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Harikrishnan S, Kaushik D, Kumar M, Kaur J, Oz E, Proestos C, Elobeid T, Karakullukcu OF, Oz F. Vitamin B12: prevention of human beings from lethal diseases and its food application. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38922926 DOI: 10.1002/jsfa.13661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Vitamin B12, a water-soluble essential micronutrient, plays a pivotal role in numerous physiological processes in the human body. This review meticulously examines the structural complexity and the diverse mechanisms through which vitamin B12 exerts its preventive effects against a spectrum of health conditions, including pernicious anaemia, neurological disorders, obesity, diabetes, dyslipidaemia and complications in foetal development. The selection of articles for this review was conducted through a systematic search across multiple scientific databases, including PubMed, Scopus and Web of Science. Criteria for inclusion encompassed relevance to the biochemical impact of vitamin B12 on health, peer-reviewed status and publication within the last decade. Exclusion criteria were non-English articles and studies lacking empirical evidence. This stringent selection process ensured a comprehensive analysis of vitamin B12's multifaceted impact on health, covering its structure, bioavailable forms and mechanisms of action. Clinical studies highlighting its therapeutic potential, applications in food fortification and other utilizations are also discussed, underscoring the nutrient's versatility. This synthesis aims to provide a clear understanding of the integral role of vitamin B12 in maintaining human health and its potential in clinical and nutritional applications. © 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- S Harikrishnan
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara, India
| | - Deepika Kaushik
- Department of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, India
| | - Mukul Kumar
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara, India
| | - Jasjit Kaur
- Department of Food Technology and Nutrition, Lovely Professional University, Phagwara, India
| | - Emel Oz
- Department of Food Engineering, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
| | - Charalampos Proestos
- Laboratory of Food Chemistry, Department of Chemistry, School of Sciences, National and Kapodistrian University of Athens Zografou, Athens, Greece
| | - Tahra Elobeid
- Department of Human Nutrition, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Omur Fatih Karakullukcu
- Republic of Türkiye, Ministry National Education, General Directorate of Support Services, Ankara, Turkey
| | - Fatih Oz
- Department of Food Engineering, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
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Torrance EL, Diop A, Bobay LM. Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596828. [PMID: 38895235 PMCID: PMC11185547 DOI: 10.1101/2024.05.31.596828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotpots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.
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Affiliation(s)
- Ellis L Torrance
- Dept. of Biology, University of North Carolina Greensboro, Greensboro, NC 27412
- Systems Biology Dept., Sandia National Laboratories, Livermore, CA 94551
| | - Awa Diop
- Dept. of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Louis-Marie Bobay
- Dept. of Biology, University of North Carolina Greensboro, Greensboro, NC 27412
- Dept. of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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Valdez-Palomares F, Aguilar JR, Pérez-Campos E, Mayoral LPC, Meraz-Cruz N, Palacios-González B. Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity. PLoS One 2024; 19:e0302726. [PMID: 38743706 PMCID: PMC11093295 DOI: 10.1371/journal.pone.0302726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Dysbiosis during childhood impacts the configuration and maturation of the microbiota. The immaturity of the infant microbiota is linked with the development of inflammatory, allergic, and dysmetabolic diseases. AIMS To identify taxonomic changes associated with age and GDM and classify the maturity of the intestinal microbiota of children of mothers with GDM and children without GDM (n-GDM). METHODS Next-generation sequencing was used to analyze the V3-V4 region of 16S rRNA gene. QIIME2 and Picrust2 were used to determine the difference in the relative abundance of bacterial genera between the study groups and to predict the functional profile of the intestinal microbiota. RESULTS According to age, the older GDM groups showed a lower alpha diversity and different abundance of Enterobacteriaceae, Veillonella, Clostridiales, and Bacteroides. Regarding the functional profile, PWY-7377 and K05895 associated with Vitamin B12 metabolism were reduced in GDM groups. Compared to n-GDM group, GDM offspring had microbiota immaturity as age-discriminatory taxa in random forest failed to classify GDM offspring according to developmental age (OOB error 81%). Conclusion. Offspring from mothers with GDM have a distinctive taxonomic profile related to taxa associated with gut microbiota immaturity.
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Affiliation(s)
- Fernanda Valdez-Palomares
- Laboratorio de Envejecimiento Saludable, Instituto Nacional de Medicina Genómica, Centro de Investigación Sobre Envejecimiento (CIE-CINVESTAV Sur), Ciudad de México, México
| | | | - Eduardo Pérez-Campos
- Unidad de Bioquímica e Inmunología, Tecnológico Nacional de México-Instituto Tecnológico de Oaxaca, Oaxaca, México
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación Facultad de Medicina UNAM-UABJO, Facultad de Medicina y Cirugía, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca, México
| | - Noemi Meraz-Cruz
- Unidad de Vinculación Científica de la Facultad de Medicina UNAM en Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Berenice Palacios-González
- Laboratorio de Envejecimiento Saludable, Instituto Nacional de Medicina Genómica, Centro de Investigación Sobre Envejecimiento (CIE-CINVESTAV Sur), Ciudad de México, México
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Simonenko SY, Bogdanova DA, Kuldyushev NA. Emerging Roles of Vitamin B 12 in Aging and Inflammation. Int J Mol Sci 2024; 25:5044. [PMID: 38732262 PMCID: PMC11084641 DOI: 10.3390/ijms25095044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Vitamin B12 (cobalamin) is an essential nutrient for humans and animals. Metabolically active forms of B12-methylcobalamin and 5-deoxyadenosylcobalamin are cofactors for the enzymes methionine synthase and mitochondrial methylmalonyl-CoA mutase. Malfunction of these enzymes due to a scarcity of vitamin B12 leads to disturbance of one-carbon metabolism and impaired mitochondrial function. A significant fraction of the population (up to 20%) is deficient in vitamin B12, with a higher rate of deficiency among elderly people. B12 deficiency is associated with numerous hallmarks of aging at the cellular and organismal levels. Cellular senescence is characterized by high levels of DNA damage by metabolic abnormalities, increased mitochondrial dysfunction, and disturbance of epigenetic regulation. B12 deficiency could be responsible for or play a crucial part in these disorders. In this review, we focus on a comprehensive analysis of molecular mechanisms through which vitamin B12 influences aging. We review new data about how deficiency in vitamin B12 may accelerate cellular aging. Despite indications that vitamin B12 has an important role in health and healthy aging, knowledge of the influence of vitamin B12 on aging is still limited and requires further research.
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Affiliation(s)
- Sergey Yu. Simonenko
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Daria A. Bogdanova
- Division of Immunobiology and Biomedicine, Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Nikita A. Kuldyushev
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
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Yang CW, Hsu HY, Lee YZ, Lee SJ. Vitamin B12 inhibits peptidylarginine deiminases and ameliorates rheumatoid arthritis in CAIA mice. Biochem Biophys Res Commun 2024; 704:149668. [PMID: 38401303 DOI: 10.1016/j.bbrc.2024.149668] [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] [Received: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/26/2024]
Abstract
Rheumatoid arthritis is an autoimmune disease whose early onset correlates with dysregulated citrullination, a process catalyzed by peptidylarginine deiminase isoform 4 (PADI-4). Here, we report that PADI-4 is a novel target of vitamin B12, a water-soluble vitamin that serves as a cofactor in DNA synthesis and the metabolism of fatty and amino acids. Vitamin B12 preferentially inhibited PADI-4 over PADI-2 with comparable inhibitory activity to the reference compound Cl-amidine in enzymatic inhibition assays, and reduced total cellular citrullination levels including that of histone H3 citrullination mediated by PADI-4. We also demonstrated that hydroxocobalamin, a manufactured form of vitamin B12, significantly ameliorated the severity of collagen type II antibody induced arthritis (CAIA) in mice and diminished gene expression of the rheumatoid inflammatory factors and cytokines IL17A, TNFα, IL-6, COX-II and ANXA2, as well PADI-4. Therefore, the use of vitamin B12 to treat rheumatoid arthritis merits further study.
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Affiliation(s)
- Cheng-Wei Yang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Hsing-Yu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Yue-Zhi Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC
| | - Shiow-Ju Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan, ROC.
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Akita Y, Ueki A, Tonouchi A, Sugawara Y, Honma S, Kaku N, Ueki K. Brooklawnia propionicigenes sp. nov., a facultatively anaerobic, propionate-producing bacterium isolated from a methanogenic reactor treating waste from cattle farms. Int J Syst Evol Microbiol 2024; 74. [PMID: 38573743 DOI: 10.1099/ijsem.0.006320] [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: 04/05/2024] Open
Abstract
Facultatively anaerobic bacterial strains were isolated from samples of a methanogenic reactor and, based on 16S rRNA gene sequences, found to be affiliated with the family Propionibacteriaceae in the phylum Actinomycetota. Four strains with almost-identical 16S rRNA gene sequences were comprehensively characterized. The most closely related species to the strains was Brooklawnia cerclae BL-34T (96.4 % sequence similarity). Although most of the phenotypic characteristics of the four strains were identical, distinct differences in some cellular and physiological properties were also detected. Cells of the strains were Gram-stain-positive, non-spore-forming, pleomorphic rods. The strains utilized carbohydrates and organic acids. The strains produced acetate, propionate and lactate from glucose, but the molar ratios of the products were variable depending on the strains. The strains grew at 10-40 °C (optimum at 35 °C) and pH 5.3-8.8 (optimum at pH 6.8-7.5.) The major cellular fatty acids of the strains were anteiso-C15 : 0, C15 : 0 and C15 : 0 dimethylacetal (as a summed feature). The major respiratory quinone was menaquinone MK-9(H4) and the diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The genome size of the type strain (SH051T) was 3.21 Mb and the genome DNA G+C content was 65.7 mol%. Genes responsible for propionate production through the Wood-Werkman pathway were detected in the genome of strain SH051T. Based on the results of phylogenetic, genomic and phenotypic analyses of the novel strains, the name Brooklawnia propionicigenes sp. nov. is proposed to accommodate the four strains. The type strain of the novel species is SH051T (=NBRC 116195T=DSM 116141T).
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Affiliation(s)
- Yasumitsu Akita
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Atsuko Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Yoshimichi Sugawara
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Sachi Honma
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan
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Li X, Li Z, Wei Y, Chen Z, Xie S. Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii. Appl Environ Microbiol 2024; 90:e0185123. [PMID: 38426790 PMCID: PMC10952539 DOI: 10.1128/aem.01851-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Yajuan Wei
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zirui Chen
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Shijie Xie
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
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Oba K, Suenaga T, Yasuda S, Kuroiwa M, Hori T, Lackner S, Terada A. Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide. Microbes Environ 2024; 39:ME23106. [PMID: 38538312 PMCID: PMC10982107 DOI: 10.1264/jsme2.me23106] [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] [Received: 12/28/2023] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria and an exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.
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Affiliation(s)
- Kohei Oba
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
| | - Toshikazu Suenaga
- Department of Chemical Engineering, Hiroshima University, 1–4–1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739–8527, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
| | - Shohei Yasuda
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Megumi Kuroiwa
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16–1 Onogawa, Tsukuba, Ibaraki, 305–8569, Japan
| | - Susanne Lackner
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
- Department of Civil and Environmental Engineering Science, Institute IWAR, Chair of Water and Environmental Biotechnology Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287, Darmstadt, Germany
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2–24–16 Naka-cho, Koganei, Tokyo, 184–8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3–8–1 Harumi-cho, Fuchu, Tokyo, 185–8538, Japan
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Herrera-Calderon AC, Leal L, Suárez-Bautista JD, Manotas-Viloria HS, Muñoz-García A, Franco D, Arenas NE, Vanegas J. Metagenomic and genomic analysis of heavy metal-tolerant and -resistant bacteria in resource islands in a semi-arid zone of the Colombian Caribbean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5596-5609. [PMID: 38127234 PMCID: PMC10799150 DOI: 10.1007/s11356-023-30253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/29/2023] [Indexed: 12/23/2023]
Abstract
Bacteria from resource islands can adapt to different extreme conditions in semi-arid regions. We aimed to determine the potential resistance and tolerance to heavy metals from the bacterial community under the canopy of three resource islands in a semi-arid zone of the Colombian Caribbean. Total DNA was extracted from soil and through a metagenomics approach, we identified genes related to heavy metal tolerance and resistance under the influence of drought and humidity conditions, as well as the presence or absence of vegetation. We characterized the genomes of bacterial isolates cultivated in the presence of four heavy metals. The abundances of genes related to heavy metal resistance and tolerance were favored by soil moisture and the presence of vegetation. We observed a high abundance of resistance genes (60.4%) for Cu, Zn, and Ni, while 39.6% represented tolerance. These genes positively correlated with clay and silt content, and negatively correlated with sand content. Resistance and tolerance were associated with detoxification mechanisms involving oxidoreductase enzymes, metalloproteases, and hydrolases, as well as transmembrane proteins involved in metal transport such as efflux pumps and ion transmembrane transporters. The Bacillus velezensis C3-3 and Cytobacillus gottheilii T106 isolates showed resistance to 5 mM of Cd, Co, Mn, and Ni through detoxification genes associated with ABC pumps, metal transport proteins, ion antiporter proteins, and import systems, among others. Overall, these findings highlight the potential of bacteria from resource islands in bioremediation processes of soils contaminated with heavy metals.
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Affiliation(s)
| | - Leslie Leal
- Department of Biological and Environmental Sciences, Universidad Jorge Tadeo Lozano, Bogotá, Colombia
| | | | | | | | - Diego Franco
- Faculty of Biology, Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Nelson Enrique Arenas
- Faculty of Sciences, Department of Biology, Universidad Antonio Nariño, Bogotá, Colombia
| | - Javier Vanegas
- Faculty of Sciences, Department of Biology, Universidad Antonio Nariño, Bogotá, Colombia.
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Hernández Villamizar S, Chica Cárdenas LA, Morales Mancera LT, Vives Florez MJ. Anaerobiosis, a neglected factor in phage-bacteria interactions. Appl Environ Microbiol 2023; 89:e0149123. [PMID: 37966212 PMCID: PMC10734468 DOI: 10.1128/aem.01491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage infection in facultative anaerobic bacteria has not yet been studied. The absence of oxygen triggers metabolic changes in facultative bacteria and this affects phage infection and viral life cycle. Understanding how an anaerobic environment can alter the behavior of phages during infection is relevant for the phage therapy success.
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Gladysh NS, Bogdanova AS, Kovalev MA, Krasnov GS, Volodin VV, Shuvalova AI, Ivanov NV, Popchenko MI, Samoilova AD, Polyakova AN, Dmitriev AA, Melnikova NV, Karpov DS, Bolsheva NL, Fedorova MS, Kudryavtseva AV. Culturable Bacterial Endophytes of Wild White Poplar ( Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential. BIOLOGY 2023; 12:1519. [PMID: 38132345 PMCID: PMC10740426 DOI: 10.3390/biology12121519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology.
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Affiliation(s)
- Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Vsevolod V. Volodin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Anastasia I. Shuvalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Nikita V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Institute of Geography, Russian Academy of Sciences, Staromonetny Pereulok, 29/4, 119017 Moscow, Russia
| | - Aleksandra D. Samoilova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Aleksandra N. Polyakova
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; (A.D.S.); (A.N.P.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Dmitry S. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (N.S.G.); (A.S.B.); (M.A.K.); (G.S.K.); (V.V.V.); (A.I.S.); (N.V.I.); (M.I.P.); (A.A.D.); (N.V.M.); (D.S.K.); (N.L.B.); (M.S.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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12
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Beauvais M, Schatt P, Montiel L, Logares R, Galand PE, Bouget FY. Functional redundancy of seasonal vitamin B 12 biosynthesis pathways in coastal marine microbial communities. Environ Microbiol 2023; 25:3753-3770. [PMID: 38031968 DOI: 10.1111/1462-2920.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.
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Affiliation(s)
- Maxime Beauvais
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Philippe Schatt
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Lidia Montiel
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - François-Yves Bouget
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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13
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Fan L, Xia Y, Wang Y, Han D, Liu Y, Li J, Fu J, Wang L, Gan Z, Liu B, Fu J, Zhu C, Wu Z, Zhao J, Han H, Wu H, He Y, Tang Y, Zhang Q, Wang Y, Zhang F, Zong X, Yin J, Zhou X, Yang X, Wang J, Yin Y, Ren W. Gut microbiota bridges dietary nutrients and host immunity. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2466-2514. [PMID: 37286860 PMCID: PMC10247344 DOI: 10.1007/s11427-023-2346-1] [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: 01/01/2023] [Accepted: 04/05/2023] [Indexed: 06/09/2023]
Abstract
Dietary nutrients and the gut microbiota are increasingly recognized to cross-regulate and entrain each other, and thus affect host health and immune-mediated diseases. Here, we systematically review the current understanding linking dietary nutrients to gut microbiota-host immune interactions, emphasizing how this axis might influence host immunity in health and diseases. Of relevance, we highlight that the implications of gut microbiota-targeted dietary intervention could be harnessed in orchestrating a spectrum of immune-associated diseases.
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Affiliation(s)
- Lijuan Fan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoyao Xia
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Youxia Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Jiahuan Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Fu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Leli Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Zhending Gan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Bingnan Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jian Fu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenhua Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinbiao Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hui Han
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiwen He
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yulong Tang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Qingzhuo Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yibin Wang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Fan Zhang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China
| | - Xin Zong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China.
| | - Xihong Zhou
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Xi'an, 712100, China.
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Yulong Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China.
| | - Wenkai Ren
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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14
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Kazemzadeh K, Pelosi L, Chenal C, Chobert SC, Hajj Chehade M, Jullien M, Flandrin L, Schmitt W, He Q, Bouvet E, Jarzynka M, Varoquaux N, Junier I, Pierrel F, Abby SS. Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution. Mol Biol Evol 2023; 40:msad219. [PMID: 37788637 PMCID: PMC10597321 DOI: 10.1093/molbev/msad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.
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Affiliation(s)
- Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Clothilde Chenal
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Mahmoud Hajj Chehade
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Margaux Jullien
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Laura Flandrin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - William Schmitt
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Qiqi He
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Emma Bouvet
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Manon Jarzynka
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Nelle Varoquaux
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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15
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Zumsteg J, Hirschler A, Carapito C, Maurer L, Villette C, Heintz D, Dahl C, El Nayal A, Sangal V, Mahmoud H, Van Dorsselaer A, Ismail W. Mechanistic insights into sulfur source-driven physiological responses and metabolic reorganization in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8. Appl Environ Microbiol 2023; 89:e0082623. [PMID: 37655899 PMCID: PMC10537767 DOI: 10.1128/aem.00826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Comparative proteomics and untargeted metabolomics were combined to study the physiological and metabolic adaptations of Rhodococcus qingshengii IGTS8 under biodesulfurization conditions. After growth in a chemically defined medium with either dibenzothiophene (DBT) or MgSO4 as the sulfur source, many differentially produced proteins and metabolites associated with several metabolic and physiological processes were detected including the metabolism of carbohydrates, amino acids, lipids, nucleotides, vitamins, protein synthesis, transcriptional regulation, cell envelope biogenesis, and cell division. Increased production of the redox cofactor mycofactocin and associated proteins was one of the most striking adaptations under biodesulfurization conditions. While most central metabolic enzymes were less abundant in the presence of DBT, a key enzyme of the glyoxylate shunt, isocitrate lyase, was up to 26-fold more abundant. Several C1 metabolism and oligotrophy-related enzymes were significantly more abundant in the biodesulfurizing culture. R. qingshengii IGTS8 exhibited oligotrophic growth in liquid and solid media under carbon starvation. Moreover, the oligotrophic growth was faster on the solid medium in the presence of DBT compared to MgSO4 cultures. In the DBT culture, the cell envelope and phospholipids were remodeled, with lower levels of phosphatidylethanolamine and unsaturated and short-chain fatty acids being the most prominent changes. Biodesulfurization increased the biosynthesis of osmoprotectants (ectoine and mannosylglycerate) as well as glutamate and induced the stringent response. Our findings reveal highly diverse and overlapping stress responses that could protect the biodesulfurizing culture not only from the associated sulfate limitation but also from chemical, oxidative, and osmotic stress, allowing efficient resource management. IMPORTANCE Despite decades of research, a commercially viable bioprocess for fuel desulfurization has not been developed yet. This is mainly due to lack of knowledge of the physiology and metabolism of fuel-biodesulfurizing bacteria. Being a stressful condition, biodesulfurization could provoke several stress responses that are not understood. This is particularly important because a thorough understanding of the microbial stress response is essential for the development of environmentally friendly and industrially efficient microbial biocatalysts. Our comparative systems biology studies provide a mechanistic understanding of the biology of biodesulfurization, which is crucial for informed developments through the rational design of recombinant biodesulfurizers and optimization of the bioprocess conditions. Our findings enhance the understanding of the physiology, metabolism, and stress response not only in biodesulfurizing bacteria but also in rhodococci, a precious group of biotechnologically important bacteria.
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Affiliation(s)
- Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Loïc Maurer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Département mécanique, ICube Laboratoire des sciences de l’ingénieur, de l’informatique et de l’imagerie, UNISTRA/CNRS/ENGEES/INSA, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ashraf El Nayal
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Huda Mahmoud
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, Université de Strasbourg, IPHC UMR 7178, Infrastructure Nationale de Protéomique ProFI FR2048, Strasbourg, France
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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16
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Gomes Soares M, Bevilaqua GC, Marcondes Tassi ÉM, Reolon Schmidt VC. Fermented foods and beverages: a potential in situ vitamin B12 biofortification - a literature review. Int J Food Sci Nutr 2023; 74:655-667. [PMID: 37612883 DOI: 10.1080/09637486.2023.2248422] [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] [Received: 05/22/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Millions of dollars have been increasingly spent on plant-based diets. Considering that vitamin B12 is obtained from the consumption of animal-derived foods, new sources of vitamin B12 and methods of food fortification are being eagerly sought. Therefore, this work aims to evaluate advances in situ fermentation processes of food and beverages produced on a large scale and industrial applications for obtaining cobalamin-rich products. Bibliometric analysis was performed and revealed that several studies report a great capacity for in situ biofortification of B12 in foods, mostly on the use of propionic (PB) and lactic (LAB) bacteria. In this context, market potentials for such products, the main microorganisms, including simultaneous cultures, and their respective applications have been presented herein. Although knowledge on potential applications is still limited, field research has been increasingly conducted, thus revealing scientific and technological opportunities, both for the production and the stability of B12 found in plant-based foods.
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Affiliation(s)
- Marcelo Gomes Soares
- Department of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
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17
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McClements IF, McClements DJ. Designing healthier plant-based foods: Fortification, digestion, and bioavailability. Food Res Int 2023; 169:112853. [PMID: 37254427 DOI: 10.1016/j.foodres.2023.112853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 06/01/2023]
Abstract
Many consumers are incorporating more plant-based foods into their diets as a result of concerns about the environmental, ethical, and health impacts of animal sourced foods like meat, seafood, egg, and dairy products. Foods derived from animals negatively impact the environment by increasing greenhouse gas emissions, land use, water use, pollution, deforestation, and biodiversity loss. The livestock industry confines and slaughters billions of livestock animals each year. There are concerns about the negative impacts of some animal sourced foods, such as red meat and processed meat, on human health. The livestock industry is a major user of antibiotics, which is leading to a rise in the resistance of several pathogenic microorganisms to antibiotics. It is often assumed that a plant-based diet is healthier than one containing more animal sourced foods, but this is not necessarily the case. Eating more fresh fruits, vegetables, nuts, and whole grain cereals has been linked to improved health outcomes but it is unclear whether next-generation plant-based foods, such as meat, seafood, egg, and dairy analogs are healthier than the products they are designed to replace. Many of these new products are highly processed foods that contain high levels of saturated fat, sugar, starch, and salt, and low levels of micronutrients, nutraceuticals, and dietary fibers. Moreover, they are often rapidly digested in the gastrointestinal tract because processing disrupts plant tissues and releases the macronutrients. Consequently, it is important to formulate plant-based foods to reduce the levels of nutrients linked to adverse health effects and increase the levels linked to beneficial health effects. Moreover, it is important to design the food matrix so that the macronutrients are not digested and absorbed too quickly, but the micronutrients are highly bioavailable. In this article, we discuss how next-generation plant-based foods can be made healthier by controlling their nutrient profile, digestibility, and bioavailability.
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Mateos G, Martínez-Bonilla A, Martínez JM, Amils R. Vitamin B 12 Auxotrophy in Isolates from the Deep Subsurface of the Iberian Pyrite Belt. Genes (Basel) 2023; 14:1339. [PMID: 37510244 PMCID: PMC10378866 DOI: 10.3390/genes14071339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Vitamin B12 is an enzymatic cofactor that is essential for both eukaryotes and prokaryotes. The development of life in extreme environments depends on cofactors such as vitamin B12 as well. The genomes of twelve microorganisms isolated from the deep subsurface of the Iberian Pyrite Belt have been analyzed in search of enzymatic activities that require vitamin B12 or are involved in its synthesis and import. Results have revealed that vitamin B12 is needed by these microorganisms for several essential enzymes such as ribonucleotide reductase, methionine synthase and epoxyqueosine reductase. Isolate Desulfosporosinus sp. DEEP is the only analyzed genome that holds a set core of proteins that could lead to the production of vitamin B12. The rest are dependent on obtaining it from the subsurface oligotrophic environment in which they grow. Sought proteins involved in the import of vitamin B12 are not widespread in the sample. The dependence found in the genomes of these microorganisms is supported by the production of vitamin B12 by microorganisms such as Desulfosporosinus sp. DEEP, showing that the operation of deep subsurface biogeochemical cycles is dependent on cofactors such as vitamin B12.
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Affiliation(s)
- Guillermo Mateos
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Adrián Martínez-Bonilla
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José M Martínez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Astrobiología (CAB-INTA), 28850 Torrejón de Ardoz, Spain
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Agrawal D, Budakoti M, Kumar V. Strategies and tools for the biotechnological valorization of glycerol to 1, 3-propanediol: Challenges, recent advancements and future outlook. Biotechnol Adv 2023; 66:108177. [PMID: 37209955 DOI: 10.1016/j.biotechadv.2023.108177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Global efforts towards decarbonization, environmental sustainability, and a growing impetus for exploiting renewable resources such as biomass have spurred the growth and usage of bio-based chemicals and fuels. In light of such developments, the biodiesel industry will likely flourish, as the transport sector is taking several initiatives to attain carbon-neutral mobility. However, this industry would inevitably generate glycerol as an abundant waste by-product. Despite being a renewable organic carbon source and assimilated by several prokaryotes, presently realizing glycerol-based biorefinery is a distant reality. Among several platform chemicals such as ethanol, lactic acid, succinic acid, 2, 3-butanediol etc. 1, 3-propanediol (1, 3-PDO) is the only chemical naturally produced by fermentation with glycerol as a native substrate. The recent commercialization of glycerol-based 1, 3-PDO by Metabolic Explorer, France, has revived research interests in developing alternate cost-competitive, scalable and marketable bioprocesses. The current review outlines natural glycerol assimilating and 1, 3-PDO-producing microbes, their metabolic pathways, and associated genes. Later, technical barriers are carefully examined, such as the direct use of industrial glycerol as input material and genetic and metabolic issues related to microbes alleviating their industrial use. Biotechnological interventions exploited in the past five years, which can substantially circumvent these challenges, such as microbial bioprospecting, mutagenesis, metabolic, evolutionary and bioprocess engineering, including their combinations, are discussed in detail. The concluding section sheds light on some of the emerging and most promising breakthroughs which have resulted in evolving new, efficient, and robust microbial cell factories and/or bioprocesses for glycerol-based 1, 3-PDO production.
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Affiliation(s)
- Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, India.
| | - Mridul Budakoti
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
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Shanmugasundaram R, Lourenco J, Hakeem WA, Dycus MM, Applegate TJ. Subclinical doses of dietary fumonisins and deoxynivalenol cause cecal microbiota dysbiosis in broiler chickens challenged with Clostridium perfringens. Front Microbiol 2023; 14:1106604. [PMID: 37082176 PMCID: PMC10111830 DOI: 10.3389/fmicb.2023.1106604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Fusarium toxins are one of the most common contaminants in poultry diets. The co-occurrence of fumonisins (FUM) and deoxynivalenol (DON), even at a subclinical dose, negatively affects the growth performance, intestinal integrity and induce subclinical necrotic enteritis in broiler chickens. Loss of gut integrity can be expected to alter the intestinal microbiota’s composition. The objective of this study was to identify the effects of combined FUM and DON on the cecal microbiome profile and predicted metabolic functions and a short chain fatty acid profile in broilers challenged with Clostridium perfringens. A total of 240 1 day-old chicks were randomly assigned to two treatments: a control diet and the control diet with 3 mg/kg FUM + 4 mg/kg DON each with eight replications. All the birds were received cocci vaccine at d0. All birds in both treatment groups were challenged with C. perfringens 1 × 108 CFU via feed on d 19 and 20 to achieve 5% mortality. On d 35, the FUM and DON contaminated diet numerically (P = 0.06) decreased the body weight gain (BWG) by 84 g compared to the control group. The bacterial compositions of the cecal contents were analyzed by sequencing the V3–V4 region of the 16S rRNA gene. Overall, microbial richness and diversity increased (P < 0.02) during the studied period (d 21–35). Cecal contents of birds in the FUM + DON group had greater (P < 0.05) microbial evenness and diversity (Shannon index) compared to the control group. FUM + DON exposure decreased (P = 0.001) the relative abundance of Proteobacteria in the cecal content, compared to the control group. The combined FUM + DON significantly increased the relative abundance of the Defluviitaleaceae and Lachnospiraceae families (P < 0.05) but decreased the abundances of the Moraxellaceae and Streptococcaceae (P < 0.05) compared to the control group birds. At the genus level, FUM + DON exposure decreased (P < 0.05) Acinetobacter and Pseudomonas abundance and had a tendency (P = 0.08) to decrease Thermincola abundance compared to the control group. In the ileum, no NE-specific microscopic abnormalities were found; however, the tip of the ileal villi were compromised. The present findings showed that dietary FUM and DON contamination, even at subclinical levels, altered cecal microbial composition, dysregulated intestinal functions, and impaired the gut immune response, potentially predisposing the birds to necrotic enteritis.
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Affiliation(s)
- Revathi Shanmugasundaram
- Toxicology and Mycotoxin Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
- *Correspondence: Revathi Shanmugasundaram,
| | - Jeferson Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
- Jeferson Lourenco,
| | - Walid Al Hakeem
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Madison M. Dycus
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Todd J. Applegate
- Department of Poultry Science, University of Georgia, Athens, GA, United States
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Kumar R, Singh U, Tiwari A, Tiwari P, Sahu JK, Sharma S. Vitamin B12: Strategies for enhanced production, fortified functional food products and health benefits. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Mantareva V, Iliev I, Sulikovska I, Durmuş M, Angelov I. Cobalamin (Vitamin B12) in Anticancer Photodynamic Therapy with Zn(II) Phthalocyanines. Int J Mol Sci 2023; 24:ijms24054400. [PMID: 36901830 PMCID: PMC10002512 DOI: 10.3390/ijms24054400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Photodynamic therapy (PDT) is a curative method, firstly developed for cancer therapy with fast response after treatment and minimum side effects. Two zinc(II) phthalocyanines (3ZnPc and 4ZnPc) and a hydroxycobalamin (Cbl) were investigated on two breast cancer cell lines (MDA-MB-231 and MCF-7) in comparison to normal cell lines (MCF-10 and BALB 3T3). The novelty of this study is a complex of non-peripherally methylpyridiloxy substituted Zn(II) phthalocyanine (3ZnPc) and the evaluation of the effects on different cell lines due to the addition of second porphyrinoid such as Cbl. The results showed the complete photocytotoxicity of both ZnPc-complexes at lower concentrations (<0.1 μM) for 3ZnPc. The addition of Cbl caused a higher phototoxicity of 3ZnPc at one order lower concentrations (<0.01 μM) with a diminishment of the dark toxicity. Moreover, it was determined that an increase of the selectivity index of 3ZnPc, from 0.66 (MCF-7) and 0.89 (MDA-MB-231) to 1.56 and 2.31, occurred by the addition of Cbl upon exposure with a LED 660 nm (50 J/cm2). The study suggested that the addition of Cbl can minimize the dark toxicity and improve the efficiency of the phthalocyanines for anticancer PDT applications.
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Affiliation(s)
- Vanya Mantareva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Bld. 9, 1113 Sofia, Bulgaria
- Correspondence: or ; Tel.: +359-9606-181
| | - Ivan Iliev
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Bld. 25, 1113 Sofia, Bulgaria
| | - Inna Sulikovska
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Bld. 25, 1113 Sofia, Bulgaria
| | - Mahmut Durmuş
- Department of Chemistry, Gebze Technical University, Gebze 41400, Turkey
| | - Ivan Angelov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Bld. 9, 1113 Sofia, Bulgaria
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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity. Int J Mol Sci 2023; 24:ijms24044158. [PMID: 36835570 PMCID: PMC9966250 DOI: 10.3390/ijms24044158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.
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Calvillo Á, Pellicer T, Carnicer M, Planas A. Developing a single-stage continuous process strategy for vitamin B 12 production with Propionibacterium freudenreichii. Microb Cell Fact 2023; 22:26. [PMID: 36759843 PMCID: PMC9912679 DOI: 10.1186/s12934-023-02029-x] [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: 11/01/2022] [Accepted: 01/21/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Vitamin B12 is a widely used compound in the feed and food, healthcare and medical industries that can only be produced by fermentation because of the complexity of its chemical synthesis. Besides, the use of Generally Recognized as Safe (GRAS) and Qualified Presumption of Safety (QPS) microorganisms, like Propionibacterium freudenreichii, especially non-GMO wild-type producers, are becoming an interesting alternative in markets where many final consumers have high health and ecological awareness. In this study, the production of vitamin B12 using the Propionibacterium freudenreichii NBRC 12391 wild-type strain was characterized and optimized in shake flasks before assessing several scale-up strategies. RESULTS Initial results established that: (i) agitation during the early stages of the culture had an inhibitory effect on the volumetric production, (ii) 5,6-dimethylbenzimidazole (DMBI) addition was necessary for vitamin B12 production, and (iii) kinetics of vitamin B12 accumulation were dependent on the induction time when DMBI was added. When scaling up in a bioreactor, both batch and fed-batch bioprocesses proved unsuitable for obtaining high volumetric productivities mainly due to carbon source limitation and propionic acid inhibition, respectively. To overcome these drawbacks, an anaerobic single-phase continuous bioprocess strategy was developed. This culture strategy was maintained stable during more than 5 residence times in two independent cultures, resulting in 5.7-fold increase in terms of volumetric productivity compared to other scale-up strategies. CONCLUSION Overall, compared to previously reported strategies aimed to reduce propionic acid inhibition, a less complex anaerobic single-phase continuous and more scalable bioprocess was achieved.
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Affiliation(s)
- Álvaro Calvillo
- grid.6162.30000 0001 2174 6723Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain
| | | | - Marc Carnicer
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain.
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain.
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The antidiabetic drug metformin aids bacteria in hijacking vitamin B12 from the environment through RcdA. Commun Biol 2023; 6:96. [PMID: 36693976 PMCID: PMC9873799 DOI: 10.1038/s42003-023-04475-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Years of use of the antidiabetic drug metformin has long been associated with the risk of vitamin B12 (B12) deficiency in type 2 diabetes (T2D) patients, although the underlying mechanisms are unclear. Accumulating evidence has shown that metformin may exert beneficial effects by altering the metabolism of the gut microbiota, but whether it induces human B12 deficiency via modulation of bacterial activity remains poorly understood. Here, we show that both metformin and the other biguanide drug phenformin markedly elevate the accumulation of B12 in E. coli. By functional and genomic analysis, we demonstrate that both biguanides can significantly increase the expression of B12 transporter genes, and depletions of vital ones, such as tonB, nearly completely abolish the drugs' effect on bacterial B12 accumulation. Via high-throughput screens in E. coli and C. elegans, we reveal that the TetR-type transcription factor RcdA is required for biguanide-mediated promotion of B12 accumulation and the expressions of B12 transporter genes in bacteria. Together, our study unveils that the antidiabetic drug metformin helps bacteria gather B12 from the environment by increasing the expressions of B12 transporter genes in an RcdA-dependent manner, which may theoretically reduce the B12 supply to T2D patients taking the drug over time.
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Shift of Choline/Betaine Pathway in Recombinant Pseudomonas for Cobalamin Biosynthesis and Abiotic Stress Protection. Int J Mol Sci 2022; 23:ijms232213934. [PMID: 36430408 PMCID: PMC9699165 DOI: 10.3390/ijms232213934] [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: 10/16/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The B12-producing strains Pseudomonas nitroreducens DSM 1650 and Pseudomonas sp. CCUG 2519 (both formerly Pseudomonas denitrificans), with the most distributed pathway among bacteria for exogenous choline/betaine utilization, are promising recombinant hosts for the endogenous production of B12 precursor betaine by direct methylation of bioavailable glycine or non-proteinogenic β-alanine. Two plasmid-based de novo betaine pathways, distinguished by their enzymes, have provided an expression of the genes encoding for N-methyltransferases of the halotolerant cyanobacterium Aphanothece halophytica or plant Limonium latifolium to synthesize the internal glycine betaine or β-alanine betaine, respectively. These betaines equally allowed the recombinant pseudomonads to grow effectively and to synthesize a high level of cobalamin, as well as to increase their protective properties against abiotic stresses to a degree comparable with the supplementation of an exogenous betaine. Both de novo betaine pathways significantly enforced the protection of bacterial cells against lowering temperature to 15 °C and increasing salinity to 400 mM of NaCl. However, the expression of the single plant-derived gene for the β-alanine-specific N-methyltransferase additionally increased the effectiveness of exogenous glycine betaine almost twofold on cobalamin biosynthesis, probably due to the Pseudomonas' ability to use two independent pathways, their own choline/betaine pathway and the plant β-alanine betaine biosynthetic pathway.
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Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
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Firat CK, Ozkan BN, Guler EM. Beneficial effects of vitamin B 12 treatment in pediatric patients diagnosed with vitamin B 12 deficiency regarding total-native thiol, oxidative stress, and mononuclear leukocyte DNA damage. Free Radic Res 2022; 56:631-639. [PMID: 36571212 DOI: 10.1080/10715762.2022.2162392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Vitamin B12 is involved in biochemical metabolic pathways. B12 deficiency is common in childhood when the need for the vitamin increases and growth and development occur. Various hematological, neurological, psychiatric, and gastrointestinal disorders are observed in its deficiency. In addition, B12 deficiency is associated with oxidative stress and DNA damage. Therefore, the aim of our study is to evaluate oxidative stress, thiol/disulfide homeostasis, and DNA damage pre and post-treatment in children diagnosed with B12 deficiency. A total of 40 children with B12 deficiency were included in the study after the consent form was approved. Blood was drawn from children pre and posttreatment. Hemoglobin (HGB), hematocrit (HCT), and red blood cells (RBC) were measured by autoanalyzer; total antioxidant status (TAS), total oxidant status (TOS), total thiol (TT), and native thiol (NT) were measured by the photometric method, and DNA damage was analyzed by the comet assay method. Oxidative stress index (OSI) and disulfide (DIS) values were calculated. As a result of the experiments, HGB, HCT, and RBC increased with treatment. While TAS, TT, and NT as antioxidant parameters increased; TOS, OSI, and DIS decreased with treatment compared to pretreatment. DNA damage was also found to decrease with treatment. Additionally, these data were statistically significant (p < 0.001). It was found that oxidative stress and DNA damage decreased with oral B12 treatment in children with B12 deficiency, and clinical parameters were also improved.
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Affiliation(s)
- Cem Koray Firat
- Department of Pediatry, Bezmialem Vakif University School of Medicine, Istanbul, Turkey
| | - Beyza Nur Ozkan
- Department of Medical Biochemistry, University of Health Sciences Turkey, Hamidiye School of Medicine, Istanbul, Turkey
| | - Eray Metin Guler
- Department of Medical Biochemistry, University of Health Sciences Turkey, Hamidiye School of Medicine, Istanbul, Turkey.,Department of Medical Biochemistry, University of Health Sciences Turkey, Hamidiye Faculty of Medicine, Haydarpasa Numune Health Application and Research Center, Istanbul, Turkey
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29
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Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt. Microorganisms 2022; 10:microorganisms10081585. [PMID: 36014003 PMCID: PMC9415397 DOI: 10.3390/microorganisms10081585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.
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Bioprocess Strategies for Vitamin B12 Production by Microbial Fermentation and Its Market Applications. Bioengineering (Basel) 2022; 9:bioengineering9080365. [PMID: 36004890 PMCID: PMC9405231 DOI: 10.3390/bioengineering9080365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Vitamin B12 is a widely used compound in the feed and food, healthcare and medical industries that can only be produced by fermentation because of the complexity of its chemical synthesis. For this reason, finding better producer strains and optimizing their bioprocesses have been the main focus of industrial producers over the last few decades. In this review, we initially provide a historical overview of vitamin B12 research and the main biosynthetic characteristics of the two microorganism families typically used for its industrial production: several strains of Propionibacterium freudenreichii and strains related to Pseudomonas denitrificans. Later, a complete summary of the current state of vitamin B12 industrial production as well as the main advances and challenges for improving it is detailed, with a special focus on bioprocess optimization, which aims not only to increase production but also sustainability. In addition, a comprehensive list of the most important and relevant patents for the present industrial strains is provided. Finally, the potential applications of vitamin B12 in different markets are discussed.
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Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [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] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
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Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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Daghio M, Pini F, Espinoza-Tofalos A, Conte G, Mari E, Giannerini F, Giovannetti L, Buccioni A, Franzetti A, Granchi L, Mele M, Rampazzo G, Gazzotti T, Zironi E, Viti C. Characterization of the microbial community in ripened Pecorino Toscano cheese affected by pink discoloration. Food Microbiol 2022; 104:104006. [DOI: 10.1016/j.fm.2022.104006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/03/2022] [Accepted: 02/17/2022] [Indexed: 02/07/2023]
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Mathur Y, Vartak AR, Hazra AB. Guardian of cobamide diversity: Probing the role of CobT in lower ligand activation in the biosynthesis of vitamin B 12 and other cobamide cofactors. Methods Enzymol 2022; 668:25-59. [PMID: 35589196 DOI: 10.1016/bs.mie.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Enzymes catalyze a wide variety of reactions with exquisite precision under crowded conditions within cellular environments. When encountered with a choice of small molecules in their vicinity, even though most enzymes continue to be specific about the substrate they pick, some others are able to accept a range of substrates and subsequently produce a variety of products. The biosynthesis of Vitamin B12, an essential nutrient required by humans involves a multi-substrate α-phosphoribosyltransferase enzyme CobT that activates the lower ligand of B12. Vitamin B12 is a member of the cobamide family of cofactors which share a common tetrapyrrolic corrin scaffold with a centrally coordinated cobalt ion, and an upper and a lower ligand. The structural difference between B12 and other cobamides mainly arises from variations in the lower ligand, which is attached to the activated corrin ring by CobT and other downstream enzymes. In this chapter, we describe the steps involved in identifying and reconstituting the activity of new CobT homologs by deriving lessons from those previously characterized. We then highlight biochemical techniques to study the unique properties of these homologs. Finally, we describe a pairwise substrate competition assay to rank CobT substrate preference, a general method that can be applied for the study of other multi-substrate enzymes. Overall, the analysis with CobT provides insights into the range of cobamides that can be synthesized by an organism or a community, complementing efforts to predict cobamide diversity from complex metagenomic data.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Aniket R Vartak
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India; Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, India.
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Vásquez L, Parra A, Quesille-Villalobos AM, Gálvez G, Navarrete P, Latorre M, Toro M, González M, Reyes-Jara A. Cobalamin cbiP mutant shows decreased tolerance to low temperature and copper stress in Listeria monocytogenes. Biol Res 2022; 55:9. [PMID: 35236417 PMCID: PMC8889760 DOI: 10.1186/s40659-022-00376-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Background Listeria monocytogenes is a foodborne pathogen that causes listeriosis in humans. This pathogen activates multiple regulatory mechanisms in response to stress, and cobalamin biosynthesis might have a potential role in bacterial protection. Low temperature is a strategy used in the food industry to control bacteria proliferation; however, L. monocytogenes can grow in cold temperatures and overcome different stress conditions. In this study we selected L. monocytogenes List2-2, a strain with high tolerance to the combination of low temperature + copper, to understand whether the cobalamin biosynthesis pathway is part of the tolerance mechanism to this stress condition. For this, we characterized the transcription level of three cobalamin biosynthesis-related genes (cbiP, cbiB, and cysG) and the eutV gene, a transcriptional regulator encoding gene involved in ethanolamine metabolism, in L. monocytogenes strain List2-2 growing simultaneously under two environmental stressors: low temperature (8 °C) + copper (0.5 mM of CuSO4 × 5H2O). In addition, the gene cbiP, which encodes an essential cobyric acid synthase required in the cobalamin pathway, was deleted by homologous recombination to evaluate the impact of this gene in L. monocytogenes tolerance to a low temperature (8 °C) + different copper concentrations. Results By analyzing the KEGG pathway database, twenty-two genes were involved in the cobalamin biosynthesis pathway in L. monocytogenes List2-2. The expression of genes cbiP, cbiB, and cysG, and eutV increased 6 h after the exposure to low temperature + copper. The cobalamin cbiP mutant strain List2-2ΔcbiP showed less tolerance to low temperature + copper (3 mM) than the wild-type L. monocytogenes List2-2. The addition of cyanocobalamin (5 nM) to the medium reverted the phenotype observed in List2-2ΔcbiP. Conclusion These results indicate that cobalamin biosynthesis is necessary for L. monocytogenes growth under stress and that the cbiP gene may play a role in the survival and growth of L. monocytogenes List2-2 at low temperature + copper. Supplementary Information The online version contains supplementary material available at 10.1186/s40659-022-00376-4.
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Affiliation(s)
- L Vásquez
- Laboratorio de Microbiología y Probióticos, INTA Universidad de Chile, Avenida El Líbano 5524 Macul, Santiago, Chile
| | - A Parra
- Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.,Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - A M Quesille-Villalobos
- Laboratorio de Microbiología y Probióticos, INTA Universidad de Chile, Avenida El Líbano 5524 Macul, Santiago, Chile
| | - G Gálvez
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - P Navarrete
- Laboratorio de Microbiología y Probióticos, INTA Universidad de Chile, Avenida El Líbano 5524 Macul, Santiago, Chile.,ANID-Millennium Science Initiative Program-Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - M Latorre
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - M Toro
- Laboratorio de Microbiología y Probióticos, INTA Universidad de Chile, Avenida El Líbano 5524 Macul, Santiago, Chile
| | - M González
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Fondap Center for Genome Regulation (CGR), Santiago, Chile
| | - A Reyes-Jara
- Laboratorio de Microbiología y Probióticos, INTA Universidad de Chile, Avenida El Líbano 5524 Macul, Santiago, Chile.
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Ma AT, Kantner DS, Beld J. Cobamide remodeling. VITAMINS AND HORMONES 2022; 119:43-63. [PMID: 35337629 DOI: 10.1016/bs.vh.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cobamides are a family of structurally-diverse cofactors which includes vitamin B12 and over a dozen natural analogs. Within the nucleotide loop structure, cobamide analogs have variable lower ligands that fall into three categories: benzimidazoles, purines, and phenols. The range of cobamide analogs that can be utilized by an organism is dependent on the specificity of its cobamide-dependent enzymes, and most bacteria are able to utilize multiple analogs but not all. Some bacteria have pathways for cobamide remodeling, a process in which imported cobamides are converted into compatible analogs. Here we discuss cobamide analog diversity and three pathways for cobamide remodeling, mediated by amidohydrolase CbiZ, phosphodiesterase CbiR, and some homologs of cobamide synthase CobS. Remodeling proteins exhibit varying degrees of specificity for cobamide substrates, reflecting different strategies to ensure that imported cobamides can be utilized.
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Affiliation(s)
- Amy T Ma
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States.
| | - Daniel S Kantner
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Joris Beld
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
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Hu J, Guo P, Mao R, Ren Z, Wen J, Yang Q, Yan T, Yu J, Zhang T, Liu Y. Gut Microbiota Signature of Obese Adults Across Different Classifications. Diabetes Metab Syndr Obes 2022; 15:3933-3947. [PMID: 36601354 PMCID: PMC9807070 DOI: 10.2147/dmso.s387523] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/28/2022] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Obesity is currently a major global public health issue. It has been shown by many that gut microbiota and microbial factors regulate the pathogenesis of obesity and metabolic abnormalities, but little is known about their roles in the different degrees of obesity. Here, we sought to investigate the microbial signatures of obesity of various severities. PATIENTS AND METHODS We did this by characterizing the intestinal microbiome signature in a Chinese cohort of obese patients and healthy controls using 16S rRNA gene sequencing. To this end, obesity was sub-divided into four subgroups, including "Overweight", Class I, Class II, and Class III obesity, based on body mass index (BMI). RESULTS Microbial diversity decreased in obese subjects, and the reduction trend was correlated with the severity of obesity. We detected an expansion of Escherichia shigella in obese patients compared to healthy controls. The family Eubacterium coprostanoligenes and Tannerellaceae, the genera Eubacterium coprostanoligenes, Lachnospiraceae NK4A136, Parabacteroides, and Akkermansia, and the species Prevotella copri were microbial biomarkers of healthy people. Gammaproteobacteria and Enterobacterales were biomarkers of being "Overweight". Erysipelatoclostridiaceae was a biomarker of Class I obesity. The class Bacilli and the order Lactobacillales were both biomarkers of Class II obesity. Negativicutes was a biomarker of Class III obesity. We further established relationships between this microbiome data and other biochemical data, including albumin, low-density lipoprotein (LDL), high-density lipoprotein (HDL), vitamin folic acid (FA) and vitamin B12 (VB12), and Interleukin-6 (IL-6) levels. Function prediction results showed a marked energy metabolism dysbiosis in obesity, especially in patients with Class III obesity. CONCLUSION These results suggested that people with different levels of obesity had distinct gut microbial signatures. Decreased microbial diversity, depletion of some specific taxa, and deviation in potential functions mirrored the severity of obesity in this cohort.
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Affiliation(s)
- Junqing Hu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- Medical Research Center, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Pengsen Guo
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Rui Mao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Zhengyun Ren
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- College of Medicine, Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Jun Wen
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- College of Medicine, Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Qin Yang
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Tong Yan
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Jiahui Yu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
| | - Tongtong Zhang
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- Medical Research Center, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
- Correspondence: Tongtong Zhang, Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, & Medical Research Center, the Third People’s Hospital of Chengdu, Chengdu, People’s Republic of China, Email ; Yanjun Liu, Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, No. 82, Qinglong Street, Qingyang District, Chengdu, 610031, People’s Republic of China, Emai
| | - Yanjun Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, People’s Republic of China
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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Stasiuk R, Krucoń T, Matlakowska R. Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline). Molecules 2021; 26:6746. [PMID: 34771152 PMCID: PMC8587615 DOI: 10.3390/molecules26216746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
This study describes for the first time the comprehensive characterization of tetrapyrrole cofactor biosynthetic pathways developed for bacterial community (BC) inhabiting shale rock. Based on the genomic and proteomic metadata, we have detailed the biosynthesis of siroheme, heme, cobalamin, and the major precursor uroporphyrinogen III by a deep BC living on a rock containing sedimentary tetrapyrrole compounds. The obtained results showed the presence of incomplete heme and cobalamin biosynthesis pathways in the studied BC. At the same time, the production of proteins containing these cofactors, such as cytochromes, catalases and sulfite reductase, was observed. The results obtained are crucial for understanding the ecology of bacteria inhabiting shale rock, as well as their metabolism and potential impact on the biogeochemistry of these rocks. Based on the findings, we hypothesize that the bacteria may use primary or modified sedimentary porphyrins and their degradation products as precursors for synthesizing tetrapyrrole cofactors. Experimental testing of this hypothesis is of course necessary, but its evidence would point to an important and unique phenomenon of the tetrapyrrole ring cycle on Earth involving bacteria.
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Affiliation(s)
- Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Renata Matlakowska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
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Shchapova E, Nazarova A, Vasilyeva U, Gurkov A, Ostyak A, Mutin A, Adelshin R, Belkova N, Timofeyev M. Cellular Immune Response of an Endemic Lake Baikal Amphipod to Indigenous Pseudomonas sp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:463-471. [PMID: 34076776 DOI: 10.1007/s10126-021-10039-2] [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: 09/02/2020] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Studies of invertebrates have shown that the internal environment of crustaceans is not always sterile in normal conditions, and in many species, it can be populated by microorganisms even in the absence of any visible pathological processes in the body. This observation raises the question of whether genetically modified indigenous hemolymph microorganisms can be used for biotechnological purposes inside the crustacean either as local producers of some compounds or as sensors to physiological parameters. In this study, we tested the ability of the bacteria isolated from the hemolymph of the amphipod Eulimnogammarus verrucosus to hide from the cellular immune response of the host as the most important feature for their potential long-term application in vivo. 16S rDNA amplicon sequencing revealed five common bacterial genera in all analyzed samples of the amphipod hemolymph, among which Pseudomonas is most easily subjected to genome modification and, thus, the most prospective for biotechnological application. Cultivation of Pseudomonas gave us a number of strains undoubtedly derived from the amphipod hemolymph, and one of them (belonging to the Pseudomonas fluorescens group) was chosen for further tests. The primary culture of amphipod hemocytes was used to analyze the immunogenicity of the strain and showed a pronounced reaction of the immune cells to a high amount of the bacteria within six hours. This result indicates that modulation of cellular immune response to metabolically active bacterial cells is not mandatory for the survival and wide distribution of these microorganisms in the hemolymph of numerous amphipod individuals.
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Affiliation(s)
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Alexander Ostyak
- Irkutsk Anti-Plague Research Institute of Siberia and Far East, Irkutsk, Russia
| | | | - Renat Adelshin
- Irkutsk State University, Irkutsk, Russia
- Irkutsk Anti-Plague Research Institute of Siberia and Far East, Irkutsk, Russia
| | - Natalia Belkova
- Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia.
- Baikal Research Centre, Irkutsk, Russia.
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Jackson HO, Taunt HN, Mordaka PM, Smith AG, Purton S. The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:708370. [PMID: 34630459 PMCID: PMC8497815 DOI: 10.3389/fpls.2021.708370] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
Sustainable and economically viable support for an ever-increasing global population requires a paradigm shift in agricultural productivity, including the application of biotechnology to generate future crop plants. Current genetic engineering approaches aimed at enhancing the photosynthetic efficiency or composition of the harvested tissues involve relatively simple manipulations of endogenous metabolism. However, radical rewiring of central metabolism using new-to-nature pathways, so-called "synthetic metabolism", may be needed to really bring about significant step changes. In many cases, this will require re-programming the metabolism of the chloroplast, or other plastids in non-green tissues, through a combination of chloroplast and nuclear engineering. However, current technologies for sophisticated chloroplast engineering ("transplastomics") of plants are limited to just a handful of species. Moreover, the testing of metabolic rewiring in the chloroplast of plant models is often impractical given their obligate phototrophy, the extended time needed to create stable non-chimeric transplastomic lines, and the technical challenges associated with regeneration of whole plants. In contrast, the unicellular green alga, Chlamydomonas reinhardtii is a facultative heterotroph that allows for extensive modification of chloroplast function, including non-photosynthetic designs. Moreover, chloroplast engineering in C. reinhardtii is facile, with the ability to generate novel lines in a matter of weeks, and a well-defined molecular toolbox allows for rapid iterations of the "Design-Build-Test-Learn" (DBTL) cycle of modern synthetic biology approaches. The recent development of combinatorial DNA assembly pipelines for designing and building transgene clusters, simple methods for marker-free delivery of these clusters into the chloroplast genome, and the pre-existing wealth of knowledge regarding chloroplast gene expression and regulation in C. reinhardtii further adds to the versatility of transplastomics using this organism. Herein, we review the inherent advantages of the algal chloroplast as a simple and tractable testbed for metabolic engineering designs, which could then be implemented in higher plants.
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Affiliation(s)
- Harry O. Jackson
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Henry N. Taunt
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Pawel M. Mordaka
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Saul Purton
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
- *Correspondence: Saul Purton
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