 1, Dongxiang Road, Xi'an 710129, China
| | - BaoShan Xian
- School of Environment and Ecology, Northwestern Polytechnical University, No. 1, Dongxiang Road, Xi'an 710129, China
| | - Kai Shu
- School of Environment and Ecology, Northwestern Polytechnical University, No. 1, Dongxiang Road, Xi'an 710129, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, No. 45, Gaoxin South 9 Road, Shenzhen 518057, China
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Covington BC, Seyedsayamdost MR. Vitamin B3 Triggers Biosynthesis of Secondary Metabolite Dormancy Signals in Streptococcus suis. J Am Chem Soc 2022; 144:14997-15001. [PMID: 35969232 PMCID: PMC10171913 DOI: 10.1021/jacs.2c05790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human-associated streptococci have not been viewed as productive sources of natural products. Against expectation, bioinformatic searches recently revealed a large collection of diverse biosynthetic gene clusters coding for ribosomally synthesized and post-translationally modified peptides (RiPPs) in streptococcal genomes. The most abundant of these, the tqq gene cluster, is specific to Streptococcus suis, a burdensome agricultural pathogen and zoonotic agent. Herein, we used high-throughput elicitor screening to identify both small molecule elicitors and products of the tqq cluster. We show that the B3 vitamin niacin effectively elicits the tqq cluster leading to the biosynthesis of a family of RiPP natural products, which we termed threoglucins and characterized structurally. The defining feature of threoglucins is an aliphatic ether bond giving rise to a substituted 1,3-oxazinane heterocycle in the peptide backbone. Isolation of 22 congeners of threoglucins facilitated structure activity relationship studies, demonstrating the requirement for the oxazinane substructure and a Trp-Tyr C-terminal dyad for biological activity, namely antibiotic persistence and allolysis at low and high doses, respectively. Potential therapeutic applications of threoglucins are discussed.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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Bicyclostreptins are radical SAM enzyme-modified peptides with unique cyclization motifs. Nat Chem Biol 2022; 18:1135-1143. [PMID: 35953547 DOI: 10.1038/s41589-022-01090-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 06/21/2022] [Indexed: 12/22/2022]
Abstract
Microbial natural products comprise diverse architectures that are generated by equally diverse biosynthetic strategies. In peptide natural products, amino acid sidechains are frequently used as sites of modification to generate macrocyclic motifs. Backbone amide groups, among the most stable of biological moieties, are rarely used for this purpose. Here we report the discovery and biosynthesis of bicyclostreptins-peptide natural products from Streptococcus spp. with an unprecedented structural motif consisting of a macrocyclic β-ether and a heterocyclic sp3-sp3 linkage between a backbone amide nitrogen and an adjacent α-carbon. Both reactions are installed, in that order, by two radical S-adenosylmethionine (RaS) metalloenzymes. Bicyclostreptins are produced at nM concentrations and are potent growth regulation agents in Streptococcus thermophilus. Our results add a distinct and unusual chemotype to the growing family of ribosomal peptide natural products, expand the already impressive catalytic scope of RaS enzymes, and provide avenues for further biological studies in human-associated streptococci.
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Arctic Psychrotolerant Pseudomonas sp. B14-6 Exhibits Temperature-Dependent Susceptibility to Aminoglycosides. Antibiotics (Basel) 2022; 11:antibiotics11081019. [PMID: 36009888 PMCID: PMC9405152 DOI: 10.3390/antibiotics11081019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria can evade antibiotics by acquiring resistance genes, as well as switching to a non-growing dormant state without accompanying genetic modification. Bacteria in this quiescent state are called persisters, and this non-inheritable ability to withstand multiple antibiotics is referred to as antibiotic tolerance. Although all bacteria are considered to be able to form antibiotic-tolerant persisters, the antibiotic tolerance of extremophilic bacteria is poorly understood. Previously, we identified the psychrotolerant bacterium Pseudomonas sp. B14-6 from the glacier foreland of Midtre Lovénbreen in High Arctic Svalbard. Herein, we investigated the resistance and tolerance of Pseudomonas sp. B14-6 against aminoglycosides at various temperatures. This bacterium was resistant to streptomycin and susceptible to apramycin, gentamicin, kanamycin, and tobramycin. The two putative aminoglycoside phosphotransferase genes aph1 and aph2 were the most likely contributors to streptomycin resistance. Notably, unlike the mesophilic Pseudomonas aeruginosa PA14, this cold-adapted bacterium demonstrated reduced susceptibility to all tested aminoglycosides in a temperature-dependent manner. Pseudomonas sp. B14-6 at a lower temperature formed the persister cells that shows tolerance to the 100-fold minimum inhibitory concentration (MIC) of gentamicin, as well as the partially tolerant cells that withstand 25-fold MIC gentamicin. The temperature-dependent gentamicin tolerance appears to result from reduced metabolic activity. Lastly, the partially tolerant Pseudomonas sp. B14-6 cells could slowly proliferate under the bactericidal concentrations of aminoglycosides. Our results demonstrate that Pseudomonas sp. B14-6 has a characteristic ability to form cells with a range of tolerance, which appears to be inversely proportional to its growth rate.
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55
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Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Junio JAB, Orfanos E, Tafakori T, Lutchman V, Mohammad K, Elsaser S, Orfali S, Rajen H, Titorenko VI. Diverse geroprotectors differently affect a mechanism linking cellular aging to cellular quiescence in budding yeast. Oncotarget 2022; 13:918-943. [PMID: 35937500 PMCID: PMC9348708 DOI: 10.18632/oncotarget.28256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | | | - Emmanuel Orfanos
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Tala Tafakori
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Harshvardhan Rajen
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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Chung CH, Chandrasekaran S. A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions. PNAS NEXUS 2022; 1:pgac132. [PMID: 36016709 PMCID: PMC9396445 DOI: 10.1093/pnasnexus/pgac132] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023]
Abstract
Drug combinations are a promising strategy to counter antibiotic resistance. However, current experimental and computational approaches do not account for the entire complexity involved in combination therapy design, such as the effect of pathogen metabolic heterogeneity, changes in the growth environment, drug treatment order, and time interval. To address these limitations, we present a comprehensive approach that uses genome-scale metabolic modeling and machine learning to guide combination therapy design. Our mechanistic approach (a) accommodates diverse data types, (b) accounts for time- and order-specific interactions, and (c) accurately predicts drug interactions in various growth conditions and their robustness to pathogen metabolic heterogeneity. Our approach achieved high accuracy (area under the receiver operating curve (AUROC) = 0.83 for synergy, AUROC = 0.98 for antagonism) in predicting drug interactions for Escherichia coli cultured in 57 metabolic conditions based on experimental validation. The entropy in bacterial metabolic response was predictive of combination therapy outcomes across time scales and growth conditions. Simulation of metabolic heterogeneity using population FBA identified two subpopulations of E. coli cells defined by the levels of three proteins (eno, fadB, and fabD) in glycolysis and lipid metabolism that influence cell tolerance to a broad range of antibiotic combinations. Analysis of the vast landscape of condition-specific drug interactions revealed a set of 24 robustly synergistic drug combinations with potential for clinical use.
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Affiliation(s)
- Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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57
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Diez S, Hydorn M, Whalen A, Dworkin J. Crosstalk between guanosine nucleotides regulates cellular heterogeneity in protein synthesis during nutrient limitation. PLoS Genet 2022; 18:e1009957. [PMID: 35594298 PMCID: PMC9173625 DOI: 10.1371/journal.pgen.1009957] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/07/2022] [Accepted: 04/24/2022] [Indexed: 11/26/2022] Open
Abstract
Phenotypic heterogeneity of microbial populations can facilitate survival in dynamic environments by generating sub-populations of cells that may have differential fitness in a future environment. Bacillus subtilis cultures experiencing nutrient limitation contain distinct sub-populations of cells exhibiting either comparatively high or low protein synthesis activity. This heterogeneity requires the production of phosphorylated guanosine nucleotides (pp)pGpp by three synthases: SasA, SasB, and RelA. Here we show that these enzymes differentially affect this bimodality: RelA and SasB are necessary to generate the sub-population of cells exhibiting low protein synthesis whereas SasA is necessary to generate cells exhibiting comparatively higher protein synthesis. Previously, it was reported that a RelA product allosterically activates SasB and we find that a SasA product competitively inhibits this activation. Finally, we provide in vivo evidence that this antagonistic interaction mediates the observed heterogeneity in protein synthesis. This work therefore identifies the mechanism underlying phenotypic heterogeneity in protein synthesis. Upon encountering conditions unfavorable to growth such as nutrient limitation, bacteria enter a quiescent phenotype that is mediated by group of guanosine nucleotides collectively known as (pp)pGpp. These nucleotides direct the down-regulation of energy intensive processes and are essential for a striking heterogeneity in protein synthesis observed during exit from rapid growth. Here, we show that a network of (pp)pGpp synthases is responsible for this heterogeneity and describe a mechanism that allows for the integration of multiple signals into the decision to down regulate the most energy intensive process in a cell.
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Affiliation(s)
- Simon Diez
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Molly Hydorn
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Abigail Whalen
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- * E-mail:
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58
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Li M, Patel HV, Cognetta AB, Smith TC, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC. Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. Cell Chem Biol 2022; 29:883-896.e5. [PMID: 34599873 PMCID: PMC8964833 DOI: 10.1016/j.chembiol.2021.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/08/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening ∼200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.
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Affiliation(s)
- Michael Li
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Hiren V Patel
- Department of Microbiology and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Armand B Cognetta
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Ivy Mallick
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | | | - Mary L Previti
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA.
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59
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Kommerein N, Vierengel N, Groß J, Opatz T, Al-Nawas B, Müller-Heupt LK. Antiplanktonic and Antibiofilm Activity of Rheum palmatum against Streptococcus oralis and Porphyromonas gingivalis. Microorganisms 2022; 10:microorganisms10050965. [PMID: 35630409 PMCID: PMC9143743 DOI: 10.3390/microorganisms10050965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/24/2022] [Accepted: 05/01/2022] [Indexed: 01/27/2023] Open
Abstract
Periodontitis and peri-implantitis are inflammatory conditions with a high global prevalence. Oral pathogens such as Porphyromonas gingivalis play a crucial role in the development of dysbiotic biofilms associated with both diseases. The aim of our study was to identify plant-derived substances which mainly inhibit the growth of “disease promoting bacteria”, by comparing the effect of Rheum palmatum root extract against P. gingivalis and the commensal species Streptococcus oralis. Antiplanktonic activity was determined by measuring optical density and metabolic activity. Antibiofilm activity was quantified using metabolic activity assays and live/dead fluorescence staining combined with confocal laser scanning microscopy. At concentrations of 3.9 mg/L, R. palmatum root extract selectively inhibited planktonic growth of the oral pathogen P. gingivalis, while not inhibiting growth of S. oralis. Selective effects also occurred in mature biofilms, as P. gingivalis was significantly more stressed and inhibited than S. oralis. Our studies show that low concentrations of R. palmatum root extract specifically inhibit P. gingivalis growth, and offer a promising approach for the development of a potential topical agent to prevent alterations in the microbiome due to overgrowth of pathogenic P. gingivalis.
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Affiliation(s)
- Nadine Kommerein
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany;
| | - Nina Vierengel
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany; (N.V.); (J.G.); (T.O.)
| | - Jonathan Groß
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany; (N.V.); (J.G.); (T.O.)
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany; (N.V.); (J.G.); (T.O.)
| | - Bilal Al-Nawas
- Department of Oral- and Maxillofacial Surgery, University Medical Center Mainz, Augustusplatz 2, 55131 Mainz, Germany;
| | - Lena Katharina Müller-Heupt
- Department of Oral- and Maxillofacial Surgery, University Medical Center Mainz, Augustusplatz 2, 55131 Mainz, Germany;
- Correspondence: ; Tel.: +49-6131-175086
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60
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Corona Ramírez A, Cailleau G, Fatton M, Dorador C, Junier P. Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco. Front Microbiol 2022; 13:826117. [PMID: 36687602 PMCID: PMC9847572 DOI: 10.3389/fmicb.2022.826117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 01/25/2023] Open
Abstract
The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland,*Correspondence: Pilar Junier,
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Roy S, Chowdhury G, Mukhopadhyay AK, Dutta S, Basu S. Convergence of Biofilm Formation and Antibiotic Resistance in Acinetobacter baumannii Infection. Front Med (Lausanne) 2022; 9:793615. [PMID: 35402433 PMCID: PMC8987773 DOI: 10.3389/fmed.2022.793615] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/31/2022] [Indexed: 07/30/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a leading cause of nosocomial infections as this pathogen has certain attributes that facilitate the subversion of natural defenses of the human body. A. baumannii acquires antibiotic resistance determinants easily and can thrive on both biotic and abiotic surfaces. Different resistance mechanisms or determinants, both transmissible and non-transmissible, have aided in this victory over antibiotics. In addition, the propensity to form biofilms (communities of organism attached to a surface) allows the organism to persist in hospitals on various medical surfaces (cardiac valves, artificial joints, catheters, endotracheal tubes, and ventilators) and also evade antibiotics simply by shielding the bacteria and increasing its ability to acquire foreign genetic material through lateral gene transfer. The biofilm formation rate in A. baumannii is higher than in other species. Recent research has shown how A. baumannii biofilm-forming capacity exerts its effect on resistance phenotypes, development of resistome, and dissemination of resistance genes within biofilms by conjugation or transformation, thereby making biofilm a hotspot for genetic exchange. Various genes control the formation of A. baumannii biofilms and a beneficial relationship between biofilm formation and "antimicrobial resistance" (AMR) exists in the organism. This review discusses these various attributes of the organism that act independently or synergistically to cause hospital infections. Evolution of AMR in A. baumannii, resistance mechanisms including both transmissible (hydrolyzing enzymes) and non-transmissible (efflux pumps and chromosomal mutations) are presented. Intrinsic factors [biofilm-associated protein, outer membrane protein A, chaperon-usher pilus, iron uptake mechanism, poly-β-(1, 6)-N-acetyl glucosamine, BfmS/BfmR two-component system, PER-1, quorum sensing] involved in biofilm production, extrinsic factors (surface property, growth temperature, growth medium) associated with the process, the impact of biofilms on high antimicrobial tolerance and regulation of the process, gene transfer within the biofilm, are elaborated. The infections associated with colonization of A. baumannii on medical devices are discussed. Each important device-related infection is dealt with and both adult and pediatric studies are separately mentioned. Furthermore, the strategies of preventing A. baumannii biofilms with antibiotic combinations, quorum sensing quenchers, natural products, efflux pump inhibitors, antimicrobial peptides, nanoparticles, and phage therapy are enumerated.
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Affiliation(s)
- Subhasree Roy
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Molecular Microbiology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Molecular Microbiology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sulagna Basu
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Khabibullina NF, Kutuzova DM, Burmistrova IA, Lyadova IV. The Biological and Clinical Aspects of a Latent Tuberculosis Infection. Trop Med Infect Dis 2022; 7:tropicalmed7030048. [PMID: 35324595 PMCID: PMC8955876 DOI: 10.3390/tropicalmed7030048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 01/22/2023] Open
Abstract
Tuberculosis (TB), caused by bacilli from the Mycobacterium tuberculosis complex, remains a serious global public health problem, representing one of the main causes of death from infectious diseases. About one quarter of the world’s population is infected with Mtb and has a latent TB infection (LTBI). According to the World Health Organization (WHO), an LTBI is characterized by a lasting immune response to Mtb antigens without any TB symptoms. Current LTBI diagnoses and treatments are based on this simplified definition, although an LTBI involves a broad range of conditions, including when Mtb remains in the body in a persistent form and the immune response cannot be detected. The study of LTBIs has progressed in recent years; however, many biological and medical aspects of an LTBI are still under discussion. This review focuses on an LTBI as a broad spectrum of states, both of the human body, and of Mtb cells. The problems of phenotypic insusceptibility, diagnoses, chemoprophylaxis, and the necessity of treatment are discussed. We emphasize the complexity of an LTBI diagnosis and its treatment due to its ambiguous nature. We consider alternative ways of differentiating an LTBI from active TB, as well as predicting TB reactivation based on using mycobacterial “latency antigens” for interferon gamma release assay (IGRA) tests and the transcriptomic analysis of human blood cells.
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63
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Graniczkowska KB, Shaffer CL, Cassone VM. Transcriptional effects of melatonin on the gut commensal bacterium Klebsiella aerogenes. Genomics 2022; 114:110321. [PMID: 35218872 PMCID: PMC8934286 DOI: 10.1016/j.ygeno.2022.110321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/26/2021] [Accepted: 02/19/2022] [Indexed: 11/04/2022]
Abstract
Klebsiella (nee Enterobacter) aerogenes is the first human gut commensal bacterium with a documented sensitivity to the pineal/gastrointestinal hormone melatonin. Exogenous melatonin specifically increases the size of macrocolonies on semisolid agar and synchronizes the circadian clock of K. aerogenes in a concentration dependent manner. However, the mechanisms driving these phenomena are unknown. In this study, we applied RNA sequencing to identify melatonin sensitive transcripts during culture maturation. This work demonstrates that the majority of melatonin sensitive genes are growth stage specific. Melatonin exposure induced differential gene expression of 81 transcripts during exponential growth and 30 during early stationary phase. This indole molecule affects genes related to biofilm formation, fimbria biogenesis, transcriptional regulators, carbohydrate transport and metabolism, phosphotransferase systems (PTS), stress response, metal ion binding and transport. Differential expression of biofilm and fimbria-related genes may be responsible for the observed differences in macrocolony area. These data suggest that melatonin enhances Klebsiella aerogenes host colonization.
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Affiliation(s)
| | - Carrie L Shaffer
- University of Kentucky, Department of Veterinary Science, USA; University of Kentucky, Department of Microbiology, Immunology, and Molecular Genetics, USA; University of Kentucky, Department of Pharmaceutical Sciences, Lexington, KY 40506, USA
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64
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Wendel U. Assessing Viability and Stress Tolerance of Probiotics—A Review. Front Microbiol 2022; 12:818468. [PMID: 35154042 PMCID: PMC8829321 DOI: 10.3389/fmicb.2021.818468] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/27/2021] [Indexed: 11/26/2022] Open
Abstract
The interest in probiotics has increased rapidly the latest years together with the global market for probiotic products. Consequently, establishing reliable microbiological methods for assuring the presence of a certain number of viable microorganisms in probiotic products has become increasingly important. To assure adequate numbers of viable cells, authorities are enquiring for information on viability rates within a certain shelf-life in colony forming units (CFU). This information is obtained from plate count enumeration, a method that enables detection of bacterial cells based on their ability to replicate. Although performing plate count enumeration is one manner of assessing viability, cells can still be viable without possessing the ability to replicate. Thus, to properly assess probiotic viability, further analysis of a broader group of characteristics using several types of methods is proposed. In addition to viability, it is crucial to identify how well the cells in a probiotic product can survive in the gastrointestinal tract (GIT) and thus be able to mediate the desired health benefit while passing through the human body. A broad spectrum of different assay designs for assessing probiotic gastric tolerance have been used in research and quality control. However, the absence of any consensus on how to assess these qualities makes it difficult to compare between laboratories and to translate the results into in vivo tolerance. This review presents and discusses the complexity of assuring that a probiotic is suitable for beneficial consumption. It summarizes the information that can be subtracted from the currently available methods for assessment of viability and stress tolerance of a probiotic, hereby altogether defined as “activity.” Strengths and limitations of the different methods are presented together with favorable method combinations. Finally, the importance of choosing a set of analyses that reveals the necessary aspects of probiotic activity for a certain product or application is emphasized.
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65
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Saggere RMS, Lee CWJ, Chan ICW, Durnford DG, Nedelcu AM. A life-history trade-off gene with antagonistic pleiotropic effects on reproduction and survival in limiting environments. Proc Biol Sci 2022; 289:20212669. [PMID: 35078364 PMCID: PMC8790358 DOI: 10.1098/rspb.2021.2669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Although life-history trade-offs are central to life-history evolution, their mechanistic basis is often unclear. Traditionally, trade-offs are understood in terms of competition for limited resources among traits within an organism, which could be mediated by signal transduction pathways at the level of cellular metabolism. Nevertheless, trade-offs are also thought to be produced as a consequence of the performance of one activity generating negative consequences for other traits, or the result of genes or pathways that simultaneously regulate two life-history traits in opposite directions (antagonistic pleiotropy), independent of resource allocation. Yet examples of genes with antagonistic effects on life-history traits are limited. This study provides direct evidence for a gene-RLS1, that is involved in increasing survival in nutrient-limiting environments at a cost to immediate reproduction in the single-celled photosynthetic alga, Chlamydomonas reinhardtii. Specifically, we show that RLS1 mutants are unable to properly suppress their reproduction in phosphate-deprived conditions. Although these mutants have an immediate reproductive advantage relative to the parental strain, their long-term survival is negatively affected. Our data suggest that RLS1 is a bona fide life-history trade-off gene that suppresses immediate reproduction and ensures survival by downregulating photosynthesis in limiting environments, as part of the general acclimation response to nutrient deprivation in photosynthetic organisms.
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Affiliation(s)
- Rani M. S. Saggere
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Christopher W. J. Lee
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Irina C. W. Chan
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Dion G. Durnford
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Aurora M. Nedelcu
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
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66
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Argüello-Miranda O, Marchand AJ, Kennedy T, Russo MAX, Noh J. Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry. J Cell Biol 2022; 221:212720. [PMID: 34694336 PMCID: PMC8548912 DOI: 10.1083/jcb.202103171] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0.
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Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ashley J Marchand
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Taylor Kennedy
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX
| | - Marielle A X Russo
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
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67
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Jara M, Barrett M, Maes I, Regnault C, Imamura H, Domagalska MA, Dujardin JC. Transcriptional Shift and Metabolic Adaptations during Leishmania Quiescence Using Stationary Phase and Drug Pressure as Models. Microorganisms 2022; 10:97. [PMID: 35056546 PMCID: PMC8781126 DOI: 10.3390/microorganisms10010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavorable conditions. Quiescent cells are characterized by slow or non-proliferation and a deep downregulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but the molecular and metabolic features enabling its maintenance are unknown. Here, we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either, through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components, such as amastins and GP63, or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. It is noteworthy that among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers afford novel insight into cell regulation and show commonly modulated features across stimuli and stages.
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Affiliation(s)
- Marlene Jara
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Michael Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.B.); (C.R.)
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Clement Regnault
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.B.); (C.R.)
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Hideo Imamura
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium;
| | - Malgorzata Anna Domagalska
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
- Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
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68
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Pshennikova ES, Voronina AS. Dormancy: There and Back Again. Mol Biol 2022; 56:735-755. [PMID: 36217335 PMCID: PMC9534470 DOI: 10.1134/s0026893322050119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/27/2022] [Accepted: 03/27/2022] [Indexed: 11/04/2022]
Abstract
Many cells are capable of maintaining viability in a non-dividing state with minimal metabolism under unfavorable conditions. These are germ cells, adult stem cells, and microorganisms. Unfortunately, a resting state, or dormancy, is possible for tuberculosis bacilli in a latent form of the disease and cancer cells, which may later form secondary tumors (metastases) in different parts of the body. These cells are resistant to therapy that can destroy intensely dividing cells and to the host immune system. A cascade of reactions that allows cells to enter and exit dormancy is triggered by regulatory factors from the microenvironment in niches that harbor the cells. A ratio of forbidding and permitting signals dictates whether the cells become dormant or start proliferation. The only difference between the cell dormancy regulation in normal and pathological conditions is that pathogens, mycobacteria, and cancer cells can influence their own fate by changing their microenvironment. Certain mechanisms of these processes are considered in the review.
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Affiliation(s)
- E. S. Pshennikova
- Bakh Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - A. S. Voronina
- Bakh Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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69
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Bagre A, Patel PR, Naqvi S, Jain K. Emerging concerns of infectious diseases and drug delivery challenges. NANOTHERANOSTICS FOR TREATMENT AND DIAGNOSIS OF INFECTIOUS DISEASES 2022. [PMCID: PMC9212246 DOI: 10.1016/b978-0-323-91201-3.00013-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Emerging infectious diseases are the infections that could be newly appeared or have existed demographic area with rapidly increasing in some geographic range. Among various types of emerging infectious diseases like Ebola, chikungunya, tuberculosis, SARS, MERS, avian flu, swine flu, Zika, and so on, very recently we have witnessed the emergence of recently recognized coronavirus infection as Covid-19 pandemic caused by SARS-CoV-2, which rapidly spread around the world. Various emerging factors precipitating disease emergence include environmental, demographic, or ecological that increase the contact of people with unfamiliar microbial agents or their host or promote dissemination. Here in this chapter, we reviewed the various emerging considerations of infectious diseases including factors responsible for emerging and re-emerging infectious diseases as well as drug delivery challenges to treat infectious diseases and various strategies to deal with these challenges including nanotheranostics. Nanotheranostics are showing potential toward real-time understanding, diagnosis, and monitoring the response of the chemotherapy during treatment with reduced nontarget toxicity and enhanced safety level in the recent research studies.
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70
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Passos ADO, Assis LHC, Ferri YG, da Silva VL, da Silva MS, Cano MIN. The Trypanosomatids Cell Cycle: A Brief Report. Methods Mol Biol 2022; 2579:25-34. [PMID: 36045195 DOI: 10.1007/978-1-0716-2736-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Trypanosomatids are protozoan parasites among which are the etiologic agents of various infectious diseases in humans, such as Trypanosoma cruzi (causative agent of Chagas disease), Trypanosoma brucei (causative agent of sleeping sickness), and species of the genus Leishmania (causative agents of leishmaniases). The cell cycle in these organisms presents a sequence of events conserved throughout evolution. However, these parasites also have unique characteristics that confer some peculiarities related to the cell cycle phases. This review compares general and peculiar aspects of the cell cycle in the replicative forms of trypanosomatids. Moreover, a brief discussion about the possible cross-talk between telomeres and the cell cycle is presented. Finally, we intend to open a discussion on how a profound understanding of the cell cycle would facilitate the search for potential targets for developing antiparasitic therapies that could help millions of people worldwide.
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Affiliation(s)
- Arthur de Oliveira Passos
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Luiz H C Assis
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Yete G Ferri
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Vitor L da Silva
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcelo S da Silva
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Maria Isabel N Cano
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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71
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Dunkers JP, Iyer H, Jones B, Camp CH, Stranick SJ, Lin NJ. Toward absolute viability measurements for bacteria. JOURNAL OF BIOPHOTONICS 2021; 14:e202100175. [PMID: 34510771 DOI: 10.1002/jbio.202100175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/13/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
We aim to develop a quantitative viability method that distinguishes individual quiescent from dead cells and is measured in time (ns) as a referenceable, comparable quantity. We demonstrate that fluorescence lifetime imaging of an anionic, fluorescent membrane voltage probe fulfills these requirements for Streptococcus mutans. A random forest machine-learning model assesses whether individual S. mutans can be correctly classified into their original populations: stationary phase (quiescent), heat killed and inactivated via chemical fixation. We compare the results to intensity using three models: lifetime variables (τ1 , τ2 and p1 ), phasor variables (G, S) or all five variables, with the five variable models having the most accurate classification. This initial work affirms the potential for using fluorescence lifetime of a membrane voltage probe as a viability marker for quiescent bacteria, and future efforts on other bacterial species and fluorophores will help refine this approach.
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Affiliation(s)
- Joy P Dunkers
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Hariharan Iyer
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Brynna Jones
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
- Department of Chemistry, University of North Florida, Jacksonville, Florida, USA
| | - Charles H Camp
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Stephan J Stranick
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nancy J Lin
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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72
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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73
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Assis LHC, Andrade-Silva D, Shiburah ME, de Oliveira BCD, Paiva SC, Abuchery BE, Ferri YG, Fontes VS, de Oliveira LS, da Silva MS, Cano MIN. Cell Cycle, Telomeres, and Telomerase in Leishmania spp.: What Do We Know So Far? Cells 2021; 10:cells10113195. [PMID: 34831418 PMCID: PMC8621916 DOI: 10.3390/cells10113195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/18/2022] Open
Abstract
Leishmaniases belong to the inglorious group of neglected tropical diseases, presenting different degrees of manifestations severity. It is caused by the transmission of more than 20 species of parasites of the Leishmania genus. Nevertheless, the disease remains on the priority list for developing new treatments, since it affects millions in a vast geographical area, especially low-income people. Molecular biology studies are pioneers in parasitic research with the aim of discovering potential targets for drug development. Among them are the telomeres, DNA–protein structures that play an important role in the long term in cell cycle/survival. Telomeres are the physical ends of eukaryotic chromosomes. Due to their multiple interactions with different proteins that confer a likewise complex dynamic, they have emerged as objects of interest in many medical studies, including studies on leishmaniases. This review aims to gather information and elucidate what we know about the phenomena behind Leishmania spp. telomere maintenance and how it impacts the parasite’s cell cycle.
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Affiliation(s)
- Luiz H. C. Assis
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Débora Andrade-Silva
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Mark E. Shiburah
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Beatriz C. D. de Oliveira
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Stephany C. Paiva
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Bryan E. Abuchery
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
| | - Yete G. Ferri
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
| | - Veronica S. Fontes
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Leilane S. de Oliveira
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
| | - Marcelo S. da Silva
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (B.E.A.); (Y.G.F.)
- Correspondence: (M.S.d.S.); (M.I.N.C.)
| | - Maria Isabel N. Cano
- Telomeres Laboratory, Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (L.H.C.A.); (D.A.-S.); (M.E.S.); (B.C.D.d.O.); (S.C.P.); (V.S.F.); (L.S.d.O.)
- Correspondence: (M.S.d.S.); (M.I.N.C.)
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74
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Daignan-Fornier B, Laporte D, Sagot I. Quiescence Through the Prism of Evolution. Front Cell Dev Biol 2021; 9:745069. [PMID: 34778256 PMCID: PMC8586652 DOI: 10.3389/fcell.2021.745069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 01/13/2023] Open
Abstract
Being able to reproduce and survive is fundamental to all forms of life. In primitive unicellular organisms, the emergence of quiescence as a reversible proliferation arrest has most likely improved cell survival under unfavorable environmental conditions. During evolution, with the repeated appearances of multicellularity, several aspects of unicellular quiescence were conserved while new quiescent cell intrinsic abilities arose. We propose that the formation of a microenvironment by neighboring cells has allowed disconnecting quiescence from nutritional cues. In this new context, non-proliferative cells can stay metabolically active, potentially authorizing the emergence of new quiescent cell properties, and thereby favoring cell specialization. Through its co-evolution with cell specialization, quiescence may have been a key motor of the fascinating diversity of multicellular complexity.
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75
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Ortiz M, Leung PM, Shelley G, Jirapanjawat T, Nauer PA, Van Goethem MW, Bay SK, Islam ZF, Jordaan K, Vikram S, Chown SL, Hogg ID, Makhalanyane TP, Grinter R, Cowan DA, Greening C. Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:e2025322118. [PMID: 34732568 PMCID: PMC8609440 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
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Affiliation(s)
- Maximiliano Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Pok Man Leung
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Philipp A Nauer
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Sean K Bay
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Zahra F Islam
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Karen Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
| | - Ian D Hogg
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- School of Science, University of Waikato, Hamilton 3240, New Zealand
- Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge Bay NU X0B 0C0, Canada
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton VIC 3800, Australia;
- School of Biological Sciences, Monash University, Clayton VIC 3800, Australia
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76
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Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife 2021; 10:e72062. [PMID: 34734806 PMCID: PMC8598167 DOI: 10.7554/elife.72062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
A longstanding hypothesis is that chromatin fiber folding mediated by interactions between nearby nucleosomes represses transcription. However, it has been difficult to determine the relationship between local chromatin fiber compaction and transcription in cells. Further, global changes in fiber diameters have not been observed, even between interphase and mitotic chromosomes. We show that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives the compaction of chromatin fibers genome-wide. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a basic patch in the histone H4 tail. This quiescence-specific fiber folding globally represses transcription and inhibits chromatin loop extrusion by condensin. These results reveal that global changes in chromatin fiber compaction can occur during cell state transitions, and establish physiological roles for local chromatin fiber folding in regulating transcription and chromatin domain formation.
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Affiliation(s)
- Sarah G Swygert
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dejun Lin
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | | | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Dakota R Hunt
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Tamar Schlick
- Department of Chemistry, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry at New York University ShanghaiShanghaiChina
| | - William S Noble
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Paul G. Allen School of Computer Science and Engineering, University of WashingtonSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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77
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Interception of host fatty acid metabolism by mycobacteria under hypoxia to suppress anti-TB immunity. Cell Discov 2021; 7:90. [PMID: 34608123 PMCID: PMC8490369 DOI: 10.1038/s41421-021-00301-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/01/2021] [Indexed: 02/08/2023] Open
Abstract
Pathogenic mycobacteria induce the formation of hypoxic granulomas during latent tuberculosis (TB) infection, in which the immune system contains, but fails to eliminate the mycobacteria. Fatty acid metabolism-related genes are relatively overrepresented in the mycobacterial genome and mycobacteria favor host-derived fatty acids as nutrient sources. However, whether and how mycobacteria modulate host fatty acid metabolism to drive granuloma progression remains unknown. Here, we report that mycobacteria under hypoxia markedly secrete the protein Rv0859/MMAR_4677 (Fatty-acid degradation A, FadA), which is also enriched in tuberculous granulomas. FadA acts as an acetyltransferase that converts host acetyl-CoA to acetoacetyl-CoA. The reduced acetyl-CoA level suppresses H3K9Ac-mediated expression of the host proinflammatory cytokine Il6, thus promoting granuloma progression. Moreover, supplementation of acetate increases the level of acetyl-CoA and inhibits the formation of granulomas. Our findings suggest an unexpected mechanism of a hypoxia-induced mycobacterial protein suppressing host immunity via modulation of host fatty acid metabolism and raise the possibility of a novel therapeutic strategy for TB infection.
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78
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Yazdani M, Croen MG, Fish TL, Thannhauser TW, Ahner BA. Overexpression of native ORANGE (OR) and OR mutant protein in Chlamydomonas reinhardtii enhances carotenoid and ABA accumulation and increases resistance to abiotic stress. Metab Eng 2021; 68:94-105. [PMID: 34571147 DOI: 10.1016/j.ymben.2021.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 09/01/2021] [Accepted: 09/18/2021] [Indexed: 01/13/2023]
Abstract
The carotenoid content of plants can be increased by overexpression of the regulatory protein ORANGE (OR) or a mutant variant known as the 'golden SNP'. In the present study, a strong light-inducible promoter was used to overexpress either wild type CrOR (CrORWT) or a mutated CrOR (CrORHis) containing a single histidine substitution for a conserved arginine in the microalgae Chlamydomonas reinhardtii. Overexpression of CrORWT and CrORHis roughly doubled and tripled, respectively, the accumulation of several different carotenoids, including β-carotene, α-carotene, lutein and violaxanthin in C. reinhardtii and upregulated the transcript abundance of nearly all relevant carotenoid biosynthetic genes. In addition, microscopic analysis revealed that the OR transgenic cells were larger than control cells and exhibited larger chloroplasts with a disrupted morphology. Moreover, both CrORWT and CrORHis cell lines showed increased tolerance to salt and paraquat stress. The levels of endogenous phytohormone abscisic acid (ABA) were also increased in CrORWT and CrORHis lines, not only in normal growth conditions but also in growth medium supplemented with salt and paraquat. Together these results offer new insights regarding the role of the native OR protein in regulating carotenoid biosynthesis and the accumulation of several carotenoids in microalgae, and establish a new functional role for OR to modulate oxidative stress tolerance potentially mediated by ABA.
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Affiliation(s)
- Mohammad Yazdani
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Michelle G Croen
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Tara L Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, USA
| | - Theodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, USA
| | - Beth A Ahner
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
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79
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Pilotto S, Fouqueau T, Lukoyanova N, Sheppard C, Lucas-Staat S, Díaz-Santín LM, Matelska D, Prangishvili D, Cheung ACM, Werner F. Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun 2021; 12:5523. [PMID: 34535646 PMCID: PMC8448823 DOI: 10.1038/s41467-021-25666-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
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Affiliation(s)
- Simona Pilotto
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Thomas Fouqueau
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | - Natalya Lukoyanova
- Institute for Structural and Molecular Biology, Birkbeck College, London, UK
| | - Carol Sheppard
- Section of Virology, Department of Infectious disease, Imperial College London, London, UK
| | | | | | - Dorota Matelska
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK
| | | | | | - Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London, UK.
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80
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Hyun H, Lee MS, Park I, Ko HS, Yun S, Jang DH, Kim S, Kim H, Kang JH, Lee JH, Kwon T. Analysis of Porcine Model of Fecal-Induced Peritonitis Reveals the Tropism of Blood Microbiome. Front Cell Infect Microbiol 2021; 11:676650. [PMID: 34527598 PMCID: PMC8435847 DOI: 10.3389/fcimb.2021.676650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have suggested the existence of a blood microbiome in the healthy host. However, changes in the blood microbiome upon bloodstream infection are not known. Here, we analyzed the dynamics of the blood microbiome in a porcine model of polymicrobial bacteremia induced by fecal peritonitis. Surprisingly, we detected bacterial populations in the bloodstream even before the infection, and these populations were maintained over time. The native blood microbiome was notably taxonomically different from the fecal microbiome that was used to induce peritonitis, reflecting microbial tropism for the blood. Although the population composition after the infection was similar to that of the native blood microbiome, new bacterial strains entered the bloodstream upon peritonitis induction as clinical symptoms relevant to sepsis developed. This indicates that the bacteria detected in the blood before peritonitis induction were derived from the blood rather than a contamination. Comparison of the functional pathways enriched in the blood and fecal microbiomes revealed that communication and stress management pathways are essential for the survival of the blood microbiome.
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Affiliation(s)
- Hwi Hyun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Min Seok Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Inwon Park
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Hwa Soo Ko
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Seongmin Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Dong-Hyun Jang
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Seonghye Kim
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Hajin Kim
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Joo H Kang
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jae Hyuk Lee
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Taejoon Kwon
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, South Korea
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81
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Zanghi G, Vaughan AM. Plasmodium vivax pre-erythrocytic stages and the latent hypnozoite. Parasitol Int 2021; 85:102447. [PMID: 34474178 DOI: 10.1016/j.parint.2021.102447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/02/2023]
Abstract
Plasmodium vivax is the most geographically widespread malaria parasite on the planet. This is largely because after mosquito transmission, P. vivax sporozoites can invade hepatocytes and form latent liver stages known as hypnozoites. These persistent liver stages can activate weeks, months or even years after an infected individual suffers a primary clinical infection. Activation then leads to replication and liver stage schizont maturation that ultimately cause relapse of blood stage infection, disease, and onward transmission. Thus, the latent hypnozoite can lie in wait during times when onward transmission is unlikely due to conditions that do not favor the mosquito. For example, in temperate climates where mosquito prevalence is only seasonal. Furthermore, the elimination of hypnozoites is challenging since the hypnozoite reservoir is currently undetectable and not killed by most antimalarial drugs. Here, we review our current knowledge of the pre-erythrocytic stages of the malaria parasite - the sporozoite and liver stages, including the elusive and enigmatic hypnozoite. We focus on our understanding of sporozoite biology, the novel animal models that are available to study the hypnozoite and hypnozoite activation and the ongoing efforts to understand the biological makeup of the hypnozoite that allow for its persistence in the human host.
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Affiliation(s)
| | - Ashley M Vaughan
- Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA.
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82
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Camacho Mateu J, Sireci M, Muñoz MA. Phenotypic-dependent variability and the emergence of tolerance in bacterial populations. PLoS Comput Biol 2021; 17:e1009417. [PMID: 34555011 PMCID: PMC8492070 DOI: 10.1371/journal.pcbi.1009417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 10/05/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well-documented to intersperse much more tightly than traditionally assumed, especially in communities of microorganisms. Advancing the development of mathematical and computational approaches to shed novel light onto eco-evolutionary problems is a challenge of utmost relevance. With this motivation in mind, here we scrutinize recent experimental results showing evidence of rapid evolution of tolerance by lag in bacterial populations that are periodically exposed to antibiotic stress in laboratory conditions. In particular, the distribution of single-cell lag times-i.e., the times that individual bacteria from the community remain in a dormant state to cope with stress-evolves its average value to approximately fit the antibiotic-exposure time. Moreover, the distribution develops right-skewed heavy tails, revealing the presence of individuals with anomalously large lag times. Here, we develop a parsimonious individual-based model mimicking the actual demographic processes of the experimental setup. Individuals are characterized by a single phenotypic trait: their intrinsic lag time, which is transmitted with variation to the progeny. The model-in a version in which the amplitude of phenotypic variations grows with the parent's lag time-is able to reproduce quite well the key empirical observations. Furthermore, we develop a general mathematical framework allowing us to describe with good accuracy the properties of the stochastic model by means of a macroscopic equation, which generalizes the Crow-Kimura equation in population genetics. Even if the model does not account for all the biological mechanisms (e.g., genetic changes) in a detailed way-i.e., it is a phenomenological one-it sheds light onto the eco-evolutionary dynamics of the problem and can be helpful to design strategies to hinder the emergence of tolerance in bacterial communities. From a broader perspective, this work represents a benchmark for the mathematical framework designed to tackle much more general eco-evolutionary problems, thus paving the road to further research avenues.
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Affiliation(s)
- José Camacho Mateu
- Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Matteo Sireci
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
| | - Miguel A. Muñoz
- Departamento de Electromagnetismo y Física de la Materia and Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
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83
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Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating. J Fungi (Basel) 2021; 7:jof7080661. [PMID: 34436200 PMCID: PMC8400180 DOI: 10.3390/jof7080661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.
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84
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Meier DV, Greve AJ, Chennu A, van Erk MR, Muthukrishnan T, Abed RMM, Woebken D, de Beer D. Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat. Appl Environ Microbiol 2021; 87:e0069821. [PMID: 34160273 PMCID: PMC8357274 DOI: 10.1128/aem.00698-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.
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Affiliation(s)
- Dimitri V. Meier
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | | | | | - Raeid M. M. Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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85
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Ravoni A. Long-term behaviours of Autocatalytic Sets. J Theor Biol 2021; 529:110860. [PMID: 34389361 DOI: 10.1016/j.jtbi.2021.110860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of Autocatalytic Sets in terms of graphs with peculiar topological properties. This formalisation has been proved to be a powerful tool for the study of the chemical networks underlying life, and it was able to identify autocatalytic structures in real metabolic networks. However, the dynamical behaviour of such networks has not been yet complitely clarified. In this work, I present a first attempt to connect the topology of an Autocatalytic Set with its dynamics. For this purpose, I represent Autocatalytic Sets in terms of Chemical Reaction Networks, and I use the Chemical Reaction Network theory to detect motifs in the networks'structure, that allow to determine the long-term behaviour of the system.
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Affiliation(s)
- Alessandro Ravoni
- Department of Mathematics and Physics, University of Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy.
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86
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Feaga HA, Dworkin J. Transcription regulates ribosome hibernation. Mol Microbiol 2021; 116:663-673. [PMID: 34152658 PMCID: PMC8628635 DOI: 10.1111/mmi.14762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
Most bacteria are quiescent, typically as a result of nutrient limitation. In order to minimize energy consumption during this potentially prolonged state, quiescent bacteria substantially attenuate protein synthesis, the most energetically costly cellular process. Ribosomes in quiescent bacteria are present as dimers of two 70S ribosomes. Dimerization is dependent on a single protein, hibernation promoting factor (HPF), that binds the ribosome in the mRNA channel. This interaction indicates that dimers are inactive, suggesting that HPF inhibits translation. However, we observe that HPF does not significantly affect protein synthesis in vivo suggesting that dimerization is a consequence of inactivity, not the cause. The HPF-dimer interaction further implies that re-initiation of translation when the bacteria exit quiescence requires dimer resolution. We show that ribosome dimers quickly resolve in the presence of nutrients, and this resolution is dependent on transcription, indicating that mRNA synthesis is required for dimer resolution. Finally, we observe that ectopic HPF expression in growing cells where mRNA is abundant does not significantly affect protein synthesis despite stimulating dimer formation, suggesting that dimerization is dynamic. Thus, the extensive transcription that occurs in response to nutrient availability rapidly re-activates the translational apparatus of a quiescent cell and induces dimer resolution.
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Affiliation(s)
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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87
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Wisnoski NI, Lennon JT. Stabilising role of seed banks and the maintenance of bacterial diversity. Ecol Lett 2021; 24:2328-2338. [PMID: 34322982 DOI: 10.1111/ele.13853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 01/09/2023]
Abstract
Coexisting species often exhibit negative frequency dependence due to mechanisms that promote population growth and persistence when rare. These stabilising mechanisms can maintain diversity through interspecific niche differences, but also through life-history strategies like dormancy that buffer populations in fluctuating environments. However, there are few tests demonstrating how seed banks contribute to long-term community dynamics and the maintenance of diversity. Using a multi-year, high-frequency time series of bacterial community data from a north temperate lake, we documented patterns consistent with stabilising coexistence. Bacterial taxa exhibited differential responses to seasonal environmental conditions, while seed bank dynamics helped maintain diversity over less-favourable winter periods. Strong negative frequency dependence in rare, but metabolically active, taxa suggested a role for biotic interactions in promoting coexistence. Together, our results provide field-based evidence that niche differences and seed banks contribute to recurring community dynamics and the long-term maintenance of diversity in nature.
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Affiliation(s)
- Nathan I Wisnoski
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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88
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Towards an ecosystem model of infectious disease. Nat Ecol Evol 2021; 5:907-918. [PMID: 34002048 DOI: 10.1038/s41559-021-01454-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Increasingly intimate associations between human society and the natural environment are driving the emergence of novel pathogens, with devastating consequences for humans and animals alike. Prior to emergence, these pathogens exist within complex ecological systems that are characterized by trophic interactions between parasites, their hosts and the environment. Predicting how disturbance to these ecological systems places people and animals at risk from emerging pathogens-and the best ways to manage this-remains a significant challenge. Predictive systems ecology models are powerful tools for the reconstruction of ecosystem function but have yet to be considered for modelling infectious disease. Part of this stems from a mistaken tendency to forget about the role that pathogens play in structuring the abundance and interactions of the free-living species favoured by systems ecologists. Here, we explore how developing and applying these more complete systems ecology models at a landscape scale would greatly enhance our understanding of the reciprocal interactions between parasites, pathogens and the environment, placing zoonoses in an ecological context, while identifying key variables and simplifying assumptions that underly pathogen host switching and animal-to-human spillover risk. As well as transforming our understanding of disease ecology, this would also allow us to better direct resources in preparation for future pandemics.
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89
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Schäfer C, Zanghi G, Vaughan AM, Kappe SHI. Plasmodium vivax Latent Liver Stage Infection and Relapse: Biological Insights and New Experimental Tools. Annu Rev Microbiol 2021; 75:87-106. [PMID: 34196569 DOI: 10.1146/annurev-micro-032421-061155] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium vivax is the most widespread human malaria parasite, in part because it can form latent liver stages known as hypnozoites after transmission by female anopheline mosquitoes to human hosts. These persistent stages can activate weeks, months, or even years after the primary clinical infection; replicate; and initiate relapses of blood stage infection, which causes disease and recurring transmission. Eliminating hypnozoites is a substantial obstacle for malaria treatment and eradication since the hypnozoite reservoir is undetectable and unaffected by most antimalarial drugs. Importantly, in some parts of the globe where P. vivax malaria is endemic, as many as 90% of P. vivax blood stage infections are thought to be relapses rather than primary infections, rendering the hypnozoite a major driver of P. vivax epidemiology. Here, we review the biology of the hypnozoite and recent discoveries concerning this enigmatic parasite stage. We discuss treatment and prevention challenges, novel animal models to study hypnozoites and relapse, and hypotheses related to hypnozoite formation and activation. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Carola Schäfer
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, USA; , , ,
| | - Gigliola Zanghi
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, USA; , , ,
| | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, USA; , , , .,Department of Pediatrics, University of Washington, Seattle, Washington 98105, USA
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, USA; , , , .,Department of Pediatrics, University of Washington, Seattle, Washington 98105, USA.,Deparment of Global Health, University of Washington, Seattle, Washington 98195, USA
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90
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Pompilio A, Scribano D, Sarshar M, Di Bonaventura G, Palamara AT, Ambrosi C. Gram-Negative Bacteria Holding Together in a Biofilm: The Acinetobacter baumannii Way. Microorganisms 2021; 9:1353. [PMID: 34206680 PMCID: PMC8304980 DOI: 10.3390/microorganisms9071353] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Bacterial biofilms are a serious public-health problem worldwide. In recent years, the rates of antibiotic-resistant Gram-negative bacteria associated with biofilm-forming activity have increased worrisomely, particularly among healthcare-associated pathogens. Acinetobacter baumannii is a critically opportunistic pathogen, due to the high rates of antibiotic resistant strains causing healthcare-acquired infections (HAIs). The clinical isolates of A. baumannii can form biofilms on both biotic and abiotic surfaces; hospital settings and medical devices are the ideal environments for A. baumannii biofilms, thereby representing the main source of patient infections. However, the paucity of therapeutic options poses major concerns for human health infections caused by A. baumannii strains. The increasing number of multidrug-resistant A. baumannii biofilm-forming isolates in association with the limited number of biofilm-eradicating treatments intensify the need for effective antibiofilm approaches. This review discusses the mechanisms used by this opportunistic pathogen to form biofilms, describes their clinical impact, and summarizes the current and emerging treatment options available, both to prevent their formation and to disrupt preformed A. baumannii biofilms.
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Affiliation(s)
- Arianna Pompilio
- Center for Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, Service of Clinical Microbiology, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (A.P.); (G.D.B.)
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy;
- Dani Di Giò Foundation-Onlus, 00193 Rome, Italy
| | - Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
| | - Giovanni Di Bonaventura
- Center for Advanced Studies and Technology (CAST), Department of Medical, Oral and Biotechnological Sciences, Service of Clinical Microbiology, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (A.P.); (G.D.B.)
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS, 00166 Rome, Italy
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91
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Cucinotta CE, Dell RH, Braceros KCA, Tsukiyama T. RSC primes the quiescent genome for hypertranscription upon cell-cycle re-entry. eLife 2021; 10:e67033. [PMID: 34042048 PMCID: PMC8186906 DOI: 10.7554/elife.67033] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Quiescence is a reversible G0 state essential for differentiation, regeneration, stem-cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.
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Affiliation(s)
| | - Rachel H Dell
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Keean CA Braceros
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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92
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Zeng MC, Jia QJ, Tang LM. rpoB gene mutations in rifampin-resistant Mycobacterium tuberculosis isolates from rural areas of Zhejiang, China. J Int Med Res 2021; 49:300060521997596. [PMID: 33715498 PMCID: PMC7952843 DOI: 10.1177/0300060521997596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective The aim was to analyze genetic mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis isolates (RIFR-MTB) from Zhejiang, China. Methods We prospectively analyzed RIFR-associated mutations in 13 rural areas of Zhejiang. Isolates were subjected to species identification, phenotype drug susceptibility testing (DST), DNA extraction, and rpoB gene sequencing. Results A total of 103 RIFR isolates were identified by DST (22 RIFR only, 14 poly-drug resistant, 49 multidrug resistant, 13 pre-extensively drug resistant [pre-XDR], and 5 extensively drug resistant [XDR]) from 2152 culture-positive sputum specimens. Gene sequencing of rpoB showed that the most frequent mutation was S450L (37.86%, 39/103); mutations P280L, E521K, and D595Y were outside the rifampicin resistance-determining region (RRDR) but may be associated with RIFR. Mutations associated with poly-drug resistant, pre-XDR, and XDR TB were mainly located at codon 445 or 450 in the RRDR. Conclusions The frequency of rpoB RRDR mutation in Zhejiang is high. Further studies are needed to clarify the relationships between RIFR and the TTC insertion at codon 433 in the RRDR and the P280L and D595Y mutations outside the RRDR.
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Affiliation(s)
- Mei-Chun Zeng
- Department of Pathology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Mei-Chun Zeng, Department of Pathology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Qingchun Road 79#, Shangcheng District, Hangzhou 310003, China.
| | - Qing-Jun Jia
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Lei-Ming Tang
- Department of Clinical Laboratory, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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93
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Fellag M, Loukil A, Drancourt M. The puzzle of the evolutionary natural history of tuberculosis. New Microbes New Infect 2021; 41:100712. [PMID: 33996102 PMCID: PMC8094893 DOI: 10.1016/j.nmni.2020.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 12/02/2022] Open
Abstract
Several pieces of the puzzle of the natural history of tuberculosis are assembled in this review to illustrate the potential reservoirs and sources of the Mycobacterium tuberculosis complex (MTBC) mycobacteria, their transmission to animals and humans, and their fate in populations, in a co-evolutionary perspective. Millennia-old companions of mammalian and human populations, MTBC are detected in the soil, in which they infect and survive within vegetative amoebae and cysts, except for Mycobacterium canettii. Never detected in the sphere of plants, they are transmissible by transcutaneous, digestive and respiratory routes and cause an infection of the lymphatic system with secondary dissemination in most tissues, in which they determine a specific and non-pathognomonic granulomatous inflammatory reaction; in which MTBC survives in dormant form irrespective of MTBC species and mammalian species; indicating that the current epidemiology in mammalian populations is essentially governed by the probabilities of contact between mammalian species and MTBC species. Individual variabilities in clinical expression of tuberculosis are related to MTBC species, strain and inoculum; host genetic factors; acquired modulations of the inflammatory response; and probably human microbiota. This review of the literature suggests an evolutionary natural history of telluric environmental mycobacteria, satellites of unicellular eukaryotes, transmissible to mammals via the digestive and then respiratory tracts, in which they determine a fatal contagious infection that is primarily lymphatic and a quiescence-mimicking encysted form. This review opens perspectives for microbiological and translational medical research.
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Affiliation(s)
- M. Fellag
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - A. Loukil
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - M. Drancourt
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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94
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Bamunuarachchi NI, Khan F, Kim YM. Inhibition of Virulence Factors and Biofilm Formation of Acinetobacter Baumannii by Naturally-derived and Synthetic Drugs. Curr Drug Targets 2021; 22:734-759. [PMID: 33100201 DOI: 10.2174/1389450121666201023122355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022]
Abstract
Acinetobacter baumannii is a gram-negative, aerobic, non-motile, and pleomorphic bacillus. A. baumannii is also a highly-infectious pathogen causing high mortality and morbidity rates in intensive care units. The discovery of novel agents against A. baumannii infections is urgently needed due to the emergence of drug-resistant A. baumannii strains and the limited number of efficacious antibiotics available for treatment. In addition to the production of several virulence factors, A. baumannii forms biofilms on the host cell surface as well. Formation of biofilms occurs through initial surface attachment, microcolony formation, biofilm maturation, and detachment stages, and is one of the major drug resistance mechanisms employed by A. baumannii. Several studies have previously reported the efficacy of naturally-derived and synthetic compounds as anti- biofilm and anti-virulence agents against A. baumannii. Here, inhibition of biofilm formation and virulence factors of A. baumannii using naturally-derived and synthetic compounds are reviewed.
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Affiliation(s)
| | - Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan 48513, South Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, South Korea
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95
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Gao Y, Chen Z, Yao W, Li D, Fu X. Gentamicin Combined With Hypoionic Shock Rapidly Eradicates Aquaculture Bacteria in vitro and in vivo. Front Microbiol 2021; 12:641846. [PMID: 33889141 PMCID: PMC8055967 DOI: 10.3389/fmicb.2021.641846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial pathogens are a major cause of infectious diseases in aquatic animals. The abuse of antibiotics in the aquatic industry has led to the proliferation of antibiotic resistance. It is therefore essential to develop more effective and safer strategies to increase the efficacy and extend the life span of the antibiotics used in aquaculture. In this study, we show that six aquaculture bacterial pathogens (i.e., Aeromonas hydrophila, Vibrio alginolyticus, Edwardsiella tarda, Streptococcus iniae, Vibrio harveyi, and Vibrio fluvialis) in the stationary phase can be rapidly killed after immersion in gentamicin- or neomycin-containing, ion-free solutions for a few minutes. Such hypoionic shock treatment enhances the bacterial uptake of gentamicin in an ATP-dependent manner. Importantly, we demonstrate, as a proof of concept, that gentamicin under hypoionic shock conditions can effectively kill A. hydrophila in vivo in a skin infection model of zebrafish (Danio rerio), completely curing the infected fish. Given that pathogenic bacteria generally adhere to the skin surface and gills of aquatic animals, our strategy is of potential significance for bacterial infection control, especially for small-scale economic fish farming and ornamental fish farming. Further, the combined treatment can be completed within 5 min with a relatively small volume of solution, thus minimizing the amount of residual antibiotics in both animals and the environment.
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Affiliation(s)
- Yuanyuan Gao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Zhongyu Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Wei Yao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Daliang Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fuzhou, China.,College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
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96
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Liu Z, Shan X, Wei H, Zhang J, Saleem M, Li D, Zhang Y, Ma R, He Y, Zhong J, Liu Y. Idiosyncratic responses of microbial communities and carbon utilization to acid rain frequency in the agricultural and forest soils. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2020.e01429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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97
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Cronan MR, Hughes EJ, Brewer WJ, Viswanathan G, Hunt EG, Singh B, Mehra S, Oehlers SH, Gregory SG, Kaushal D, Tobin DM. A non-canonical type 2 immune response coordinates tuberculous granuloma formation and epithelialization. Cell 2021; 184:1757-1774.e14. [PMID: 33761328 PMCID: PMC8055144 DOI: 10.1016/j.cell.2021.02.046] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
The central pathogen-immune interface in tuberculosis is the granuloma, a complex host immune structure that dictates infection trajectory and physiology. Granuloma macrophages undergo a dramatic transition in which entire epithelial modules are induced and define granuloma architecture. In tuberculosis, relatively little is known about the host signals that trigger this transition. Using the zebrafish-Mycobacterium marinum model, we identify the basis of granuloma macrophage transformation. Single-cell RNA-sequencing analysis of zebrafish granulomas and analysis of Mycobacterium tuberculosis-infected macaques reveal that, even in the presence of robust type 1 immune responses, countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling, mediated via stat6, is absolutely required for epithelialization and granuloma formation. In mixed chimeras, stat6 acts cell autonomously within macrophages, where it is required for epithelioid transformation and incorporation into necrotic granulomas. These findings establish the signaling pathway that produces the hallmark structure of mycobacterial infection.
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MESH Headings
- Animals
- Animals, Genetically Modified/genetics
- Animals, Genetically Modified/metabolism
- Cadherins/genetics
- Cadherins/metabolism
- Cell Differentiation
- Disease Models, Animal
- Epithelioid Cells/cytology
- Epithelioid Cells/immunology
- Epithelioid Cells/metabolism
- Granuloma/immunology
- Granuloma/metabolism
- Granuloma/pathology
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism
- Immunity/physiology
- Interferon-gamma/metabolism
- Interleukin-12/metabolism
- Macrophages/cytology
- Macrophages/immunology
- Macrophages/metabolism
- Mycobacterium Infections, Nontuberculous/immunology
- Mycobacterium Infections, Nontuberculous/pathology
- Mycobacterium marinum/isolation & purification
- Mycobacterium marinum/physiology
- Necrosis
- Receptors, Interleukin-4/antagonists & inhibitors
- Receptors, Interleukin-4/genetics
- Receptors, Interleukin-4/metabolism
- STAT6 Transcription Factor/antagonists & inhibitors
- STAT6 Transcription Factor/genetics
- STAT6 Transcription Factor/metabolism
- Signal Transduction
- Zebrafish/growth & development
- Zebrafish/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Mark R Cronan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emily G Hunt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bindu Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Smriti Mehra
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Stefan H Oehlers
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, NSW, Australia; The University of Sydney, Faculty of Medicine and Health & Marie Bashir Institute, Camperdown, NSW, Australia
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27710, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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98
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Bezrukov F, Prados J, Renzoni A, Panasenko OO. MazF toxin causes alterations in Staphylococcus aureus transcriptome, translatome and proteome that underlie bacterial dormancy. Nucleic Acids Res 2021; 49:2085-2101. [PMID: 33544858 PMCID: PMC7913683 DOI: 10.1093/nar/gkaa1292] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance is a serious problem which may be caused by bacterial dormancy. It has been suggested that bacterial toxin-antitoxin systems induce dormancy. We analyzed the genome-wide role of Staphylococcus aureus endoribonuclease toxin MazF using RNA-Seq, Ribo-Seq and quantitative proteomics. We characterized changes in transcriptome, translatome and proteome caused by MazF, and proposed that MazF decreases translation directly by cleaving mRNAs, and indirectly, by decreasing translation factors and by promoting ribosome hibernation. Important pathways affected during the early stage of MazF induction were identified: MazF increases cell wall thickness and decreases cell division; MazF activates SsrA-system which rescues stalled ribosomes, appearing as a result of MazF mRNA cleavage. These pathways may be promising targets for new antibacterial drugs that prevent bacteria dormancy. Finally, we described the overall impact of MazF on S. aureus cell physiology, and propose one of the mechanisms by which MazF might regulate cellular changes leading to dormancy.
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Affiliation(s)
- Fedor Bezrukov
- Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Adriana Renzoni
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.,Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
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99
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Doello S, Burkhardt M, Forchhammer K. The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium. Curr Biol 2021; 31:1606-1615.e2. [PMID: 33571435 DOI: 10.1016/j.cub.2021.01.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
The ability to resume growth after a dormant period is an important strategy for the survival and spreading of bacterial populations. Energy homeostasis is critical in the transition into and out of a quiescent state. Synechocystis sp. PCC 6803, a non-diazotrophic cyanobacterium, enters metabolic dormancy as a response to nitrogen starvation. We used Synechocystis as a model to investigate the regulation of ATP homeostasis during dormancy, and we unraveled a critical role for sodium bioenergetics in dormant cells. During nitrogen starvation, cells reduce their ATP levels and engage sodium bioenergetics to maintain the minimum ATP content required for viability. When nitrogen becomes available, energy requirements rise, and cells immediately increase ATP levels, employing sodium bioenergetics and glycogen catabolism. These processes allow them to restore the photosynthetic machinery and resume photoautotrophic growth. Our work reveals a precise regulation of the energy metabolism essential for bacterial survival during periods of nutrient deprivation.
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Affiliation(s)
- Sofia Doello
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Markus Burkhardt
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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Bazurto JV, Riazi S, D’Alton S, Deatherage DE, Bruger EL, Barrick JE, Marx CJ. Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition. Microorganisms 2021; 9:347. [PMID: 33578755 PMCID: PMC7916467 DOI: 10.3390/microorganisms9020347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. Herein, we investigate growth and changes in gene expression to understand how M. extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response, and how this mechanism compares to antibiotic-mediated translation inhibition. These distinct mechanisms of translation inhibition have notable differences: they each involve different specific players and in addition, formaldehyde also acts as a general, multi-target stressor and a potential carbon source. We present findings demonstrating that in addition to its characterized impact on translation, functional EfgA allows for a rapid and robust transcriptional response to formaldehyde and that removal of EfgA leads to heightened proteotoxic and genotoxic stress in the presence of increased formaldehyde levels. We also found that many downstream consequences of translation inhibition were shared by EfgA-formaldehyde- and kanamycin-mediated translation inhibition. Our work uncovered additional layers of regulatory control enacted by functional EfgA upon experiencing formaldehyde stress, and further demonstrated the importance this protein plays at both transcriptional and translational levels in this model methylotroph.
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Affiliation(s)
- Jannell V. Bazurto
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (J.V.B.); (S.R.); (E.L.B.)
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, MN 55108, USA
- Microbial and Plant Genomics Institute, University of Minnesota, Twin Cities, MN 55108, USA
- Biotechnology Institute, University of Minnesota, Twin Cities, MN 55108, USA
| | - Siavash Riazi
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (J.V.B.); (S.R.); (E.L.B.)
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Simon D’Alton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; (S.D.); (D.E.D.); (J.E.B.)
| | - Daniel E. Deatherage
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; (S.D.); (D.E.D.); (J.E.B.)
| | - Eric L. Bruger
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (J.V.B.); (S.R.); (E.L.B.)
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Jeffrey E. Barrick
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; (S.D.); (D.E.D.); (J.E.B.)
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA; (J.V.B.); (S.R.); (E.L.B.)
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID 83844, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
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