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Boone CHT, Gutzmann DJ, Kramer JJ, Urbin SD, Navarathna DH, Atkin AL, Nickerson KW. Micronutrient availability alters Candida albicans growth and farnesol accumulation: implications for studies using RPMI-1640. Microbiol Spectr 2024:e0157124. [PMID: 39315785 DOI: 10.1128/spectrum.01571-24] [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: 06/27/2024] [Accepted: 08/19/2024] [Indexed: 09/25/2024] Open
Abstract
Science is challenging because we do not know what we do not know. Commercial chemicals are often marketed with >99% purity, but 0.5-1% impurity can impact results and cloud data interpretation. We recently developed an assay for farnesol and aromatic fusel alcohols from Candida albicans. During proof-of-concept experiments using RPMI-1640 growth media, the buffering compound was switched from MOPS obtained from Acros Organics to MOPS obtained from Sigma-Aldrich, both labeled 99% + purity. We observed a twofold decrease in growth, along with a three- to fivefold increase in farnesol production per cell upon the switch. ICP-MS showed that trace Mn(II) was present in Acros MOPS but absent in Sigma MOPS. Optimal growth was achieved by the addition of Mn(II), Zn(II), and Fe(II). We established upper and lower limits for Fe(II), Zn(II), Cu(II), and Mn(II) that allowed similar growth and then assessed 16 different mineral combinations in RPMI-1640 base media. The results show an increased production of farnesol and the aromatic fusel alcohols when Zn(II) is abundant, and a further increase in the aromatic fusel alcohols when both Fe(II) and Zn(II) are abundant. Finally, antifungal susceptibility testing displayed no significant difference between RPMI/MOPS with and without mineral supplementation. Supplemental Mn(II) was most needed for cell growth, while supplemental Zn(II) was most needed for the production of farnesol and the aromatic fusel alcohols. To avoid these artifacts due to metal contamination, we now use a modified RPMI supplemented with 1 mg/ L of Cu(II), Zn(II), Mn(II), and Fe(II). IMPORTANCE The dimorphic fungus Candida albicans is a major opportunistic pathogen of humans. RPMI-1640 is a chemically defined growth medium commonly used with C. albicans. We identified over 32,000 publications with keywords RPMI and C. albicans. Additionally, Antifungal Susceptibility Testing (AFST) protocols in the United States (CLSI) and Europe (EUCAST) utilize RPMI as a base media to assess drug efficacy against clinical fungal isolates. RPMI contains many nutrients but no added trace metals. We found that the growth characteristics with RPMI were dependent on which MOPS buffer was chosen and the contamination of that buffer by trace levels of Mn(II) and Zn(II). Added Mn(II) was most needed for cell growth while added Zn(II) was most needed for secretion of farnesol and other signaling molecules.
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Affiliation(s)
- Cory H T Boone
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Daniel J Gutzmann
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Jaxon J Kramer
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Shyanne D Urbin
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | | | - Audrey L Atkin
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Kenneth W Nickerson
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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2
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Islam DT, Williams MR, Teppen BJ, Johnston CT, Li H, Boyd SA, Zylstra GJ, Fennell DE, Cupples AM, Hashsham SA. Comprehensive model for predicting toxic equivalents (TEQ) reduction due to dechlorination of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/F congeners). JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135749. [PMID: 39276747 DOI: 10.1016/j.jhazmat.2024.135749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/17/2024] [Accepted: 09/03/2024] [Indexed: 09/17/2024]
Abstract
Remediation-focused predictive tools for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) rely on transformation models to evaluate the reduction in total contaminant load and toxic equivalency (TEQ). In this study, a comprehensive model predicting the profiles of PCDD/F congeners and the associated TEQs was developed. The model employs first-order kinetics to describe the transformation of 256 reactions for 75 PCDD congeners and 421 reactions for 135 PCDF congeners. It integrates the growth of anaerobic microbial guilds using Monod kinetics on hydrogen release compounds and stoichiometric growth for Dehalococcoides sp. The effects of temperature, salinity, pH, and availability of vitamin B12 (a cofactor) were also integrated. The PCDD/F congeners model was used to extract the first-order dechlorination rate constants from a number of pure culture and mixed microbial microcosm studies. Simulations for the transformation of PCDD/F congeners at concentrations representative of the Tittabawassee or Saginaw Rivers and watershed in MI, USA were carried out. For a starting TEQ of 5000 ng per kg dry sediment (ppt), the model predicted a decrease in the overall TEQ to below 2000 ppt after 2.6 years and below 250 ppt after ∼21 years. The developed model may be used for extracting rates from microcosm studies and to evaluate the effect of engineering interventions on TEQ reduction.
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Affiliation(s)
- Dar Tafazul Islam
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Maggie R Williams
- School of Engineering and Technology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Brian J Teppen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Cliff T Johnston
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Stephen A Boyd
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Gerben J Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Donna E Fennell
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
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3
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Martínez Felices JM, Barreto YB, Thangaratnarajah C, Whittaker JJ, Alencar AM, Guskov A, Slotboom DJ. Cobalamin decyanation by the membrane transporter BtuM. Structure 2024; 32:1165-1173.e3. [PMID: 38733996 DOI: 10.1016/j.str.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
BtuM is a bacterial cobalamin transporter that binds the transported substrate in the base-off state, with a cysteine residue providing the α-axial coordination of the central cobalt ion via a sulfur-cobalt bond. Binding leads to decyanation of cobalamin variants with a cyano group as the β-axial ligand. Here, we report the crystal structures of untagged BtuM bound to two variants of cobalamin, hydroxycobalamin and cyanocobalamin, and unveil the native residue responsible for the β-axial coordination, His28. This coordination had previously been obscured by non-native histidines of His-tagged BtuM. A model in which BtuM initially binds cobinamide reversibly with low affinity (KD = 4.0 μM), followed by the formation of a covalent bond (rate constant of 0.163 s-1), fits the kinetics data of substrate binding and decyanation of the cobalamin precursor cobinamide by BtuM. The covalent binding mode suggests a mechanism not used by any other transport protein.
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Affiliation(s)
- Jose M Martínez Felices
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Yan Borges Barreto
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands; Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Jacob J Whittaker
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Adriano M Alencar
- Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Albert Guskov
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Dirk J Slotboom
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands.
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4
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Lu Y, Lu F, Zhang J, Tang Q, Yang D, Liu Y. Understanding the sources, function, and irreplaceable role of cobamides in organohalide-respiring bacteria. Front Microbiol 2024; 15:1435674. [PMID: 39139376 PMCID: PMC11321594 DOI: 10.3389/fmicb.2024.1435674] [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: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 08/15/2024] Open
Abstract
Halogenated organic compounds are persistent pollutants that pose a serious threat to human health and the safety of ecosystems. Cobamides are essential cofactors for reductive dehalogenases (RDase) in organohalide-respiring bacteria (OHRB), which catalyze the dehalogenation process. This review systematically summarizes the impact of cobamides on organohalide respiration. The catalytic processes of cobamide in dehalogenation processes are also discussed. Additionally, we examine OHRB, which cannot synthesize cobamide and must obtain it from the environment through a salvage pathway; the co-culture with cobamide producer is more beneficial and possible. This review aims to help readers better understand the importance and function of cobamides in reductive dehalogenation. The presented information can aid in the development of bioremediation strategies.
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Affiliation(s)
- Yongfeng Lu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Fancheng Lu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Jian Zhang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Qianwei Tang
- College & Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Dan Yang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
- Guangxi Yuhuacheng Environmental Protection Technology Co., Nanning, China
| | - Yaqing Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
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Voshall A, Gutzmann DJ, Verdaguer IB, Crispim M, Boone CH, Atkin AL, Nickerson KW. Absence of farnesol salvage in Candida albicans and probably in other fungi. Appl Environ Microbiol 2024; 90:e0087424. [PMID: 38940563 PMCID: PMC11267938 DOI: 10.1128/aem.00874-24] [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: 05/02/2024] [Accepted: 06/08/2024] [Indexed: 06/29/2024] Open
Abstract
Farnesol salvage, a two-step pathway converting farnesol to farnesyl pyrophosphate (FPP), occurs in bacteria, plants, and animals. This paper investigates the presence of this pathway in fungi. Through bioinformatics, biochemistry, and physiological analyses, we demonstrate its absence in the yeasts Saccharomyces cerevisiae and Candida albicans, suggesting a likely absence across fungi. We screened 1,053 fungal genomes, including 34 from C. albicans, for potential homologs to four genes (Arabidopsis thaliana AtFOLK, AtVTE5, AtVTE6, and Plasmodium falciparum PfPOLK) known to accomplish farnesol/prenol salvage in other organisms. Additionally, we showed that 3H-farnesol was not converted to FPP or any other phosphorylated prenol, and exogenous farnesol was not metabolized within 90 minutes at any phase of growth and did not rescue cells from the toxic effects of atorvastatin, but it did elevate the levels of intracellular farnesol (Fi). All these experiments were conducted with C. albicans. In sum, we found no evidence for farnesol salvage in fungi. IMPORTANCE The absence of farnesol salvage constitutes a major difference in the metabolic capabilities of fungi. In terms of fungal physiology, the lack of farnesol salvage pathways relates to how farnesol acts as a quorum-sensing molecule in Candida albicans and why farnesol should be investigated for use in combination with other known antifungal antibiotics. Its absence is essential for a model (K. W. Nickerson et al., Microbiol Mol Biol Rev 88:e00081-22, 2024), wherein protein farnesylation, protein chaperones, and the unfolded protein response are combined under the unifying umbrella of a cell's intracellular farnesol (Fi). In terms of human health, farnesol should have at least two different modes of action depending on whether those cells have farnesol salvage. Because animals have farnesol salvage, we can now see the importance of dietary prenols as well as the potential importance of farnesol in treating neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, and multiple sclerosis.
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Affiliation(s)
- Adam Voshall
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel J. Gutzmann
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Cory H.T. Boone
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Audrey L. Atkin
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kenneth W. Nickerson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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6
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Muhammad N, Avila F, Kim SG. Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov. BMC Microbiol 2024; 24:245. [PMID: 38970021 PMCID: PMC11225308 DOI: 10.1186/s12866-024-03393-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. RESULTS To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5-76.5% for ANI and 18.1-25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3-6), Cu2+ (0.2-0.4), Ni2+ (3-5), Zn2+ (2-4), Mn2+ (20-50), and Hg2+ (0.3). CONCLUSIONS Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).
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Affiliation(s)
- Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea
| | - Forbes Avila
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea ResearchInstitute of Bioscience and Biotechnology, Jeongeup, Jeonbuk, 56212, the Republic of Korea.
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon, 34113, the Republic of Korea.
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7
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B 12. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580003. [PMID: 38405713 PMCID: PMC10888822 DOI: 10.1101/2024.02.12.580003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Alexa M. Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zoila I. Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Ella T. Sieradzki
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, 94550 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | - Jillian F. Banfield
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Hans K. Carlson
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Mary K. Firestone
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
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8
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Diver P, Ward BA, Cunliffe M. Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean. FEMS Microbiol Ecol 2024; 100:fiae053. [PMID: 38599628 PMCID: PMC11062419 DOI: 10.1093/femsec/fiae053] [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: 08/09/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterized the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilization is present but not universal in marine yeasts, consistent with existing knowledge of nonmarine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.
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Affiliation(s)
- Poppy Diver
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Ben A Ward
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, United Kingdom
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9
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12. THE ISME JOURNAL 2024; 18:wrae094. [PMID: 38832716 PMCID: PMC11287211 DOI: 10.1093/ismejo/wrae094] [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: 03/01/2024] [Revised: 04/30/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ella T Sieradzki
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jennifer Pett-Ridge
- Physical & Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
| | - Jillian F Banfield
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, United States
- Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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10
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Muhammad N, Avila F, Nedashkovskaya OI, Kim SG. Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides. Front Microbiol 2023; 14:1265676. [PMID: 38156005 PMCID: PMC10752948 DOI: 10.3389/fmicb.2023.1265676] [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: 07/23/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023] Open
Abstract
Three novel strains designated ABR2-5T, BKB1-1T, and WSW4-B4T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%-94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%-97.2%. The genome sizes of the strains ABR2-5T, BKB1-1T, and WSW4-B4T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%-42.0%. The average nucleotide identity and the digital DNA-DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%-75.5% and 17.7-18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C15:0 (37.7%-47.4%) and C16:1 ω5c (14.4%-22.9%). Specifically, strain ABR2-5T displayed an additional higher proportion of C16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5T = KCTC 82990T = JCM 35839T), R. agarivorans sp. nov. (BKB1-1T = KCTC 82964T = JCM 35840T), and R. carrageenanivorans sp. nov. (WSW4-B4T = KCTC 82706T = JCM 35841T).
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Affiliation(s)
- Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Forbes Avila
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Olga I. Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
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11
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Michalik A, Bauer E, Szklarzewicz T, Kaltenpoth M. Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects. THE ISME JOURNAL 2023; 17:2221-2231. [PMID: 37833524 PMCID: PMC10689751 DOI: 10.1038/s41396-023-01528-4] [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: 06/25/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Hemipterans are known as hosts to bacterial or fungal symbionts that supplement their unbalanced diet with essential nutrients. Among them, scale insects (Coccomorpha) are characterized by a particularly large diversity of symbiotic systems. Here, using microscopic and genomic approaches, we functionally characterized the symbionts of two scale insects belonging to the Eriococcidae family, Acanthococcus aceris and Gossyparia spuria. These species host Burkholderia bacteria that are localized in the cytoplasm of the fat body cells. Metagenome sequencing revealed very similar and highly reduced genomes (<900KBp) with a low GC content (~38%), making them the smallest and most AT-biased Burkholderia genomes yet sequenced. In their eroded genomes, both symbionts retain biosynthetic pathways for the essential amino acids leucine, isoleucine, valine, threonine, lysine, arginine, histidine, phenylalanine, and precursors for the semi-essential amino acid tyrosine, as well as the cobalamin-dependent methionine synthase MetH. A tryptophan biosynthesis pathway is conserved in the symbiont of G. spuria, but appeared pseudogenized in A. aceris, suggesting differential availability of tryptophan in the two host species' diets. In addition to the pathways for essential amino acid biosynthesis, both symbionts maintain biosynthetic pathways for multiple cofactors, including riboflavin, cobalamin, thiamine, and folate. The localization of Burkholderia symbionts and their genome traits indicate that the symbiosis between Burkholderia and eriococcids is younger than other hemipteran symbioses, but is functionally convergent. Our results add to the emerging picture of dynamic symbiont replacements in sap-sucking Hemiptera and highlight Burkholderia as widespread and versatile intra- and extracellular symbionts of animals, plants, and fungi.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland.
| | - Eugen Bauer
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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12
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Majee CK, Ali SY, Padhy PK. Effects of atmospheric dust particles on common medicinal plants in an industrial area of West Bengal, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:978. [PMID: 37477710 DOI: 10.1007/s10661-023-11573-3] [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: 12/15/2022] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The exposure of atmospheric dust particles on four common medicinal plants (Ocimum sanctum, Andrographis paniculata, Catharanthus roseous, and Kaempferia galanga, which are available in the study area and cultivated by the local people for medicinal purposes) affects their growth, levels of essential biochemical constituents and heavy metal concentration. The plant species were grown by pot cultivation in an industrial area with high levels of coal dust to assess the capacity of heavy metals accumulation in their leaves and changes in allometry and biochemical parameters. The results showed that annual average SPM and dustfall varied between 195.88 to 645.97 μg/m3 and 17.55 to 41.16 g/m2/month, respectively. Dustfall at different polluted sites was 2.4, 2.1, 1.5, 1.4, and 2.3 times higher than at the control site. The most prevalent heavy metal in atmospheric particulate matter was Zn, followed by Pb, Ni, Cu, Co, and Cd. Plant allometry measurements such as height, stem width, root length, petiole length, and leaf area are shown to have a strong and significant (p<0.05) negative correlation with dustfall and SPM. Total chlorophyll and RWC were inversely proportional to the dust load present in all the species. Except for Andrographis paniculata, chlorophyll and leaf-extracted pH of plant species were moderately correlated with APTI, whereas no correlation was noticed for ascorbic acid. A positive correlation between SPM and heavy metals in leaves was observed. The results implied that the cultivation and collection of medicinal plants from the study area could be potentially toxic to human health.
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Affiliation(s)
- C K Majee
- Department of Environmental Studies, Institute of Science, Visva-Bharati, Santiniketan, Birbhum, West Bengal, 731235, India
| | - S Y Ali
- Central Pollution Control Board, Eastern Regional Directorate, Kolkata, India
| | - P K Padhy
- Department of Environmental Studies, Institute of Science, Visva-Bharati, Santiniketan, Birbhum, West Bengal, 731235, India.
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13
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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14
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Martins DOS, Souza RAC, Freire MCLC, de Moraes Roso Mesquita NC, Santos IA, de Oliveira DM, Junior NN, de Paiva REF, Harris M, Oliveira CG, Oliva G, Jardim ACG. Insights into the role of the cobalt(III)-thiosemicarbazone complex as a potential inhibitor of the Chikungunya virus nsP4. J Biol Inorg Chem 2023; 28:101-115. [PMID: 36484824 PMCID: PMC9735056 DOI: 10.1007/s00775-022-01974-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever, a disease that can result in disability. Until now, there is no antiviral treatment against CHIKV, demonstrating that there is a need for development of new drugs. Studies have shown that thiosemicarbazones and their metal complexes possess biological activities, and their synthesis is simple, clean, versatile, and results in high yields. Here, we evaluated the mechanism of action (MOA) of a cobalt(III) thiosemicarbazone complex named [CoIII(L1)2]Cl based on its in vitro potent antiviral activity against CHIKV previously evaluated (80% of inhibition on replication). Furthermore, the complex has no toxicity in healthy cells, as confirmed by infecting BHK-21 cells with CHIKV-nanoluciferase in the presence of the compound, showing that [CoIII(L1)2]Cl inhibited CHIKV infection with the selective index of 3.26. [CoIII(L1)2]Cl presented a post-entry effect on viral replication, emphasized by the strong interaction of [CoIII(L1)2]Cl with CHIKV non-structural protein 4 (nsP4) in the microscale thermophoresis assay, suggesting a potential mode of action of this compound against CHIKV. Moreover, in silico analyses by molecular docking demonstrated potential interaction of [CoIII(L1)2]Cl with nsP4 through hydrogen bonds, hydrophobic and electrostatic interactions. The evaluation of ADME-Tox properties showed that [CoIII(L1)2]Cl presents appropriate lipophilicity, good human intestinal absorption, and has no toxicological effect as irritant, mutagenic, reproductive, and tumorigenic side effects.
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Affiliation(s)
- Daniel Oliveira Silva Martins
- Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil
- São Paulo State University, IBILCE, São José do Rio Preto, SP, Brazil
| | | | | | | | - Igor Andrade Santos
- Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil
| | - Débora Moraes de Oliveira
- Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil
| | - Nilson Nicolau Junior
- Molecular Modeling Laboratory, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Mark Harris
- Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Carolina Gonçalves Oliveira
- Bioinorganic Chemistry Group, Institute of Chemistry, Federal University of Uberlândia, Uberlândia, MG, 38408-100, Brazil.
| | - Glaucius Oliva
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil.
- São Paulo State University, IBILCE, São José do Rio Preto, SP, Brazil.
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15
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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16
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Zhang Y, Jiang Y, Gao K, Sui D, Yu P, Su M, Wei GW, Hu J. Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter. Nat Commun 2023; 14:385. [PMID: 36693843 PMCID: PMC9873690 DOI: 10.1038/s41467-023-36048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 Å toward the extracellular side against the static TMs which mediate dimerization. These findings allow us to conclude that BbZIP is an elevator-type transporter.
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Affiliation(s)
- Yao Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Yuhan Jiang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Kaifu Gao
- Department of Mathematics, Michigan State University, East Lansing, MI, USA
| | - Dexin Sui
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Peixuan Yu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Guo-Wei Wei
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Mathematics, Michigan State University, East Lansing, MI, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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17
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Ren Y, Jin L, Zeng H, Busquets R, He G, Deng S, He Q, Khan MR, Deng R, Chi Y. Primer-Engineered Transferase Enzyme for One-Pot and Amplified Detection of Cobalt Pollution and Peptide Remover Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:877-883. [PMID: 36563311 DOI: 10.1021/acs.jafc.2c07223] [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: 06/17/2023]
Abstract
Extensive consumption of cobalt in the chemical field such as for battery materials, alloy, pigments, and dyes has aggravated the pollution of cobalt both in food and the environment, and assays for its on-site monitoring are urgently demanded. Herein, we utilized enzyme dependence on metal cofactors to develop terminal transferase (TdT) as a recognition element, achieving a one-pot sensitive and specific assay for detecting cobalt pollution. We engineered a 3'-OH terminus primer to improve the discrimination capacity of TdT for Co2+ from other bivalent cations. The TdT extension reaction amplified the recognition of Co2+ and yielded a limit of detection of 0.99 μM for Co2+ detection. Then, the TdT-based assay was designed to precisely detect cobalt in food and agricultural soil samples. By end-measurement of fluorescence using a microplate reader, the multiplexing assay enabled the rapid screening of the peptide remover for cobalt pollution. The TdT-based assay can be a promising tool for cobalt pollution monitoring and control.
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Affiliation(s)
- Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Lulu Jin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hongling Zeng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Rosa Busquets
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, Penrhyn Road, KT1 2EE Kingston Upon Thames, United Kingdom
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan 610065, China
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18
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A Review of Pseudomonas aeruginosa Metallophores: Pyoverdine, Pyochelin and Pseudopaline. BIOLOGY 2022; 11:biology11121711. [PMID: 36552220 PMCID: PMC9774294 DOI: 10.3390/biology11121711] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
P. aeruginosa is a common Gram-negative bacterium found in nature that causes severe infections in humans. As a result of its natural resistance to antibiotics and the ability of biofilm formation, the infection with this pathogen can be therapeutic challenging. During infection, P. aeruginosa produces secondary metabolites such as metallophores that play an important role in their virulence. Metallophores are metal ions chelating molecules secreted by bacteria, thus allowing them to survive in the host under metal scarce conditions. Pyoverdine, pyochelin and pseudopaline are the three metallophores secreted by P. aeruginosa. Pyoverdines are the primary siderophores that acquire iron from the surrounding medium. These molecules scavenge and transport iron to the bacterium intracellular compartment. Pyochelin is another siderophore produced by this bacterium, but in lower quantities and its affinity for iron is less than that of pyoverdine. The third metallophore, pseudopaline, is an opine narrow spectrum ion chelator that enables P. aeruginosa to uptake zinc in particular but can transport nickel and cobalt as well. This review describes all the aspects related to these three metallophore, including their main features, biosynthesis process, secretion and uptake when loaded by metals, in addition to the genetic regulation responsible for their synthesis and secretion.
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Abstract
The skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining the skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. Here, we provide the first large-scale metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin encode cobamide-dependent enzymes, relatively few species encode de novo cobamide biosynthesis. We show that cobamide producers and users are integrated into the network structure of microbial communities across the different microenvironments of the skin and that changes in microbiome community structure and diversity are associated with the abundance of cobamide producers in the Corynebacterium genus, for both healthy and diseased skin states. Finally, we find that de novo cobamide biosynthesis is enriched only in Corynebacterium species associated with hosts, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by human skin-associated species isolated in the laboratory. Taken together, our results reveal the potential for cobamide sharing within skin microbial communities, which we hypothesize mediates microbiome community dynamics and host interactions. IMPORTANCE The skin microbiome is essential for maintaining skin health and function. However, the microbial interactions that dictate microbiome structure, stability, and function are not well understood. Here, we investigate the biosynthesis and use of cobamides, a cofactor needed by many organisms but only produced by select prokaryotes, within the human skin microbiome. We found that while a large proportion of skin taxa encode cobamide-dependent enzymes, only a select few encode de novo cobamide biosynthesis. Further, the abundance of cobamide-producing Corynebacterium species is associated with skin microbiome diversity and structure, and within this genus, de novo biosynthesis is enriched in host-associated species compared to environment-associated species. These findings identify cobamides as a potential mediator of skin microbiome dynamics and skin health.
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Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses. Microbiol Spectr 2022; 10:e0277922. [PMID: 36094208 PMCID: PMC9603385 DOI: 10.1128/spectrum.02779-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of "collaborative pathways" for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems. IMPORTANCE The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as "collaborative pathways". To date, collaborative pathways have only been reported from sap-feeding insects. Here, we examined metabolic interactions between cockroaches, a group of detritivorous insects, and their obligate endosymbiont, Blattabacterium, and only found evidence of collaborative pathways for arginine biosynthesis. The rarity of collaborative pathways in cockroaches and Blattabacterium contrasts with their prevalence in insect hosts feeding on phloem-sap. Our results suggest that host diet is a factor affecting metabolic integration in obligate symbiotic systems.
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Fischer F, Vorontsov E, Turlin E, Malosse C, Garcia C, Tabb DL, Chamot-Rooke J, Percudani R, Vinella D, De Reuse H. Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2022; 14:6674772. [PMID: 36002005 DOI: 10.1093/mtomcs/mfac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/17/2022] [Indexed: 11/14/2022]
Abstract
Acquisition and homeostasis of essential metals during host colonization by bacterial pathogens rely on metal uptake, trafficking and storage proteins. How these factors have evolved within bacterial pathogens is poorly defined. Urease, a nickel enzyme, is essential for Helicobacter pylori to colonize the acidic stomach. Our previous data suggest that acquisition of nickel transporters and a Histidine-rich protein (HRP) involved in nickel storage in H. pylori and gastric Helicobacter spp. have been essential evolutionary events for gastric colonization. Using bioinformatics, proteomics and phylogenetics, we extended this analysis to determine how evolution has framed the repertoire of HRPs among 39 Epsilonproteobacteria; 18 gastric and 11 non-gastric enterohepatic (EH) Helicobacter spp., as well as 10 other Epsilonproteobacteria. We identified a total of 213 HRPs distributed in 22 protein families named orthologous groups (OG) with His-rich domains, including 15 newly described OGs. Gastric Helicobacter spp. are enriched in HRPs (7.7 ± 1.9 HRPs/strain) as compared to EH Helicobacter spp. (1.9 ± 1.0 HRPs/strain) with a particular prevalence of HRPs with C-terminal Histidine-rich domains in gastric species. The expression and nickel-binding capacity of several HRPs was validated in five gastric Helicobacter spp. We established the evolutionary history of new HRP families, such as the periplasmic HP0721-like proteins and the HugZ-type heme-oxygenases. The expansion of Histidine-rich extensions in gastric Helicobacter spp. proteins is intriguing but can tentatively be associated with the presence of the urease nickel-enzyme. We conclude that this HRP expansion is associated with unique properties of organisms that rely on large intracellular nickel amounts for their survival.
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Affiliation(s)
- Frédéric Fischer
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE.,Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Université de Strasbourg, Institut de Physiologie et Chimie Biologiques, 4 allée Konrad Roentgen, 67084 Strasbourg, FRANCE
| | - Egor Vorontsov
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE.,Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 413, 40530 Gothenburg, SWEDEN
| | - Evelyne Turlin
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Christian Malosse
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Camille Garcia
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - David L Tabb
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Julia Chamot-Rooke
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, ITALY
| | - Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
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22
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Nef C, Dittami S, Kaas R, Briand E, Noël C, Mairet F, Garnier M. Sharing Vitamin B 12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea. Microorganisms 2022; 10:1337. [PMID: 35889056 PMCID: PMC9323062 DOI: 10.3390/microorganisms10071337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Haptophyte microalgae are key contributors to microbial communities in many environments. It has been proposed recently that members of this group would be virtually all dependent on vitamin B12 (cobalamin), an enzymatic cofactor produced only by some bacteria and archaea. Here, we examined the processes of vitamin B12 acquisition by haptophytes. We tested whether co-cultivating the model species Tisochrysis lutea with B12-producing bacteria in vitamin-deprived conditions would allow the microalga to overcome B12 deprivation. While T. lutea can grow by scavenging vitamin B12 from bacterial extracts, co-culture experiments showed that the algae did not receive B12 from its associated bacteria, despite bacteria/algae ratios supposedly being sufficient to allow enough vitamin production. Since other studies reported mutualistic algae-bacteria interactions for cobalamin, these results question the specificity of such associations. Finally, cultivating T. lutea with a complex bacterial consortium in the absence of the vitamin partially rescued its growth, highlighting the importance of microbial interactions and diversity. This work suggests that direct sharing of vitamin B12 is specific to each species pair and that algae in complex natural communities can acquire it indirectly by other mechanisms (e.g., after bacterial lysis).
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Affiliation(s)
- Charlotte Nef
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
| | - Simon Dittami
- Station Biologique de Roscoff, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne University, F-29680 Roscoff, France;
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
| | - Enora Briand
- GENALG, PHYTOX, IFREMER, F-44000 Nantes, France; (E.B.); (M.G.)
| | - Cyril Noël
- SEBIMER, IRSI, IFREMER, F-29280 Brest, France;
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23
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Poddar H, Heyes DJ, Zhang S, Hardman SJ, Sakuma M, Scrutton NS. An unusual light-sensing function for coenzyme B 12 in bacterial transcription regulator CarH. Methods Enzymol 2022; 668:349-372. [PMID: 35589201 DOI: 10.1016/bs.mie.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coenzyme B12 is one of the most complex cofactors found in nature and synthesized de novo by certain groups of bacteria. Although its use in various enzymatic reactions is well characterized, only recently an unusual light-sensing function has been ascribed to coenzyme B12. It has been reported that the coenzyme B12 binding protein CarH, found in the carotenoid biosynthesis pathway of several thermostable bacteria, binds to the promoter region of DNA and suppresses transcription. To overcome the harmful effects of light-induced damage in the cells, CarH releases DNA in the presence of light and promotes transcription and synthesis of carotenoids, thereby working as a photoreceptor. CarH is able to achieve this by exploiting the photosensitive nature of the CoC bond between the adenosyl moiety and the cobalt atom in the coenzyme B12 molecule. Extensive structural and spectroscopy studies provided a mechanistic understanding of the molecular basis of this unique light-sensitive reaction. Most studies on CarH have used the ortholog from the thermostable bacterium Thermus thermophilus, due to the ease with which it can be expressed and purified in high quantities. In this chapter we give an overview of this intriguing class of photoreceptors and report a step-by-step protocol for expression, purification and spectroscopy experiments (both static and time-resolved techniques) employed in our laboratory to study CarH from T. thermophilus. We hope the contents of this chapter will be of interest to the wider coenzyme B12 community and apprise them of the potential and possibilities of using coenzyme B12 as a light-sensing probe in a protein scaffold.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samantha J Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom.
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24
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Jia X, Dong T, Han Y, Yue Z, Zhang P, Ren J, Wang Y, Wu W, Yang H, Guo H, Zhang GH, Cao J. Identifying the dose response relationship between seminal metal at low levels and semen quality using restricted cubic spline function. CHEMOSPHERE 2022; 295:133805. [PMID: 35134404 DOI: 10.1016/j.chemosphere.2022.133805] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Environmental exposure to metals, including essential and nonessential elements, may be related to semen quality. Our goal was to explore the continuous relationship between seminal metals and sperm parameters. A restricted cubic spline (RCS) was applied to automatic selection criteria to ascertain the optimal smoothing degree. We recruited 841 male volunteers from Henan Province, China. Eighteen seminal metals, namely Al, Cr, Mn, Cu, Zn, Se, As, Ni, Cd, Pb, Co, V, Rb, Ag, Ba, TI, Fe, and Li, and 21 semen parameters were detected. Seminal malondialdehyde (MDA) was also detected to express oxidative stress. We revealed a non-linear relationship of the vanadium and chromium exposure to semen parameters. There were inverse 'U' shapes found between seminal Cr and sperm concentrations, total sperm count, and semen quality. The best semen quality was observed when the seminal Cr concentration was 5.05 ppb, and an increase or decrease in chromium concentration led to decreased semen quality. The V concentration was associated with reduced sperm concentration, total sperm count, normal morphology, and progressive motility at high doses (V > 0.58 ppb). Seminal MDA had a strong adverse association with sperm motility parameters, such as curve line velocity (VCL) (P < 0.001), straight line velocity (VSL) (P = 0.004), velocity of average path (VAP) (P < 0.001), and lateral head movement (ALH) (P = 0.001), whereas it was adversely associated with seminal Zn (β [95% confidence interval (CI)], -0.28(-0.41-0.16), P < 0.001) after adjusting for confounding factors. Our findings represent the curves of the dose-response relationship between seminal Cr, seminal V, and semen quality, in which seminal MDA was a good indicator of sperm movement. These models provide new insight into the dose-relationship between metal exposure and semen quality, and further investigation is needed to validate this.
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Affiliation(s)
- Xueshan Jia
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China; Reproductive Center, Henan Provincial Peoples Hospital, Zhengzhou, 450003, China
| | - Tingting Dong
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Yufen Han
- Puyang Maternity and Child Care Centers, 59 South Section of Kaizhou Road, Puyang, 457000, China
| | - Zhongyi Yue
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Pingyang Zhang
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Jingchao Ren
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Yongbin Wang
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Weidong Wu
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China
| | - Huan Yang
- Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Haibin Guo
- Reproductive Center, Henan Provincial Peoples Hospital, Zhengzhou, 450003, China.
| | - Guang-Hui Zhang
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China; Department of Environmental Health, College of Preventive Medicine, Army Medical University, Chongqing, China.
| | - Jia Cao
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Xinxiang, 453003, China; Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China.
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25
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Padmanabhan S, Pérez-Castaño R, Osete-Alcaraz L, Polanco MC, Elías-Arnanz M. Vitamin B 12 photoreceptors. VITAMINS AND HORMONES 2022; 119:149-184. [PMID: 35337618 DOI: 10.1016/bs.vh.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B12 or 5'-deoxyadenosylcobalamin, a biological form of vitamin B12, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B12-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B12-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Lucía Osete-Alcaraz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
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26
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Guéant JL, Guéant-Rodriguez RM, Alpers DH. Vitamin B12 absorption and malabsorption. VITAMINS AND HORMONES 2022; 119:241-274. [PMID: 35337622 DOI: 10.1016/bs.vh.2022.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Vitamin B12 is assimilated and transported by complex mechanisms that involve three transport proteins, intrinsic factor (IF), haptocorrin (HC) and transcobalamin (TC) and their respective membrane receptors. Vitamin deficiency is mainly due to inadequate dietary intake in vegans, and B12 malabsorption is related to digestive diseases. This review explores the physiology of vitamin B12 absorption and the mechanisms and diseases that produce malabsorption. In the stomach, B12 is released from food carrier proteins and binds to HC. The degradation of HC by pancreatic proteases and the pH change trigger the transfer of B12 to IF in the duodenum. Cubilin and amnionless are the two components of the receptor that mediates the uptake of B12 in the distal ileum. Part of liver B12 is excreted in bile, and undergoes an enterohepatic circulation. The main causes of B12 malabsorption include inherited disorders (Intrinsic factor deficiency, Imerslund-Gräsbeck disease, Addison's pernicious anemia, obesity, bariatric surgery and gastrectomies. Other causes include pancreatic insufficiency, obstructive Jaundice, tropical sprue and celiac disease, bacterial overgrowth, parasitic infestations, Zollinger-Ellison syndrome, inflammatory bowel diseases, chronic radiation enteritis of the distal ileum and short bowel. The assessment of B12 deficit is recommended in the follow-up of subjects with bariatric surgery. The genetic causes of B12 malabsorption are probably underestimated in adult cases with B12 deficit. Despite its high prevalence in the general population and in the elderly, B12 malabsorption cannot be anymore assessed by the Schilling test, pointing out the urgent need for an equivalent reliable test.
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Affiliation(s)
- Jean-Louis Guéant
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France; Department of Hepato-Gastroenterology, University Hospital of Nancy, Nancy, France.
| | - Rosa-Maria Guéant-Rodriguez
- University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, Nancy, France; Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, Nancy, France
| | - David H Alpers
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St Louis, MO, United States.
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27
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Nijland M, Martínez Felices JM, Slotboom DJ, Thangaratnarajah C. Membrane transport of cobalamin. VITAMINS AND HORMONES 2022; 119:121-148. [PMID: 35337617 DOI: 10.1016/bs.vh.2022.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A wide variety of organisms encode cobalamin-dependent enzymes catalyzing essential metabolic reactions, but the cofactor cobalamin (vitamin B12) is only synthesized by a subset of bacteria and archaea. The biosynthesis of cobalamin is complex and energetically costly, making cobalamin variants and precursors metabolically valuable. Auxotrophs for these molecules have evolved uptake mechanisms to compensate for the lack of a synthesis pathway. Bacterial transport of cobalamin involves the passage over one or two lipidic membranes in Gram-positive and -negative bacteria, respectively. In higher eukaryotes, a complex system of carriers, receptors and transporters facilitates the delivery of the essential molecule to the tissues. Biochemical and genetic approaches have identified different transporter families involved in cobalamin transport. The majority of the characterized cobalamin transporters are active transport systems that belong to the ATP-binding cassette (ABC) superfamily of transporters. In this chapter, we describe the different cobalamin transport systems characterized to date that are present in bacteria and humans, as well as yet-to-be-identified transporters.
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Affiliation(s)
- Mark Nijland
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
| | - Jose M Martínez Felices
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
| | - Dirk J Slotboom
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands.
| | - Chancievan Thangaratnarajah
- University of Groningen, Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, Groningen, Netherlands
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28
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Abstract
Soil micronutrients limit crop productivity in many regions worldwide, and micronutrient deficiencies affect over two billion people globally. Microbial biofertilizers could combat these issues by inoculating arable soils with microorganisms that mobilize micronutrients, increasing their availability to crop plants in an environmentally sustainable and cost-effective manner. However, the widespread application of biofertilizers is limited by complex micronutrient–microbe–plant interactions, which reduce their effectiveness under field conditions. Here, we review the current state of seven micronutrients in food production. We examine the mechanisms underpinning microbial micronutrient mobilization in natural ecosystems and synthesize the state-of-knowledge to improve our overall understanding of biofertilizers in food crop production. We demonstrate that, although soil micronutrient concentrations are strongly influenced by soil conditions, land management practices can also substantially affect micronutrient availability and uptake by plants. The effectiveness of biofertilizers varies, but several lines of evidence indicate substantial benefits in co-applying biofertilizers with conventional inorganic or organic fertilizers. Studies of micronutrient cycling in natural ecosystems provide examples of microbial taxa capable of mobilizing multiple micronutrients whilst withstanding harsh environmental conditions. Research into the mechanisms of microbial nutrient mobilization in natural ecosystems could, therefore, yield effective biofertilizers to improve crop nutrition under global changes.
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29
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Frye KA, Piamthai V, Hsiao A, Degnan PH. Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe. Cell Rep 2021; 37:110164. [PMID: 34965410 PMCID: PMC8759732 DOI: 10.1016/j.celrep.2021.110164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
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30
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Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? Comput Struct Biotechnol J 2021; 19:5752-5761. [PMID: 34765092 PMCID: PMC8566771 DOI: 10.1016/j.csbj.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.
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Key Words
- ABC, ATP-binding cassette
- ECF transporter
- ECF, energy-coupling factor
- Fur, ferric uptake regulator
- Hrl, histidine-rich lipoprotein
- Iron homeostasis
- Metal acquisition
- Metalloenzyme
- Mge, Mycoplasma genitalium
- Mho, Mycoplasma hominis
- Mollicutes
- Mpe, Mycoplasma penetrans
- Mpn, Mycoplasma pneumonia
- Mycoplasmas
- PDB, protein data bank
- RNR, ribonucleotide reductase
- XRF, X-ray fluorescence
- ZIP, zinc-iron permease
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31
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Newsome L, Falagán C. The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health. GEOHEALTH 2021; 5:e2020GH000380. [PMID: 34632243 PMCID: PMC8490943 DOI: 10.1029/2020gh000380] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/13/2023]
Abstract
Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.
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Affiliation(s)
- Laura Newsome
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
| | - Carmen Falagán
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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32
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Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem J 2021; 478:3265-3279. [PMID: 34409984 PMCID: PMC8454699 DOI: 10.1042/bcj20210565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.
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33
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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Tibbett M, Green I, Rate A, De Oliveira VH, Whitaker J. The transfer of trace metals in the soil-plant-arthropod system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146260. [PMID: 33744587 DOI: 10.1016/j.scitotenv.2021.146260] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Essential and non-essential trace metals are capable of causing toxicity to organisms above a threshold concentration. Extensive research has assessed the behaviour of trace metals in biological and ecological systems, but has typically focused on single organisms within a trophic level and not on multi-trophic transfer through terrestrial food chains. This reinforces the notion of metal toxicity as a closed system, failing to consider one trophic level as a pollution source to another; therefore, obscuring the full extent of ecosystem effects. Given the relatively few studies on trophic transfer of metals, this review has taken a compartment-based approach, where transfer of metals through trophic pathways is considered as a series of linked compartments (soil-plant-arthropod herbivore-arthropod predator). In particular, we consider the mechanisms by which trace metals are taken up by organisms, the forms and transformations that can occur within the organism and the consequences for trace metal availability to the next trophic level. The review focuses on four of the most prevalent metal cations in soil which are labile in terrestrial food chains: Cd, Cu, Zn and Ni. Current knowledge of the processes and mechanisms by which these metals are transformed and moved within and between trophic levels in the soil-plant-arthropod system are evaluated. We demonstrate that the key factors controlling the transfer of trace metals through the soil-plant-arthropod system are the form and location in which the metal occurs in the lower trophic level and the physiological mechanisms of each organism in regulating uptake, transformation, detoxification and transfer. The magnitude of transfer varies considerably depending on the trace metal concerned, as does its toxicity, and we conclude that biomagnification is not a general property of plant-arthropod and arthropod-arthropod systems. To deliver a more holistic assessment of ecosystem toxicity, integrated studies across ecosystem compartments are needed to identify critical pathways that can result in secondary toxicity across terrestrial food-chains.
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Affiliation(s)
- Mark Tibbett
- Department of Sustainable Land Management & Soil Research Centre, School of Agriculture Policy and Development, University of Reading, Whiteknights, RG6 6AR, UK.
| | - Iain Green
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, Dorset BH12 5BB, UK
| | - Andrew Rate
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Vinícius H De Oliveira
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo 13083-970, Brazil
| | - Jeanette Whitaker
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Lancaster LA1 4AP, UK
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Petushkova E, Mayorova E, Tsygankov A. TCA Cycle Replenishing Pathways in Photosynthetic Purple Non-Sulfur Bacteria Growing with Acetate. Life (Basel) 2021; 11:711. [PMID: 34357087 PMCID: PMC8307300 DOI: 10.3390/life11070711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/27/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Purple non-sulfur bacteria (PNSB) are anoxygenic photosynthetic bacteria harnessing simple organic acids as electron donors. PNSB produce a-aminolevulinic acid, polyhydroxyalcanoates, bacteriochlorophylls a and b, ubiquinones, and other valuable compounds. They are highly promising producers of molecular hydrogen. PNSB can be cultivated in organic waste waters, such as wastes after fermentation. In most cases, wastes mainly contain acetic acid. Therefore, understanding the anaplerotic pathways in PNSB is crucial for their potential application as producers of biofuels. The present review addresses the recent data on presence and diversity of anaplerotic pathways in PNSB and describes different classifications of these pathways.
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Affiliation(s)
- Ekaterina Petushkova
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
| | - Ekaterina Mayorova
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
- Pushchino State Institute of Natural Science, The Federal State Budget Educational Institution of Higher Education, 3, Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Anatoly Tsygankov
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
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Kumar A, Jigyasu DK, Kumar A, Subrahmanyam G, Mondal R, Shabnam AA, Cabral-Pinto MMS, Malyan SK, Chaturvedi AK, Gupta DK, Fagodiya RK, Khan SA, Bhatia A. Nickel in terrestrial biota: Comprehensive review on contamination, toxicity, tolerance and its remediation approaches. CHEMOSPHERE 2021; 275:129996. [PMID: 33647680 DOI: 10.1016/j.chemosphere.2021.129996] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Nickel (Ni) has been a subject of interest for environmental, physiological, biological scientists due to its dual effect (toxicity and essentiality) in terrestrial biota. In general, the safer limit of Ni is 1.5 μg g-1 in plants and 75-150 μg g-1 in soil. Litreature review indicates that Ni concentrations have been estimated up to 26 g kg-1 in terrestrial, and 0.2 mg L-1 in aquatic resources. In case of vegetables and fruits, mean Ni content has been reported in the range of 0.08-0.26 and 0.03-0.16 mg kg-1. Considering, Ni toxicity and its potential health hazards, there is an urgent need to find out the suitable remedial approaches. Plant vascular (>80%) and cortical (<20%) tissues are the major sequestration site (cation exchange) of absorbed Ni. Deciphering molecular mechanisms in transgenic plants have immense potential for enhancing Ni phytoremediation and microbial remediation efficiency. Further, it has been suggested that integrated bioremediation approaches have a potential futuristic path for Ni decontamination in natural resources. This systematic review provides insight on Ni effects on terrestrial biota including human and further explores its transportation, bioaccumulation through food chain contamination, human health hazards, and possible Ni remediation approaches.
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Affiliation(s)
- Amit Kumar
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing, Jiangsu, 210044, China
| | - Dharmendra K Jigyasu
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Amit Kumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Gangavarapu Subrahmanyam
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - Raju Mondal
- Central Sericultural Germplasm Resources Centre (CSGRC), Central Silk Board, Ministry of Textiles, Thally Road, Hosur, Tamil Nadu, 635109, India.
| | - Aftab A Shabnam
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam, 785700, India.
| | - M M S Cabral-Pinto
- Department of Geosciences, Geobiotec Research Centre, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sandeep K Malyan
- Research Management and Outreach Division, National Institute of Hydrology, Jalvigyan Bhawan, Roorkee, Uttarakhand, 247667, India.
| | - Ashish K Chaturvedi
- Land and Water Management Research Group, Centre for Water Resources Development and Management, Kozhikode, Kerala, 673571, India.
| | - Dipak Kumar Gupta
- ICAR-Central Arid Zone Research Institute Regional Research Station Pali Marwar, Rajasthan, 342003, India.
| | - Ram Kishor Fagodiya
- Division of Irrigation and Drainage Engineering, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India.
| | - Shakeel A Khan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Buetti-Dinh A, Ruinelli M, Czerski D, Scapozza C, Martignier A, Roman S, Caminada A, Tonolla M. Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps. PLoS One 2021; 16:e0248877. [PMID: 33784327 PMCID: PMC8009434 DOI: 10.1371/journal.pone.0248877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/07/2021] [Indexed: 12/02/2022] Open
Abstract
The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.
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Affiliation(s)
- Antoine Buetti-Dinh
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (ABD); (MT)
| | - Michela Ruinelli
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Dorota Czerski
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Cristian Scapozza
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Agathe Martignier
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Annapaola Caminada
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (ABD); (MT)
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De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis. J Bacteriol 2021; 203:JB.00620-20. [PMID: 33468593 PMCID: PMC8088520 DOI: 10.1128/jb.00620-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remain poorly understood. Cobalamin is an essential cofactor in all domains of life, yet its biosynthesis is restricted to some bacteria and archaea. Mycobacterium smegmatis, an environmental saprophyte frequently used as surrogate for the obligate human pathogen M. tuberculosis, carries approximately 30 genes predicted to be involved in de novo cobalamin biosynthesis. M. smegmatis also encodes multiple cobalamin-dependent enzymes, including MetH, a methionine synthase that catalyzes the final reaction in methionine biosynthesis. In addition to metH, M. smegmatis possesses a cobalamin-independent methionine synthase, metE, suggesting that enzyme use—MetH versus MetE—is regulated by cobalamin availability. Consistent with this notion, we previously described a cobalamin-sensing riboswitch controlling metE expression in M. tuberculosis. Here, we apply a targeted mass spectrometry-based approach to confirm de novo cobalamin biosynthesis in M. smegmatis during aerobic growth in vitro. We also demonstrate that M. smegmatis can transport and assimilate exogenous cyanocobalamin (CNCbl; also known as vitamin B12) and its precursor, dicyanocobinamide ([CN]2Cbi). However, the uptake of CNCbl and (CN)2Cbi in this organism is restricted and seems dependent on the conditional essentiality of the cobalamin-dependent methionine synthase. Using gene and protein expression analyses combined with single-cell growth kinetics and live-cell time-lapse microscopy, we show that transcription and translation of metE are strongly attenuated by endogenous cobalamin. These results support the inference that metH essentiality in M. smegmatis results from riboswitch-mediated repression of MetE expression. Moreover, differences observed in cobalamin-dependent metabolism between M. smegmatis and M. tuberculosis provide some insight into the selective pressures which might have shaped mycobacterial metabolism for pathogenicity. IMPORTANCE Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remains poorly understood. Using the nonpathogenic saprophyte M. smegmatis, we investigated the production of cobalamin, transport and assimilation of cobalamin precursors, and the role of cobalamin in regulating methionine biosynthesis. We confirm constitutive de novo cobalamin biosynthesis in M. smegmatis, in contrast with M. tuberculosis, which appears to lack de novo cobalamin biosynthetic capacity. We also show that uptake of cyanocobalamin (vitamin B12) and its precursors is restricted in M. smegmatis, apparently depending on the cofactor requirements of the cobalamin-dependent methionine synthase. These observations establish M. smegmatis as an informative foil to elucidate key metabolic adaptations enabling mycobacterial pathogenicity.
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Orłowska M, Steczkiewicz K, Muszewska A. Utilization of cobalamin is ubiquitous in early-branching fungal phyla. Genome Biol Evol 2021; 13:6157828. [PMID: 33682003 PMCID: PMC8085122 DOI: 10.1093/gbe/evab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/15/2021] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all non-Dikarya fungi lineages. This observation is supported by the genomic presence of both B12-dependent enzymes and cobalamin modifying enzymes. Fungal cobalamin-dependent enzymes are highly similar to their animal homologs. Phylogenetic analyses support a scenario of vertical inheritance of the cobalamin usage with several losses. Cobalamin usage was probably lost in Mucorinae and at the base of Dikarya which groups most of the model organisms and which hindered B12-dependent metabolism discovery in fungi. Our results indicate that cobalamin dependence was a widely distributed trait at least in Opisthokonta, across diverse microbial eukaryotes and was likely present in the LECA.
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Affiliation(s)
- Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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40
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Wang X, Wei W, Zhao J. Using a Riboswitch Sensor to Detect Co 2+/Ni 2+ Transport in E. coli. Front Chem 2021; 9:631909. [PMID: 33659237 PMCID: PMC7917058 DOI: 10.3389/fchem.2021.631909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Intracellular concentrations of essential mental ions must be tightly maintained to avoid metal deprivation and toxicity. However, their levels in cells are still difficult to monitor. In this report, the combination of a Co2+Ni2+-specific riboswitch and an engineered downstream mCherry fluorescent protein allowed a highly sensitive and selective whole-cell Co2+/Ni2+ detection process. The sensors were applied to examine the resistance system of Co2+/Ni2+ in E. coli, and the sensors were able to monitor the effects of genetic deletions. These results indicate that riboswitch-based sensors can be employed in the study of related cellular processes.
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Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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41
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Luo ZH, Narsing Rao MP, Chen H, Hua ZS, Li Q, Hedlund BP, Dong ZY, Liu BB, Guo SX, Shu WS, Li WJ. Genomic Insights of " Candidatus Nitrosocaldaceae" Based on Nine New Metagenome-Assembled Genomes, Including " Candidatus Nitrosothermus" Gen Nov. and Two New Species of " Candidatus Nitrosocaldus". Front Microbiol 2021; 11:608832. [PMID: 33488549 PMCID: PMC7819960 DOI: 10.3389/fmicb.2020.608832] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 01/11/2023] Open
Abstract
“Candidatus Nitrosocaldaceae” are globally distributed in neutral or slightly alkaline hot springs and geothermally heated soils. Despite their essential role in the nitrogen cycle in high-temperature ecosystems, they remain poorly understood because they have never been isolated in pure culture, and very few genomes are available. In the present study, a metagenomics approach was employed to obtain “Ca. Nitrosocaldaceae” metagenomic-assembled genomes (MAGs) from hot spring samples collected from India and China. Phylogenomic analysis placed these MAGs within “Ca. Nitrosocaldaceae.” Average nucleotide identity and average amino acid identity analysis suggested the new MAGs represent two novel species of “Candidatus Nitrosocaldus” and a novel genus, herein proposed as “Candidatus Nitrosothermus.” Key genes responsible for chemolithotrophic ammonia oxidation and a thaumarchaeal 3HP/4HB cycle were detected in all MAGs. Furthermore, genes coding for urea degradation were only present in “Ca. Nitrosocaldus,” while biosynthesis of the vitamins, biotin, cobalamin, and riboflavin were detected in almost all MAGs. Comparison of “Ca. Nitrosocaldales/Nitrosocaldaceae” with other AOA revealed 526 specific orthogroups. This included genes related to thermal adaptation (cyclic 2,3-diphosphoglycerate, and S-adenosylmethionine decarboxylase), indicating their importance for life at high temperature. In addition, these MAGs acquired genes from members from archaea (Crenarchaeota) and bacteria (Firmicutes), mainly involved in metabolism and stress responses, which might play a role to allow this group to adapt to thermal habitats.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
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Osman D, Cooke A, Young TR, Deery E, Robinson NJ, Warren MJ. The requirement for cobalt in vitamin B 12: A paradigm for protein metalation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118896. [PMID: 33096143 PMCID: PMC7689651 DOI: 10.1016/j.bbamcr.2020.118896] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
Abstract
Vitamin B12, cobalamin, is a cobalt-containing ring-contracted modified tetrapyrrole that represents one of the most complex small molecules made by nature. In prokaryotes it is utilised as a cofactor, coenzyme, light sensor and gene regulator yet has a restricted role in assisting only two enzymes within specific eukaryotes including mammals. This deployment disparity is reflected in another unique attribute of vitamin B12 in that its biosynthesis is limited to only certain prokaryotes, with synthesisers pivotal in establishing mutualistic microbial communities. The core component of cobalamin is the corrin macrocycle that acts as the main ligand for the cobalt. Within this review we investigate why cobalt is paired specifically with the corrin ring, how cobalt is inserted during the biosynthetic process, how cobalt is made available within the cell and explore the cellular control of cobalt and cobalamin levels. The partitioning of cobalt for cobalamin biosynthesis exemplifies how cells assist metalation.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Anastasia Cooke
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Tessa R Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; Department of Chemistry, Durham University, Durham DH1 3LE, UK.
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Biomedical Research Centre, University of East Anglia, Norwich NR4 7TJ, UK.
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Hu X, Wei X, Ling J, Chen J. Cobalt: An Essential Micronutrient for Plant Growth? FRONTIERS IN PLANT SCIENCE 2021; 12:768523. [PMID: 34868165 PMCID: PMC8635114 DOI: 10.3389/fpls.2021.768523] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 05/19/2023]
Abstract
Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the family Fabaceae or Leguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2 fixation. In addition to symbiosis, a group of N2 fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2 fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.
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Affiliation(s)
- Xiu Hu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangying Wei
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Xiangying Wei
| | - Jie Ling
- He Xiangning College of Art and Design, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States
- *Correspondence: Jianjun Chen
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Du W, Li G, Ho N, Jenkins L, Hockaday D, Tan J, Cao H. CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms. Brief Bioinform 2020; 22:6035272. [PMID: 33320930 DOI: 10.1093/bib/bbaa375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/14/2022] Open
Abstract
CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH.
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Affiliation(s)
| | | | - Nicholas Ho
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Landon Jenkins
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Drew Hockaday
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
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Pekarsky A, Mihalyi S, Weiss M, Limbeck A, Spadiut O. Depletion of Boric Acid and Cobalt from Cultivation Media: Impact on Recombinant Protein Production with Komagataella phaffii. Bioengineering (Basel) 2020; 7:bioengineering7040161. [PMID: 33322107 PMCID: PMC7763993 DOI: 10.3390/bioengineering7040161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The REACH regulation stands for “Registration, Evaluation, Authorization and Restriction of Chemicals” and defines certain substances as harmful to human health and the environment. This urges manufacturers to adapt production processes. Boric acid and cobalt dichloride represent such harmful ingredients, but are commonly used in yeast cultivation media. The yeast Komagataella phaffii (Pichia pastoris) is an important host for heterologous protein production and compliance with the REACH regulation is desirable. Boric acid and cobalt dichloride are used as boron and cobalt sources, respectively. Boron and cobalt support growth and productivity and a number of cobalt-containing enzymes exist. Therefore, depletion of boric acid and cobalt dichloride could have various negative effects, but knowledge is currently scarce. Herein, we provide an insight into the impact of boric acid and cobalt depletion on recombinant protein production with K. phaffii and additionally show how different vessel materials affect cultivation media compositions through leaking elements. We found that boric acid could be substituted through boron leakiness from borosilicate glassware. Furthermore, depletion of boric acid and cobalt dichloride neither affected high cell density cultivation nor cell morphology and viability on methanol. However, final protein quality of three different industrially relevant enzymes was affected in various ways.
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Affiliation(s)
- Alexander Pekarsky
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Sophia Mihalyi
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Maximilian Weiss
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
- Correspondence: ; Tel.: +43-1-58801-166473
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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Fernandes LDP, Silva JMB, Martins DOS, Santiago MB, Martins CHG, Jardim ACG, Oliveira GS, Pivatto M, Souza RAC, Franca EDF, Deflon VM, Machado AEH, Oliveira CG. Fragmentation Study, Dual Anti-Bactericidal and Anti-Viral Effects and Molecular Docking of Cobalt(III) Complexes. Int J Mol Sci 2020; 21:ijms21218355. [PMID: 33171773 PMCID: PMC7664407 DOI: 10.3390/ijms21218355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
Considering our previous findings on the remarkable activity exhibited by cobalt(III) with 2-acetylpyridine-N(4)-R-thiosemicarbazone (Hatc-R) compounds against Mycobacterium tuberculosis, the present study aimed to explored new structure features of the complexes of the type [Co(atc--R)2]Cl, where R = methyl (Me, 1) or phenyl (Ph, 2) (13C NMR, high-resolution mass spectrometry, LC-MS/MS, fragmentation study) together with its antibacterial and antiviral biological activities. The minimal inhibitory and minimal bactericidal concentrations (MIC and MBC) were determined, as well as the antiviral potential of the complexes on chikungunya virus (CHIKV) infection in vitro and cell viability. [Co(atc-Ph)2]Cl revealed promising MIC and MBC values which ranged from 0.39 to 0.78 µg/mL in two strains tested and presented high potential against CHIKV by reducing viral replication by up to 80%. The results showed that the biological activity is strongly influenced by the peripheral substituent groups at the N(4) position of the atc-R1- ligands. In addition, molecular docking analysis was performed. The relative binding energy of the docked compound with five bacteria strains was found in the range of -3.45 and -9.55 kcal/mol. Thus, this work highlights the good potential of cobalt(III) complexes and provide support for future studies on this molecule aiming at its antibacterial and antiviral therapeutic application.
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Affiliation(s)
- Laísa de P. Fernandes
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil; (L.d.P.F.); (G.S.O.); (M.P.); (R.A.C.S.)
| | - Júlia M. B. Silva
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil; (J.M.B.S.); (D.O.S.M.); (M.B.S.); (C.H.G.M.); (A.C.G.J.)
| | - Daniel O. S. Martins
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil; (J.M.B.S.); (D.O.S.M.); (M.B.S.); (C.H.G.M.); (A.C.G.J.)
| | - Mariana B. Santiago
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil; (J.M.B.S.); (D.O.S.M.); (M.B.S.); (C.H.G.M.); (A.C.G.J.)
| | - Carlos H. G. Martins
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil; (J.M.B.S.); (D.O.S.M.); (M.B.S.); (C.H.G.M.); (A.C.G.J.)
| | - Ana C. G. Jardim
- Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia 38408-100, MG, Brazil; (J.M.B.S.); (D.O.S.M.); (M.B.S.); (C.H.G.M.); (A.C.G.J.)
| | - Guedmiller S. Oliveira
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil; (L.d.P.F.); (G.S.O.); (M.P.); (R.A.C.S.)
| | - Marcos Pivatto
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil; (L.d.P.F.); (G.S.O.); (M.P.); (R.A.C.S.)
| | - Rafael A. C. Souza
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil; (L.d.P.F.); (G.S.O.); (M.P.); (R.A.C.S.)
| | - Eduardo de F. Franca
- Laboratório de Cristalografia e Química Computacional, Instituto de Química, Universidade Federal de Uberlândia, UFU, Uberlândia 38408-100, MG, Brazil;
| | - Victor M. Deflon
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos 13566-590, SP, Brazil;
| | - Antonio E. H. Machado
- Laboratório de Fotoquímica e Ciências dos Materiais, Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil;
- Unidade Acadêmica Especial de Física, Programa de Pós-Graduação em Ciências Exatas e Tecnol., Universidade Federal de Catalão, Catalão 75705-220, GO, Brasil
| | - Carolina G. Oliveira
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia 38400-902, MG, Brazil; (L.d.P.F.); (G.S.O.); (M.P.); (R.A.C.S.)
- Correspondence: ; Tel.: +55-34-9997-9271
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Schneider NO, Tassoulas LJ, Zeng D, Laseke AJ, Reiter NJ, Wackett LP, Maurice MS. Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine. Biochemistry 2020; 59:3258-3270. [PMID: 32786413 DOI: 10.1021/acs.biochem.0c00537] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Free guanidine is increasingly recognized as a relevant molecule in biological systems. Recently, it was reported that urea carboxylase acts preferentially on guanidine, and consequently, it was considered to participate directly in guanidine biodegradation. Urea carboxylase combines with allophanate hydrolase to comprise the activity of urea amidolyase, an enzyme predominantly found in bacteria and fungi that catalyzes the carboxylation and subsequent hydrolysis of urea to ammonia and carbon dioxide. Here, we demonstrate that urea carboxylase and allophanate hydrolase from Pseudomonas syringae are insufficient to catalyze the decomposition of guanidine. Rather, guanidine is decomposed to ammonia through the combined activities of urea carboxylase, allophanate hydrolase, and two additional proteins of the DUF1989 protein family, expansively annotated as urea carboxylase-associated family proteins. These proteins comprise the subunits of a heterodimeric carboxyguanidine deiminase (CgdAB), which hydrolyzes carboxyguanidine to N-carboxyurea (allophanate). The genes encoding CgdAB colocalize with genes encoding urea carboxylase and allophanate hydrolase. However, 25% of urea carboxylase genes, including all fungal urea amidolyases, do not colocalize with cgdAB. This subset of urea carboxylases correlates with a notable Asp to Asn mutation in the carboxyltransferase active site. Consistent with this observation, we demonstrate that fungal urea amidolyase retains a strong substrate preference for urea. The combined activities of urea carboxylase, carboxyguanidine deiminase and allophanate hydrolase represent a newly recognized pathway for the biodegradation of guanidine. These findings reinforce the relevance of guanidine as a biological metabolite and reveal a broadly distributed group of enzymes that act on guanidine in bacteria.
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Affiliation(s)
- Nicholas O Schneider
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Lambros J Tassoulas
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108-6106, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108-6106, United States
| | - Danyun Zeng
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Amanda J Laseke
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Nicholas J Reiter
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108-6106, United States.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota 55108-6106, United States
| | - Martin St Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
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Uebanso T, Shimohata T, Mawatari K, Takahashi A. Functional Roles of B‐Vitamins in the Gut and Gut Microbiome. Mol Nutr Food Res 2020; 64:e2000426. [DOI: 10.1002/mnfr.202000426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Indexed: 01/19/2023]
Affiliation(s)
- Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences Tokushima University Graduate School Tokushima 770–8503 Japan
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50
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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