1
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Nguyen HNA, Sharp L, Lyman E, Saenz JP. Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering. Biophys J 2024; 123:1896-1902. [PMID: 38850024 PMCID: PMC11267422 DOI: 10.1016/j.bpj.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the ordering of hydrocarbon chains and the packing of lipids. Many eukaryotes synthesize sterols, which are uniquely capable of modulating the lipid order to decouple membrane stability from fluidity. Ancient sterol analogs known as hopanoids are found in many bacteria and proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. In this work, simulations, monolayer experiments, and cellular assays show that hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid acyl chain. We find that cholesterol and diplopterol's methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterol's constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest that cholesterol's broader lipid-ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.
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Affiliation(s)
- Ha Ngoc Anh Nguyen
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware; College of Arts and Sciences, Fairfield University, Fairfield, Connecticut
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware; Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - James P Saenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany; Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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2
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van Aalst EJ, Yekefallah M, A M van Beekveld R, Breukink E, Weingarth M, Wylie BJ. Coordination of bilayer properties by an inward-rectifier K + channel is a cooperative process driven by protein-lipid interaction. J Struct Biol X 2024; 9:100101. [PMID: 38883399 PMCID: PMC11176924 DOI: 10.1016/j.yjsbx.2024.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Physical properties of biological membranes directly or indirectly govern biological processes. Yet, the interplay between membrane and integral membrane proteins is difficult to assess due to reciprocal effects between membrane proteins, individual lipids, and membrane architecture. Using solid-state NMR (SSNMR) we previously showed that KirBac1.1, a bacterial Inward-Rectifier K+ channel, nucleates bilayer ordering and microdomain formation through tethering anionic lipids. Conversely, these lipids cooperatively bind cationic residues to activate the channel and initiate K+ flux. The mechanistic details governing the relationship between cooperative lipid loading and bilayer ordering are, however, unknown. To investigate, we generated KirBac1.1 samples with different concentrations of 13C-lableded phosphatidyl glycerol (PG) lipids and acquired a full suite of SSNMR 1D temperature series experiments using the ordered all-trans (AT) and disordered trans-gauche (TG) acyl conformations as markers of bilayer dynamics. We observed increased AT ordered signal, decreased TG disordered signal, and increased bilayer melting temperature with increased PG concentration. Further, we identified cooperativity between ordering and direct binding of PG lipids, indicating KirBac1.1-driven bilayer ordering and microdomain formation is a classically cooperative Hill-type process driven by and predicated upon direct binding of PG lipids. Our results provide unique mechanistic insight into how proteins and lipids in tandem contribute to supramolecular bilayer heterogeneity in the lipid membrane.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Roy A M van Beekveld
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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3
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Lam M, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Gluconobacter frateurii ML.ISBL3, an endophytic strain isolated from aerial roots of Syngonium podophyllum. Microbiol Resour Announc 2024; 13:e0110623. [PMID: 38470266 PMCID: PMC11008163 DOI: 10.1128/mra.01106-23] [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: 11/16/2023] [Accepted: 03/02/2024] [Indexed: 03/13/2024] Open
Abstract
The endophytic strain Gluconobacter frateurii ML.ISBL3 was isolated from aerial roots of Syngonium podophyllum in Hong Kong. Its complete genome, established through hybrid assembly, comprises a single chromosome of 3,309,710 bp (56.30% G+C).
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Affiliation(s)
- M. Lam
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - K. M. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - G. K. K. Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - F. C. C. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - S. D. J. Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
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4
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Pan H, Shim A, Lubin MB, Belin BJ. Hopanoid lipids promote soybean -Bradyrhizobium symbiosis. mBio 2024; 15:e0247823. [PMID: 38445860 PMCID: PMC11005386 DOI: 10.1128/mbio.02478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/04/2024] [Indexed: 03/07/2024] Open
Abstract
The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu-shc::∆shc. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta, Pcu-shc::∆shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility. A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
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Affiliation(s)
- Huiqiao Pan
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
| | - Ashley Shim
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew B. Lubin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Brittany J. Belin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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5
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Willdigg JR, Patel Y, Arquilevich BE, Subramanian C, Frank MW, Rock CO, Helmann JD. The Bacillus subtilis cell envelope stress-inducible ytpAB operon modulates membrane properties and contributes to bacitracin resistance. J Bacteriol 2024; 206:e0001524. [PMID: 38323910 PMCID: PMC10955860 DOI: 10.1128/jb.00015-24] [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: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σM responds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall-inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependent ytpAB operon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35 terpenoids. Using targeted lipidomics, we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless, ytpA was critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression of ytpA increased membrane fluidity as monitored by fluorescence anisotropy. The ytpA gene contributes to bacitracin resistance in mutants additionally lacking the bceAB or bcrC genes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of the ytpAB operon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes involved in cell wall homeostasis.IMPORTANCEPeptidoglycan synthesis inhibitors include some of our most important antibiotics. In Bacillus subtilis, peptidoglycan synthesis inhibitors induce the σM regulon, which is critical for intrinsic antibiotic resistance. The σM-dependent ytpAB operon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35 terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Furthermore, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the undecaprenyl-pyrophosphate lipid carrier that sustains peptidoglycan synthesis.
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Affiliation(s)
| | - Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | | | - Chitra Subramanian
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Matthew W. Frank
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Charles O. Rock
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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6
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Lee TH, Charchar P, Separovic F, Reid GE, Yarovsky I, Aguilar MI. The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes. Chem Sci 2024; 15:3408-3427. [PMID: 38455013 PMCID: PMC10915831 DOI: 10.1039/d3sc04523d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Patrick Charchar
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
| | - Gavin E Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
- Department of Biochemistry and Pharmacology, University of Melbourne Parkville VIC 3010 Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
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7
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de Oliveira Costa G, Mansur Pontes CL, Parize AL, Sandjo LP. Unveiling chemical responses in the kombucha-based fermentation of black tea, banana flower, and grape juice: LC-ESIMS, GNPS, MS-DIAL, and MS-FINDER-assisted chemical characterization. Food Funct 2024; 15:2497-2523. [PMID: 38334749 DOI: 10.1039/d3fo04977a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The lack of studies evaluating the chemical responses of kombucha microorganisms when exposed to plants is notable in the literature. Therefore, this work investigates the chemical behaviour of 7-, 14- and 21 day-fermentation of kombucha derived from three extracts obtained from banana inflorescence, black tea, and grape juice. After the acquisition of UPLC-ESI-MS data, GNPS molecular networking, MS-Dial, and MS-Finder were used to chemically characterize the samples. The microbial chemical responses were enzymatic hydrolysis, oxidation, and biosynthesis. The biosynthesis was different among the kombucha samples. In fermented black tea, gallic and dihydrosinapic acids were found as hydrolysis products alongside a sugar-derived product namely 7-(α-D-glucopyranosyloxy)-2,3,4,5,6-pentahydroxyheptanoic acid. The sphingolipids, safingol and cedefingol alongside capryloyl glycine and palmitoyl proline were identified. In fermented grapes, sugar degradation and chemical transformation products were detected together with three cell membrane hopanoids characterized as hydroxybacteriohopanetetrol cyclitol ether, (Δ6 or Δ11)-hydroxybacteriohopanetetrol cyclitol ether, and methyl (Δ6 or Δ11)-hydroxybacteriohopanetetrol cyclitol. The fermented banana blossom showed the presence of methyl (Δ6 or Δ11)-hydroxybacteriohopanetetrol cyclitol together with sphingofungin B, sphinganine and other fatty acid derivatives. Parts of these samples were tested for their inhibition against α-glucosidase and their antioxidant effects. Except for the 14-day fermented extracts, other black tea extracts showed significant inhibition of α-glucosidase ranging from 42.5 to 42.8%. A 14-day fermented extract of the banana blossom infusion showed an inhibition of 29.1%, while grape samples were less active than acarbose. The 21-day fermented black tea extract showed moderate antioxidant properties on a DPPH-based model with an EC50 of 5.29 ± 0.10 μg mL-1, while the other extracts were weakly active (EC50 between 80.76 and 168.12 μg mL-1).
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Affiliation(s)
| | - Carime L Mansur Pontes
- Department of Chemistry, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, SC, Brazil.
| | - Alexandre L Parize
- Department of Chemistry, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, SC, Brazil.
| | - Louis P Sandjo
- Department of Chemistry, Universidade Federal de Santa Catarina, 88040-900, Florianópolis, SC, Brazil.
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8
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Nguyen HNA, Sharp L, Lyman E, Saenz JP. Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556521. [PMID: 38370701 PMCID: PMC10871177 DOI: 10.1101/2023.09.06.556521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the thermodynamic ordering of lipids. Most Eukaryotes employ sterols, which are uniquely capable of modulating lipid order to decouple membrane stability from fluidity. Ancient sterol analogues known as hopanoids are found in many bacteria and are proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. We reveal that both hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipid's acyl chain. We find that cholesterol and diplopterol's methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterol's constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest cholesterol's broader lipid ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.
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Affiliation(s)
- Ha-Ngoc-Anh Nguyen
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark DE 19716
- College of Arts and Sciences, Fairfield University, Fairfield, CT 06824
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark DE 19716
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - James P Saenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
- Medical Faculty, Technische Universität Dresden, 01062 Dresden, Germany
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9
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Wycisk V, Wagner MC, Urner LH. Trends in the Diversification of the Detergentome. Chempluschem 2024; 89:e202300386. [PMID: 37668309 DOI: 10.1002/cplu.202300386] [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: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/06/2023]
Abstract
Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of detergents is determined empirically, which leads to failed preparations, and raising costs. To facilitate project planning, here we review synthesis strategies that drive the diversification of the detergentome. Synthesis strategies relevant for industrial and academic applications include linear, modular, combinatorial, bio-based, and metric-assisted detergent synthesis. Scopes and limitations of individual synthesis strategies in context with industrial product development and academic research are discussed. Furthermore, when designing detergents, the selection of molecular building blocks, i. e., head, linker, tail, is as important as the employed synthesis strategy. To facilitate the design of safe-to-use and tailor-made detergents, we provide an overview of established head, linker, and tail groups and highlight selected scopes and limitations for applications. It becomes apparent that most recent contributions to the increasing chemical diversity of detergent building blocks originate from the development of detergents for membrane protein studies. The overview of synthesis strategies and molecular blocks will bring us closer to the ability to predictably design and synthesize optimal detergents for challenging future applications.
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Affiliation(s)
- Virginia Wycisk
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Marc-Christian Wagner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Leonhard H Urner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
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Hoshino Y, Nettersheim BJ, Gold DA, Hallmann C, Vinnichenko G, van Maldegem LM, Bishop C, Brocks JJ, Gaucher EA. Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago. Nat Ecol Evol 2023; 7:2045-2054. [PMID: 37884688 PMCID: PMC10697835 DOI: 10.1038/s41559-023-02223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/06/2023] [Indexed: 10/28/2023]
Abstract
Fossilized lipids offer a rare glimpse into ancient ecosystems. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of cyanobacteria as primary producers throughout geological history. However, the discovery of hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including recently proposed candidate phyla and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free samples. We show that HpnP was probably present in the last common ancestor of cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago (Ma). A subsequent rise of sedimentary 2-methylhopanes around 600 Ma probably reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae-possibly connected by algal dependency on microbially produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers before 750 Ma and thus as a potential tool to measure the importance of oxygenic cyanobacteria as primary producers on early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.
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Affiliation(s)
- Yosuke Hoshino
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
- Department of Biology, Georgia State University, Atlanta, GA, USA.
| | - Benjamin J Nettersheim
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany.
| | - David A Gold
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, USA
| | | | - Galina Vinnichenko
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lennart M van Maldegem
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Caleb Bishop
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jochen J Brocks
- Research School of Earth Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, USA
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11
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Kan Y, Zhang L, Wang Y, Ma Q, Zhou Y, Jiang X, Zhang W, Ruan Z. Endophytic Bacterium Flexivirga meconopsidis sp. nov. with Plant Growth-Promoting Function, Isolated from the Seeds of Meconopsis integrifolia. Microorganisms 2023; 11:2899. [PMID: 38138043 PMCID: PMC10745605 DOI: 10.3390/microorganisms11122899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Strain Q11T of an irregular coccoid Gram-positive bacterium, aerobic and non-motile, was isolated from Meconopsis integrifolia seeds. Strain Q11T grew optimally in 1% (w/v) NaCl, pH 7, at 30 °C. Strain Q11T is most closely related to Flexivirga, as evidenced by 16S rRNA gene analysis, and shares the highest similarity with Flexivirga aerilata ID2601ST (99.24%). Based on genome sequence analysis, the average nucleotide identity and digital DNA-DNA hybridization values of strains Q11T and D2601ST were 88.82% and 36.20%, respectively. Additionally, strain Q11T showed the abilities of nitrogen fixation and indole acetic acid production and was shown to promote maize growth under laboratory conditions. Its genome contains antibiotic resistance genes (the vanY gene in the vanB cluster and the vanW gene in the vanI cluster) and extreme environment tolerance genes (ectoine biosynthetic gene cluster). Shotgun proteomics also detected antibiotic resistance proteins (class A beta-lactamases, D-alanine ligase family proteins) and proteins that improve plant cold tolerance (multispecies cold shock proteins). Strain Q11T was determined to be a novel species of the genus Flexivirga, for which the name Flexivirga meconopsidis sp. nov. is proposed. The strain type is Q11T (GDMCC 1.3002T = JCM 36020 T).
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Affiliation(s)
- Yongtao Kan
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China;
| | - Yan Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China
| | - Qingyun Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Jiang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi 830017, China;
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (Q.M.); (Y.Z.); (X.J.)
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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12
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Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H. Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales. THE ISME JOURNAL 2023; 17:2123-2133. [PMID: 37749300 PMCID: PMC10579370 DOI: 10.1038/s41396-023-01518-6] [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: 04/19/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Anne Daebeler
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 7, 370 05, Budweis, Czech Republic
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | - Rasmus H Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Vienna, Austria.
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13
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Pan H, Shim A, Lubin MB, Belin BJ. Hopanoid lipids promote soybean- Bradyrhizobium symbiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556284. [PMID: 37732186 PMCID: PMC10508751 DOI: 10.1101/2023.09.04.556284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, the most economically significant Bradyrhizobium host, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu- shc ::Δ shc . GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta , Pcu- shc ::Δ shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within host tissue. RNA-seq revealed that hopanoid loss reduces expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility. IMPORTANCE A major problem for global sustainability is feeding our exponentially growing human population while available arable land is decreasing, especially in areas with the greatest population growth. Harnessing the power of plant-beneficial microbes has gained attention as a potential solution, including the increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically important host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
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14
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Ji Z, Fan B, Chen Y, Yue J, Chen J, Zhang R, Tong Y, Liu Z, Liang J, Duan L. Functional characterization of triterpene synthases in Cibotium barometz. Synth Syst Biotechnol 2023; 8:437-444. [PMID: 37416896 PMCID: PMC10320381 DOI: 10.1016/j.synbio.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023] Open
Abstract
Cibotium barometz (Linn.) J. Sm., a tree fern in the Dicksoniaceae family, is an economically important industrial exported plant in China and widely used in Traditional Chinese Medicine. C. barometz produces a range of bioactive triterpenes and their metabolites. However, the biosynthetic pathway of triterpenes in C. barometz remains unknown. To clarify the origin of diverse triterpenes in C. barometz, we conducted de novo transcriptome sequencing and analysis of C. barometz rhizomes and leaves to identify the candidate genes involved in C. barometz triterpene biosynthesis. Three C. barometz triterpene synthases (CbTSs) candidate genes were obtained. All of them were highly expressed in C. barometz rhizomes, consisting of the accumulation pattern of triterpenes in C. barometz. To characterize the function of these CbTSs, we constructed a squalene- and oxidosqualene-overproducing yeast chassis by overexpressing all the enzymes in the MVA pathway under the control of GAL-regulated promoter and disrupted the GAL80 gene in Saccharomyces cerevisiae simultaneously. Heterologous expressing CbTS1, CbTS2, and CbTS3 in engineering yeast strain produced cycloartenol, dammaradiene, and diploptene, respectively. Phylogenetic analysis revealed that CbTS1 belongs to oxidosqualene cyclase, while CbTS2 and CbTS3 belong to squalene cyclase. These results decipher enzymatic mechanisms underlying the origin of diverse triterpene in C. barometz.
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15
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Mitchison-Field LM, Belin BJ. Bacterial lipid biophysics and membrane organization. Curr Opin Microbiol 2023; 74:102315. [PMID: 37058914 PMCID: PMC10523990 DOI: 10.1016/j.mib.2023.102315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The formation of lateral microdomains is emerging as a central organizing principle in bacterial membranes. These microdomains are targets of antibiotic development and have the potential to enhance natural product synthesis, but the rules governing their assembly are unclear. Previous studies have suggested that microdomain formation is promoted by lipid phase separation, particularly by cardiolipin (CL) and isoprenoid lipids, and there is strong evidence that CL biosynthesis is required for recruitment of membrane proteins to cell poles and division sites. New work demonstrates that additional bacterial lipids may mediate membrane protein localization and function, opening the field for mechanistic evaluation of lipid-driven membrane organization in vivo.
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Affiliation(s)
- Lorna My Mitchison-Field
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Brittany J Belin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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16
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Di Lorenzo F, Nicolardi S, Marchetti R, Vanacore A, Gallucci N, Duda K, Nieto Fabregat F, Nguyen HNA, Gully D, Saenz J, Giraud E, Paduano L, Molinaro A, D’Errico G, Silipo A. Expanding Knowledge of Methylotrophic Capacity: Structure and Properties of the Rough-Type Lipopolysaccharide from Methylobacterium extorquens and Its Role on Membrane Resistance to Methanol. JACS AU 2023; 3:929-942. [PMID: 37006758 PMCID: PMC10052234 DOI: 10.1021/jacsau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
The ability of Methylobacterium extorquens to grow on methanol as the sole carbon and energy source has been the object of intense research activity. Unquestionably, the bacterial cell envelope serves as a defensive barrier against such an environmental stressor, with a decisive role played by the membrane lipidome, which is crucial for stress resistance. However, the chemistry and the function of the main constituent of the M. extorquens outer membrane, the lipopolysaccharide (LPS), is still undefined. Here, we show that M. extorquens produces a rough-type LPS with an uncommon, non-phosphorylated, and extensively O-methylated core oligosaccharide, densely substituted with negatively charged residues in the inner region, including novel monosaccharide derivatives such as O-methylated Kdo/Ko units. Lipid A is composed of a non-phosphorylated trisaccharide backbone with a distinctive, low acylation pattern; indeed, the sugar skeleton was decorated with three acyl moieties and a secondary very long chain fatty acid, in turn substituted by a 3-O-acetyl-butyrate residue. Spectroscopic, conformational, and biophysical analyses on M. extorquens LPS highlighted how structural and tridimensional features impact the molecular organization of the outer membrane. Furthermore, these chemical features also impacted and improved membrane resistance in the presence of methanol, thus regulating membrane ordering and dynamics.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Roberta Marchetti
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Adele Vanacore
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Noemi Gallucci
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Katarzyna Duda
- Research
Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Ferran Nieto Fabregat
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Ha Ngoc Anh Nguyen
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Djamel Gully
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - James Saenz
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Eric Giraud
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Luigi Paduano
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Gerardino D’Errico
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Alba Silipo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
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17
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Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem. mSystems 2022; 7:e0063222. [PMID: 36445112 PMCID: PMC9765116 DOI: 10.1128/msystems.00632-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.
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18
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Wahia H, Fakayode OA, Mustapha AT, Zhou C, Dabbour M. Application and potential of multifrequency ultrasound in juice industry: Comprehensive analysis of inactivation and germination of Alicyclobacillus acidoterrestris spores. Crit Rev Food Sci Nutr 2022; 64:4561-4586. [PMID: 36412233 DOI: 10.1080/10408398.2022.2143475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The majority of acidic fruits are perishable owing to their high-water activity, which promotes microbial activity, thus exhibiting metabolic functions that cause spoilage. Along with sanitary practices, several treatments are used during processing and/or storage to inhibit the development of undesirable bacteria. To overcome the challenges caused by mild heat treatment, juice manufacturers have recently increased their involvement in developing novel non-thermal processing procedures. Ultrasonication alone or in combination with other hurdle technologies may be used to pasteurize processed fruit juices. Multifrequency ultrasound has gained popularity due to the fact that mono-frequency ultrasound has less impact on bacterial inactivation and bioactive compound enhancement of fruit juice. Here, we present and discuss the fundamental information and technological knowledge of how spoilage bacteria, specifically Alicyclobacillus acidoterrestris, assemble resistant spores and inactivate and germinate dormant spores in response to nutrient germinants and physical treatments such as heat and ultrasound. To the authors' knowledge, no prior review of ultrasonic inactivation and germination of A. acidoterrestris in fruit juice exists. Therefore, this article aims to provide a review of previously published research on the inactivation and germination of A. acidoterrestris in fruit juice by ultrasound and heat.
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Affiliation(s)
- Hafida Wahia
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | | | | | - Cunshan Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
- School of Biological and Food Engineering, Chuzhou University, Chuzhou, PR China
| | - Mokhtar Dabbour
- Department of Agricultural and Biosystems Engineering, Faculty of Agriculture, Benha University, Moshtohor, Qaluobia, Egypt
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19
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Abstract
Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.
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20
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Lima CODC, De Castro GM, Solar R, Vaz ABM, Lobo F, Pereira G, Rodrigues C, Vandenberghe L, Martins Pinto LR, da Costa AM, Koblitz MGB, Benevides RG, Azevedo V, Uetanabaro APT, Soccol CR, Góes-Neto A. Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics. Front Microbiol 2022; 13:994524. [PMID: 36406426 PMCID: PMC9671152 DOI: 10.3389/fmicb.2022.994524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/04/2022] [Indexed: 03/23/2024] Open
Abstract
Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.
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Affiliation(s)
- Carolina O. de C. Lima
- Department of Biological Sciences, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
| | - Giovanni M. De Castro
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo Solar
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Aline B. M. Vaz
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Francisco Lobo
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gilberto Pereira
- Bioprocess Engineering and Biotechnology Department, Federal University of the Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Cristine Rodrigues
- Bioprocess Engineering and Biotechnology Department, Federal University of the Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Luciana Vandenberghe
- Bioprocess Engineering and Biotechnology Department, Federal University of the Paraná (UFPR), Curitiba, Paraná, Brazil
| | | | - Andréa Miura da Costa
- Department of Biological Sciences, State University of Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Maria Gabriela Bello Koblitz
- Food and Nutrition Graduate Program (PPGAN), Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Guimarães Benevides
- Department of Biological Sciences, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Ana Paula Trovatti Uetanabaro
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
- Department of Biological Sciences, State University of Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of the Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Aristóteles Góes-Neto
- Department of Biological Sciences, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
- Institute of Biological Sciences, Federal University of the Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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21
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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22
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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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Aukema KG, Wang M, de Souza B, O'Keane S, Clipsham M, Wackett LP, Aksan A. Core-shell encapsulation formulations to stabilize desiccated Bradyrhizobium against high environmental temperature and humidity. Microb Biotechnol 2022; 15:2391-2400. [PMID: 35730421 PMCID: PMC9437883 DOI: 10.1111/1751-7915.14078] [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: 01/25/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Engineered materials to improve the shelf-life of desiccated microbial strains are needed for cost-effective bioaugmentation strategies. High temperatures and humidity of legume-growing regions challenge long-term cell stabilization at the desiccated state. A thermostable xeroprotectant core and hydrophobic water vapour barrier shell encapsulation technique was developed to protect desiccated cells from the environment. A trehalose core matrix increased the stability of desiccated Bradyrhizobium by three orders of magnitude over 20 days at 32°C and 50% relative humidity (RH) compared to buffer alone; however, the improvement was not deemed sufficient for a shelf-stable bioproduct. We tested common additives (skim milk, albumin, gelatin and dextran) to increase the glass transition temperature of the desiccated product to provide further stabilization. Albumin increased the glass transition temperature of the trehalose-based core by 40°C and stabilized desiccated Bradyrhizobium for 4 months during storage at high temperature (32°C) and moderate humidity (50% RH) with only 1 log loss of viability. Although the albumin-trehalose core provided exceptional protection against high temperature, it was ineffective at higher humidity conditions (75%). We therefore incorporated a paraffin shell, which protected desiccated cells against 75% RH providing proof of concept that core and shell encapsulation is an effective strategy to stabilize desiccated cells.
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Affiliation(s)
- Kelly G. Aukema
- Department of BiochemistryMolecular Biology and BiophysicsMinneapolisMNUSA
- BioTechnology Institute University of MinnesotaSt. PaulMNUSA
| | - Mian Wang
- Department of Mechanical EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Beatriz de Souza
- Department of Mechanical EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Sophie O'Keane
- Department of Mechanical EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Maia Clipsham
- Microbial EngineeringUniversity of MinnesotaSt. PaulMNUSA
| | - Lawrence P. Wackett
- Department of BiochemistryMolecular Biology and BiophysicsMinneapolisMNUSA
- BioTechnology Institute University of MinnesotaSt. PaulMNUSA
| | - Alptekin Aksan
- BioTechnology Institute University of MinnesotaSt. PaulMNUSA
- Department of Mechanical EngineeringUniversity of MinnesotaMinneapolisMNUSA
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Hopanoids Confer Robustness to Physicochemical Variability in the Niche of the Plant Symbiont Bradyrhizobium diazoefficiens. J Bacteriol 2022; 204:e0044221. [PMID: 35657706 DOI: 10.1128/jb.00442-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobia are a group of bacteria that increase soil nitrogen content through symbiosis with legume plants. The soil and symbiotic host are potentially stressful environments, and the soil will likely become even more stressful as the climate changes. Many rhizobia within the Bradyrhizobium clade, like Bradyrhizobium diazoefficiens, possess the genetic capacity to synthesize hopanoids, steroid-like lipids similar in structure and function to cholesterol. Hopanoids are known to protect against stresses relevant to the niche of B. diazoefficiens. Paradoxically, mutants unable to synthesize the extended class of hopanoids participate in symbioses with success similar to that of the wild type, despite being delayed in root nodule initiation. Here, we show that in B. diazoefficiens, the growth defects of extended-hopanoid-deficient mutants can be at least partially compensated for by the physicochemical environment, specifically, by optimal osmotic and divalent cation concentrations. Through biophysical measurements of lipid packing and membrane permeability, we show that extended hopanoids confer robustness to environmental variability. These results help explain the discrepancy between previous in-culture and in planta results and indicate that hopanoids may provide a greater fitness advantage to rhizobia in the variable soil environment than the more controlled environments within root nodules. To improve the legume-rhizobium symbiosis through either bioengineering or strain selection, it will be important to consider the full life cycle of rhizobia, from soil to symbiosis. IMPORTANCE Rhizobia, such as B. diazoefficiens, play an important role in the nitrogen cycle by making nitrogen gas bioavailable through symbiosis with legume plants. As climate change threatens soil health, this symbiosis has received increased attention as a more sustainable source of soil nitrogen than the energy-intensive Haber-Bosch process. Efforts to use rhizobia as biofertilizers have been effective; however, long-term integration of rhizobia into the soil community has been less successful. This work represents a small step toward improving the legume-rhizobium symbiosis by identifying a cellular component-hopanoid lipids-that confers robustness to environmental stresses rhizobia are likely to encounter in soil microenvironments as sporadic desiccation and flooding events become more common.
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Ferreira EGC, Gomes DF, Delai CV, Barreiros MAB, Grange L, Rodrigues EP, Henning LMM, Barcellos FG, Hungria M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiol 2022; 22:122. [PMID: 35513812 PMCID: PMC9069715 DOI: 10.1186/s12866-022-02527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. RESULTS A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF. CONCLUSIONS All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.
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Affiliation(s)
- Everton Geraldo Capote Ferreira
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
| | | | - Caroline Vanzzo Delai
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | | | - Luciana Grange
- Federal University of Paraná (UFPR), Estrada dos Pioneiros 2153, CEP 85950-000 Palotina, PR Brazil
| | - Elisete Pains Rodrigues
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | | | - Fernando Gomes Barcellos
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
| | - Mariangela Hungria
- Londrina State University (UEL), Celso Garcia Cid Road (PR 445), km 380, CEP 86057-970 Londrina, PR Brazil
- Embrapa Soja, Rodovia Carlos João Strass, C.P. 231, CEP 86001-970 Londrina, PR Brazil
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Elling FJ, Evans TW, Nathan V, Hemingway JD, Kharbush JJ, Bayer B, Spieck E, Husain F, Summons RE, Pearson A. Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols. GEOBIOLOGY 2022; 20:399-420. [PMID: 35060273 DOI: 10.1111/gbi.12484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia- and nitrite-oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia-oxidizing (AOB), nitrite-oxidizing (NOB), and complete ammonia-oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen-containing bacteriohopanepolyols were tentatively identified, of which the so called BHP-743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin-Benson-Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids.
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Affiliation(s)
- Felix J Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Vinitra Nathan
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jordon D Hemingway
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Jenan J Kharbush
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Department of Earth and Environmental Science, University of Michigan, Ann Arbor, Michigan, USA
| | - Barbara Bayer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Fatima Husain
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roger E Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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27
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Tahoun M, Engeser M, Namasivayam V, Sander PM, Müller CE. Chemistry and Analysis of Organic Compounds in Dinosaurs. BIOLOGY 2022; 11:670. [PMID: 35625398 PMCID: PMC9138232 DOI: 10.3390/biology11050670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.
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Affiliation(s)
- Mariam Tahoun
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
| | - Marianne Engeser
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany;
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
| | - Paul Martin Sander
- Institute of Geosciences, Section Paleontology, University of Bonn, D-53113 Bonn, Germany;
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
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28
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Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
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Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
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29
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Salt Stress Tolerance-Promoting Proteins and Metabolites under Plant-Bacteria-Salt Stress Tripartite Interactions. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The rapid increase in soil salinization has impacted agricultural output and poses a threat to food security. There is an urgent need to focus on improving soil fertility and agricultural yield, both of which are severely influenced by abiotic variables such as soil salinity and sodicity. Abiotic forces have rendered one-third of the overall land unproductive. Microbes are the primary answer to the majority of agricultural production’s above- and below-ground problems. In stressful conditions, proper communication between plants and beneficial microbes is critical for avoiding plant cell damage. Many chemical substances such as proteins and metabolites synthesized by bacteria and plants mediate communication and stress reduction. Metabolites such as amino acids, fatty acids, carbohydrates, vitamins, and lipids as well as proteins such as aquaporins and antioxidant enzymes play important roles in plant stress tolerance. Plant beneficial bacteria have an important role in stress reduction through protein and metabolite synthesis under salt stress. Proper genomic, proteomic and metabolomics characterization of proteins and metabolites’ roles in salt stress mitigation aids scientists in discovering a profitable avenue for increasing crop output. This review critically examines recent findings on proteins and metabolites produced during plant-bacteria interaction essential for the development of plant salt stress tolerance.
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30
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Hwang S, Lee N, Choe D, Lee Y, Kim W, Kim JH, Kim G, Kim H, Ahn NH, Lee BH, Palsson BO, Cho BK. System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus. Front Bioeng Biotechnol 2022; 10:844200. [PMID: 35284422 PMCID: PMC8914203 DOI: 10.3389/fbioe.2022.844200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3'-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5'-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Neung-Ho Ahn
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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31
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Lipopolysaccharide O-antigen molecular and supramolecular modifications of plant root microbiota are pivotal for host recognition. Carbohydr Polym 2022; 277:118839. [PMID: 34893256 DOI: 10.1016/j.carbpol.2021.118839] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022]
Abstract
Lipopolysaccharides, the major outer membrane components of Gram-negative bacteria, are crucial actors of the host-microbial dialogue. They can contribute to the establishment of either symbiosis or bacterial virulence, depending on the bacterial lifestyle. Plant microbiota shows great complexity, promotes plant health and growth and assures protection from pathogens. How plants perceive LPS from plant-associated bacteria and discriminate between beneficial and pathogenic microbes is an open and urgent question. Here, we report on the structure, conformation, membrane properties and immune recognition of LPS isolated from the Arabidopsis thaliana root microbiota member Herbaspirillum sp. Root189. The LPS consists of an O-methylated and variously acetylated D-rhamnose containing polysaccharide with a rather hydrophobic surface. Plant immunology studies in A. thaliana demonstrate that the native acetylated O-antigen shields the LPS from immune recognition whereas the O-deacylated one does not. These findings highlight the role of Herbaspirillum LPS within plant-microbial crosstalk, and how O-antigen modifications influence membrane properties and modulate LPS host recognition.
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Garby TJ, Jordan M, Timms V, Walter MR, Neilan BA. 2-Methylhopanoids in geographically distinct, arid biological soil crusts are primarily cyanobacterial in origin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:164-169. [PMID: 34898023 DOI: 10.1111/1758-2229.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/10/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Microbial palaeontology is largely reliant on the interpretation of geologically stable biomarkers or molecular fossils. Biomolecules that are both specific to particular groups of organisms and stable on a geological scale are invaluable for tracing the emergence and diversification of lifeforms, particularly in cases where mineral fossils are lacking. 2-Methylhopanoids and their diagenic product, 2-methylhopanes, are highly abundant bacterial membrane lipids, recoverable from samples in excess of a billion years old. In this work we used degenerate PCR, targeting 2-methylhopanoid biosynthesis genes, and sequencing to show that the ability to produce these molecules in arid biological soil crusts from deserts in diverse geographical locations (Utah, USA, and the Pilbara, Australia) is largely confined to cyanobacteria. These data suggest that 2-methylhopanes can be used as a proxy for cyanobacterial presence within these environments, contributing to our understanding of the emergence of terrestrial life on Earth.
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Affiliation(s)
- Tamsyn J Garby
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew Jordan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Verlaine Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Malcolm R Walter
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
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Waschulin V, Borsetto C, James R, Newsham KK, Donadio S, Corre C, Wellington E. Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing. THE ISME JOURNAL 2022; 16:101-111. [PMID: 34253854 PMCID: PMC8692599 DOI: 10.1038/s41396-021-01052-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 12/31/2022]
Abstract
The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.
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Affiliation(s)
| | - Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | | | - Christophe Corre
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Chemistry, University of Warwick, Coventry, UK
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Drost M, Diamanti E, Fuhrmann K, Goes A, Shams A, Haupenthal J, Koch M, Hirsch AKH, Fuhrmann G. Bacteriomimetic Liposomes Improve Antibiotic Activity of a Novel Energy-Coupling Factor Transporter Inhibitor. Pharmaceutics 2021; 14:4. [PMID: 35056900 PMCID: PMC8779172 DOI: 10.3390/pharmaceutics14010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/21/2022] Open
Abstract
Liposomes have been studied for decades as nanoparticulate drug delivery systems for cytostatics, and more recently, for antibiotics. Such nanoantibiotics show improved antibacterial efficacy compared to the free drug and can be effective despite bacterial recalcitrance. In this work, we present a loading method of bacteriomimetic liposomes for a novel, hydrophobic compound (HIPS5031) inhibiting energy-coupling factor transporters (ECF transporters), an underexplored antimicrobial target. The liposomes were composed of DOPG (18:1 (Δ9-cis) phosphatidylglycerol) and CL (cardiolipin), resembling the cell membrane of Gram-positive Staphylococcus aureus and Streptococcus pneumoniae, and enriched with cholesterol (Chol). The size and polydispersity of the DOPG/CL/± Chol liposomes remained stable over 8 weeks when stored at 4 °C. Loading of the ECF transporter inhibitor was achieved by thin film hydration and led to a high encapsulation efficiency of 33.19% ± 9.5% into the DOPG/CL/Chol liposomes compared to the phosphatidylcholine liposomes (DMPC/DPPC). Bacterial growth inhibition assays on the model organism Bacillus subtilis revealed liposomal HIPS5031 as superior to the free drug, showing a 3.5-fold reduction in CFU/mL at a concentration of 9.64 µM. Liposomal HIPS5031 was also shown to reduce B. subtilis biofilm. Our findings present an explorative basis for bacteriomimetic liposomes as a strategy against drug-resistant pathogens by surpassing the drug-formulation barriers of innovative, yet unfavorably hydrophobic, antibiotics.
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Affiliation(s)
- Menka Drost
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
- Department of Biology, Pharmaceutical Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Staudtstr. 5, 91058 Erlangen, Germany
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
- Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
| | - Kathrin Fuhrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
| | - Adriely Goes
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
| | - Marcus Koch
- INM-Leibniz-Institut für Neue Materialien, Campus D2.2, 66123 Saarbrücken, Germany;
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
- Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus C1.7, 66123 Saarbrücken, Germany
| | - Gregor Fuhrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; (M.D.); (E.D.); (K.F.); (A.G.); (A.S.); (J.H.); (A.K.H.H.)
- Department of Biology, Pharmaceutical Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Staudtstr. 5, 91058 Erlangen, Germany
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van Tilburg AY, Warmer P, van Heel AJ, Sauer U, Kuipers OP. Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10. Microb Biotechnol 2021; 15:1633-1651. [PMID: 34856064 PMCID: PMC9049611 DOI: 10.1111/1751-7915.13978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent‐resistant and detergent‐sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive miniBacillus PG10 strain. Our study supports previous work suggesting that cardiolipin and prenol lipids are enriched in FMMs of B. subtilis. Additionally, structural analysis of acyl chains of major phospholipids indicated that FMMs display increased order and thickness compared with the surrounding bilayer. Despite the 36% genome reduction, membrane and FMM integrity are largely preserved in miniBacillus PG10, as supported by analysis of membrane fluidity, flotillin distribution and gene expression data. The novel insights in FMM architecture reported here will contribute to further explore the biological significance of FMMs and the means by which FMMs can be exploited as heterologous production platforms. Moreover, our lipidomics method enables comparative FMM lipid profiling between different bacteria.
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Affiliation(s)
- Amanda Y van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Philipp Warmer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.,Life Science Zürich PhD Program on Systems Biology, Zürich, Switzerland
| | - Auke J van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
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Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie van Leeuwenhoek 2021; 115:41-58. [PMID: 34761294 PMCID: PMC8776678 DOI: 10.1007/s10482-021-01676-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022]
Abstract
Acetobacteraceae is an economically important family of bacteria that is used for industrial fermentation in the food/feed sector and for the preparation of sorbose and bacterial cellulose. It comprises two major groups: acetous species (acetic acid bacteria) associated with flowers, fruits and insects, and acidophilic species, a phylogenetically basal and physiologically heterogeneous group inhabiting acid or hot springs, sludge, sewage and freshwater environments. Despite the biotechnological importance of the family Acetobacteraceae, the literature does not provide any information about its ability to produce specialized metabolites. We therefore constructed a phylogenomic tree based on concatenated protein sequences from 141 type strains of the family and predicted the presence of small-molecule biosynthetic gene clusters (BGCs) using the antiSMASH tool. This dual approach allowed us to associate certain biosynthetic pathways with particular taxonomic groups. We found that acidophilic and acetous species contain on average ~ 6.3 and ~ 3.4 BGCs per genome, respectively. All the Acetobacteraceae strains encoded proteins involved in hopanoid biosynthesis, with many also featuring genes encoding type-1 and type-3 polyketide and non-ribosomal peptide synthases, and enzymes for aryl polyene, lactone and ribosomal peptide biosynthesis. Our in silico analysis indicated that the family Acetobacteraceae is a potential source of many undiscovered bacterial metabolites and deserves more detailed experimental exploration.
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Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria. Appl Microbiol Biotechnol 2021; 105:8805-8822. [PMID: 34716462 DOI: 10.1007/s00253-021-11659-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.
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Alvares DS, Crosio M, Wilke N. Hopanoid Hopene Locates in the Interior of Membranes and Affects Their Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11900-11908. [PMID: 34585578 DOI: 10.1021/acs.langmuir.1c02030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hopanoids are proposed as sterol surrogates in some bacteria, and it has been proved that some hopanoids are able to induce a liquid-order phase state in lipid membranes. The members of this group of molecules have diverse structures, and not all of them have been studied in detail yet. Here, we study membranes with the hopanoid hopene (hop-22 (29)-ene or diploptene), which is the product of the cycling of squalene by squalene-hopene cyclase, and thus is present in the first step of hopanoid biosynthesis. Hopene is particularly interesting because it lacks a polar head group, which opens the question of how does this molecule accommodate in a lipid membrane, and what are the effects promoted by its presence. In order to get an insight into this, we prepared monolayers and bilayers of a phospholipid with hopene and studied their properties in comparison with pure phospholipid membranes, and with the sterol cholesterol or the hopanoid diplopterol. Film stiffness, shear viscosity, and bending dynamics were very affected by the presence of hopene, while zeta-potential, generalized polarization of Laurdan, and conductivity were affected moderately by this molecule. The results suggest that at very low percentages, hopene locates parallel to the phospholipid molecules, while the excess of the hopene molecules stays between leaflets, as previously proposed using molecular dynamics simulations.
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Affiliation(s)
- Dayane S Alvares
- Department of Physics, UNESP-São Paulo State University, IBILCE, São José do Rio Preto, 15054-000 São Paulo, Brazil
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Matias Crosio
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Natalia Wilke
- Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
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Avalos M, Garbeva P, Vader L, van Wezel GP, Dickschat JS, Ulanova D. Biosynthesis, evolution and ecology of microbial terpenoids. Nat Prod Rep 2021; 39:249-272. [PMID: 34612321 DOI: 10.1039/d1np00047k] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.
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Affiliation(s)
- Mariana Avalos
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lisa Vader
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jeroen S Dickschat
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,University of Bonn, Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Dana Ulanova
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan.
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Sato S, Kudo F, Rohmer M, Eguchi T. Biochemical and Mutational Analysis of Radical S-Adenosyl-L-Methionine Adenosylhopane Synthase HpnH from Zymomonas mobilis Reveals that the Conserved Residue Cysteine-106 Reduces a Radical Intermediate and Determines the Stereochemistry. Biochemistry 2021; 60:2865-2874. [PMID: 34506710 DOI: 10.1021/acs.biochem.1c00536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosylhopane is a crucial precursor of C35 hopanoids, which are believed to modulate the fluidity and permeability of bacterial cell membranes. Adenosylhopane is formed by a crosslinking reaction between diploptene and a 5'-deoxyadenosyl radical that is generated by the radical S-adenosyl-L-methionine (SAM) enzyme HpnH. We previously showed that HpnH from Streptomyces coelicolor A3(2) (ScHpnH) converts diploptene to (22R)-adenosylhopane. However, the mechanism of the stereoselective C-C bond formation was unclear. Thus, here, we performed biochemical and mutational analysis of another HpnH, from the ethanol-producing bacterium Zymomonas mobilis (ZmHpnH). Similar to ScHpnH, wild-type ZmHpnH afforded (22R)-adenosylhopane. Conserved cysteine and tyrosine residues were suggested as possible hydrogen sources to quench the putative radical reaction intermediate. A Cys106Ala mutant of ZmHpnH had one-fortieth the activity of the wild-type enzyme and yielded both (22R)- and (22S)-adenosylhopane along with some related byproducts. Radical trapping experiments with a spin-trapping agent supported the generation of a radical intermediate in the ZmHpnH-catalyzed reaction. We propose that the thiol of Cys106 stereoselectively reduces the radical intermediate generated at the C22 position by the addition of the 5'-deoxadenosyl radical to diploptene, to complete the reaction.
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Affiliation(s)
- Shusuke Sato
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Michel Rohmer
- Institut de Chimie de Strasbourg, Université de Strasbourg/CNRS, 4 rue Blaise Pascal, Strasbourg Cedex 67070, France
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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Anaerobic 3-methylhopanoid production by an acidophilic photosynthetic purple bacterium. Arch Microbiol 2021; 203:6041-6052. [PMID: 34528111 PMCID: PMC8590665 DOI: 10.1007/s00203-021-02561-7] [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: 04/02/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022]
Abstract
Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.
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Rizk S, Henke P, Santana-Molina C, Martens G, Gnädig M, Nguyen NA, Devos DP, Neumann-Schaal M, Saenz JP. Functional diversity of isoprenoid lipids in Methylobacterium extorquens PA1. Mol Microbiol 2021; 116:1064-1078. [PMID: 34387371 DOI: 10.1111/mmi.14794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 11/29/2022]
Abstract
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE, and crtB we disrupted the production of squalene, and phytoene in Methylobacterium extorquens PA1, which are the presumed precursors for hopanoids and carotenoids, respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
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Affiliation(s)
- Sandra Rizk
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Petra Henke
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carlos Santana-Molina
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Gesa Martens
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marén Gnädig
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | | | - Damien P Devos
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - James P Saenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
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Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals. ENERGIES 2021. [DOI: 10.3390/en14164903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.
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Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT. A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments. Proc Natl Acad Sci U S A 2021; 118:e2105225118. [PMID: 34353908 PMCID: PMC8364164 DOI: 10.1073/pnas.2105225118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353-358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sanne J Wiersma
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Eline S R Doornenbal
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Petrik Buitenhuis
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximillians University Munich, 81377 Munich, Germany
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands;
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Di Lorenzo F, Duda KA, Lanzetta R, Silipo A, De Castro C, Molinaro A. A Journey from Structure to Function of Bacterial Lipopolysaccharides. Chem Rev 2021; 122:15767-15821. [PMID: 34286971 DOI: 10.1021/acs.chemrev.0c01321] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lipopolysaccharide (LPS) is a crucial constituent of the outer membrane of most Gram-negative bacteria, playing a fundamental role in the protection of bacteria from environmental stress factors, in drug resistance, in pathogenesis, and in symbiosis. During the last decades, LPS has been thoroughly dissected, and massive information on this fascinating biomolecule is now available. In this Review, we will give the reader a third millennium update of the current knowledge of LPS with key information on the inherent peculiar carbohydrate chemistry due to often puzzling sugar residues that are uniquely found on it. Then, we will drive the reader through the complex and multifarious immunological outcomes that any given LPS can raise, which is strictly dependent on its chemical structure. Further, we will argue about issues that still remain unresolved and that would represent the immediate future of LPS research. It is critical to address these points to complete our notions on LPS chemistry, functions, and roles, in turn leading to innovative ways to manipulate the processes involving such a still controversial and intriguing biomolecule.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Katarzyna A Duda
- Research Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Cristina De Castro
- Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Department of Agricultural Sciences, University of Naples Federico II, Via Università 96, 80055 Portici, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Department of Chemistry, School of Science, Osaka University, 1-1 Osaka University Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Vitiello G, Oliva R, Petraccone L, Vecchio PD, Heenan RK, Molinaro A, Silipo A, D'Errico G, Paduano L. Covalently bonded hopanoid-Lipid A from Bradyrhizobium: The role of unusual molecular structure and calcium ions in regulating the lipid bilayers organization. J Colloid Interface Sci 2021; 594:891-901. [DOI: 10.1016/j.jcis.2021.03.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 01/31/2023]
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Transposon sequencing analysis of Bradyrhizobium diazoefficiens 110spc4. Sci Rep 2021; 11:13211. [PMID: 34168197 PMCID: PMC8225791 DOI: 10.1038/s41598-021-92534-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Bradyrhizobium diazoefficiens USDA110 is one of the most effective nitrogen-fixing symbionts of soybeans. Here we carried out a large-scale transposon insertion sequencing (Tn-seq) analysis of strain Bd110spc4, which is derived from USDA110, with the goal of increasing available resources for identifying genes crucial for the survival of this plant symbiont under diverse conditions. We prepared two transposon (Tn) insertion libraries of Bd110spc4 with 155,042 unique Tn insertions when the libraries were combined, which is an average of one insertion every 58.7 bp of the reference USDA110 genome. Application of bioinformatic filtering steps to remove genes too small to be expected to have Tn insertions, resulted in a list of genes that were classified as putatively essential. Comparison of this gene set with genes putatively essential for the growth of the closely related alpha-proteobacterium, Rhodopseudomonas palustris, revealed a small set of five genes that may be collectively essential for closely related members of the family Bradyrhizobiaceae. This group includes bacteria with diverse lifestyles ranging from plant symbionts to animal-associated species to free-living species.
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Abstract
Fungal pathogens, among other stressors, negatively impact the productivity and population size of honey bees, one of our most important pollinators (1, 2), in particular their brood (larvae and pupae) (3, 4). Understanding the factors that influence disease incidence and prevalence in brood may help us improve colony health and productivity. Here, we examined the capacity of a honey bee-associated bacterium, Bombella apis, to suppress the growth of fungal pathogens and ultimately protect bee brood from infection. Our results showed that strains of B. apis inhibit the growth of two insect fungal pathogens, Beauveria bassiana and Aspergillus flavus, in vitro. This phenotype was recapitulated in vivo; bee broods supplemented with B. apis were significantly less likely to be infected by A. flavus. Additionally, the presence of B. apis reduced sporulation of A. flavus in the few bees that were infected. Analyses of biosynthetic gene clusters across B. apis strains suggest antifungal candidates, including a type 1 polyketide, terpene, and aryl polyene. Secreted metabolites from B. apis alone were sufficient to suppress fungal growth, supporting the hypothesis that fungal inhibition is mediated by an antifungal metabolite. Together, these data suggest that B. apis can suppress fungal infections in bee brood via secretion of an antifungal metabolite.
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Tookmanian EM, Belin BJ, Sáenz JP, Newman DK. The role of hopanoids in fortifying rhizobia against a changing climate. Environ Microbiol 2021; 23:2906-2918. [PMID: 33989442 DOI: 10.1111/1462-2920.15594] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.
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Affiliation(s)
- Elise M Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Brittany J Belin
- Department of Embryology, The Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - James P Sáenz
- B CUBE Center for Molecular Bioengineering, Tatzberg 41, Technische Universität Dresden, Dresden, 01307, Germany
| | - Dianne K Newman
- Division of Biology & Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
- Division of Geology & Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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50
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Jin Y, Xu Y, Huang Z, Zhou Z, Wei X. Metabolite pattern in root nodules of the actinorhizal plant Casuarina equisetifolia. PHYTOCHEMISTRY 2021; 186:112724. [PMID: 33721795 DOI: 10.1016/j.phytochem.2021.112724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Casuarina equisetifolia L. (Casuarinaceae), an actinorhizal plant, exhibits mutualistic symbiosis with Frankia and promotes nitrogen fixation in root nodules. While the exchange of metabolites between host plant and microsymbiont is well understood in legume symbioses, the situation in the symbiosis between nitrogen-fixing Frankia and actinorhizal plants is less clear. In this study, a metabolomic approach was applied to root nodules of mature C. equisetifolia trees, leading to the identification of an undescribed taraxerane-type triterpenoid ester, 3-O-dihydrocoumaroyl β-taraxerol, along with twelve known compounds. An abundant component was tyramine with a content of 2.76 ± 0.315 mg/g FW in mature nodules. Tyramine specifically and abundantly accumulated in mature nitrogen-fixing nodules compared to senescent nodules, stems, leaves, and seeds. In addition, the potential function of tyramine was preliminarily examined and discussed.
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Affiliation(s)
- Yu Jin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yingting Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhengwan Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhongyu Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; South China Branch of Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China; South China Branch of Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Guangzhou, 510650, China
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