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Denic M, Turlin E, Zamble DB, Betton JM, Vinella D, De Reuse H. The SlyD metallochaperone targets iron-sulfur biogenesis pathways and the TCA cycle. mBio 2023; 14:e0096723. [PMID: 37584558 PMCID: PMC10653786 DOI: 10.1128/mbio.00967-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
IMPORTANCE Correct folding of proteins represents a crucial step for their functions. Among the chaperones that control protein folding, the ubiquitous PPIases catalyze the cis/trans-isomerization of peptidyl-prolyl bonds. Only few protein targets of PPIases have been reported in bacteria. To fill this knowledge gap, we performed a large-scale two-hybrid screen to search for targets of the Escherichia coli and Helicobacter pylori SlyD PPIase-metallochaperone. SlyD from both organisms interacts with enzymes (i) containing metal cofactors, (ii) from the central metabolism tricarboxylic acid (TCA) cycle, and (iii) involved in the formation of the essential and ancestral Fe-S cluster cofactor. E. coli and H. pylori ∆slyD mutants present similar phenotypes of diminished susceptibility to antibiotics and to oxidative stress. In H. pylori, measurements of the intracellular ATP content, proton motive force, and activity of TCA cycle proteins suggest that SlyD regulates TCA cycle enzymes by controlling the formation of their indispensable Fe-S clusters.
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Affiliation(s)
- Milica Denic
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Evelyne Turlin
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Michel Betton
- Unité Adaptation au stress et Métabolisme chez les entérobactéries, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Daniel Vinella
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
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Thompson CC, Tschoeke D, Coutinho FH, Leomil L, Garcia GD, Otsuki K, Turcq BJ, Moreira LS, Turcq PFM, Cordeiro RC, Asp NE, Thompson FL. Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment. MICROBIAL ECOLOGY 2023; 86:2202-2209. [PMID: 37017718 DOI: 10.1007/s00248-023-02202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.
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Affiliation(s)
- Cristiane C Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Biomedical Engineer Program, COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Felipe H Coutinho
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Luciana Leomil
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto de Ciências Médicas, Centro Multidisciplinar UFRJ Macae, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Macae, Brazil
| | - Koko Otsuki
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno J Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Luciane S Moreira
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Patrícia F M Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Renato C Cordeiro
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Nils E Asp
- Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará (UFPA), Bragança, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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Torres J, Touati E. Mitochondrial Function in Health and Disease: Responses to Helicobacter pylori Metabolism and Impact in Gastric Cancer Development. Curr Top Microbiol Immunol 2023; 444:53-81. [PMID: 38231215 DOI: 10.1007/978-3-031-47331-9_3] [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: 01/18/2024]
Abstract
Mitochondria are major cellular organelles that play an essential role in metabolism, stress response, immunity, and cell fate. Mitochondria are organized in a network with other cellular compartments, functioning as a signaling hub to maintain cells' health. Mitochondrial dysfunctions and genome alterations are associated with diseases including cancer. Mitochondria are a preferential target for pathogens, which have developed various mechanisms to hijack cellular functions for their benefit. Helicobacter pylori is recognized as the major risk factor for gastric cancer development. H. pylori induces oxidative stress and chronic gastric inflammation associated with mitochondrial dysfunction. Its pro-apoptotic cytotoxin VacA interacts with the mitochondrial inner membrane, leading to increased permeability and decreased ATP production. Furthermore, H. pylori induces mitochondrial DNA damage and mutation, concomitant with the development of gastric intraepithelial neoplasia as observed in infected mice. In this chapter, we present diverse aspects of the role of mitochondria as energy supplier and signaling hubs and their adaptation to stress conditions. The metabolic activity of mitochondria is directly linked to biosynthetic pathways. While H. pylori virulence factors and derived metabolites are essential for gastric colonization and niche adaptation, they may also impact mitochondrial function and metabolism, and may have consequences in gastric pathogenesis. Importantly, during its long way to reach the gastric epithelium, H. pylori faces various cellular types along the gastric mucosa. We discuss how the mitochondrial response of these different cells is affected by H. pylori and impacts the colonization and bacterium niche adaptation and point to areas that remain to be investigated.
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Affiliation(s)
- Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatriıa, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Eliette Touati
- Equipe DMic01-Infection, Génotoxicité et Cancer, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, F-75015, Paris, France.
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Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function. Curr Opin Genet Dev 2022; 77:101987. [PMID: 36183585 DOI: 10.1016/j.gde.2022.101987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.
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Artificial Intelligence-based Blockchain Technology for Skin Cancer Investigation Complemented with Dietary Assessment and Recommendation using Correlation Analysis in Elder Individuals. J FOOD QUALITY 2022. [DOI: 10.1155/2022/3958596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the modern world, due to the usage of high-power chemical-based cosmetics, climate change, and other major factors, skin cancer has been increasing among individuals. Skin cancer is considered as the most common malignant disorder, and there are more than a million cases being recorded with this disease every year. Extensive studies have already been performed to identify the risk factors and causative agents for skin cancer, including lifestyle changes and eatery patterns among individuals. The most common type of skin cancer is classified into basal cell carcinoma and squamous cell carcinoma. The researcher intends to conduct the research with the primary goal of determining the important factors in blockchain technology in the treatment of skin cancer in senior people. The application of new technologies such as blockchain has enabled offering better promises to health care professionals in addressing skin cancer in a more effective manner. These tools supported in evaluating the nature and severity of psoriasis has been regarded as much support for health care professionals in detecting skin cancer and offer better health care guidance for better living. The detection of melanomas supports the patient in enhancing the prognosis and support in discriminating between the melanomas and less impact lesions. The blockchain-based classification system offers more benefits and reduces the cost of detecting skin cancer in an effective manner. It also helps the medical professionals by assisting them in developing a custom diet plan for each patient on the basis of their health records and food intake. The researchers are focused on applying both the primary data sources and secondary data sources for performing the study. A detailed questionnaire is designed, and it is shared with the participants through university hospitals, support groups, etc. so as to gather the information. Nearly 156 respondents were chosen through nonprobability sampling, and the information was collected. The researcher performs critical descriptive analysis, and correlation analysis is performed to understand the overall association between the variables. The researchers intend to perform the study with the basic goal of understanding the critical factors in blockchain technology in skin cancer for elderly individuals. The major factors involved are enhanced data privacy, support in forecasting patterns, and enhanced medical services to patients complemented with personalized dietary assessment and recommendations. The result demonstrates that artificial intelligence-based blockchain technology allows for the efficient processing of huge amounts of data in order to complete the assigned task and correctly determine and predict the model.
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