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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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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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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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Ginez LD, Osorio A, Vázquez-Ramírez R, Arenas T, Mendoza L, Camarena L, Poggio S. Changes in fluidity of the E. coli outer membrane in response to temperature, divalent cations and polymyxin-B show two different mechanisms of membrane fluidity adaptation. FEBS J 2022; 289:3550-3567. [PMID: 35038363 DOI: 10.1111/febs.16358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/23/2021] [Accepted: 01/13/2022] [Indexed: 12/28/2022]
Abstract
The outer membrane (OM) is an essential component of the Gram-negative bacterial cell envelope. Restricted diffusion of integral OM proteins and lipopolysaccharide (LPS) that constitute the outer leaflet of the OM support a model in which the OM is in a semi-crystalline state. The low fluidity of the OM has been suggested to be an important property of this membrane that even contributes to cell rigidity. The LPS characteristics strongly determine the properties of the OM and the LPS layer fluidity has been measured using different techniques that require specific conditions or are technically challenging. Here, we characterize the Escherichia coli LPS fluidity by evaluating the lateral diffusion of the styryl dye FM4-64FX in fluorescence recovery after photobleaching experiments. This technique allowed us to determine the effect of different conditions and genetic backgrounds on the LPS fluidity. Our results show that a fraction of the LPS can slowly diffuse and that the fluidity of the LPS layer adapts by modifying the diffusion of the LPS and the fraction of mobile LPS molecules.
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Affiliation(s)
- Luis David Ginez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Aurora Osorio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Ricardo Vázquez-Ramírez
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Thelma Arenas
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Luis Mendoza
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Laura Camarena
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
| | - Sebastian Poggio
- Departamento Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
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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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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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González-Rosales C, Vergara E, Dopson M, Valdés JH, Holmes DS. Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle. Front Microbiol 2022; 12:822229. [PMID: 35242113 PMCID: PMC8886135 DOI: 10.3389/fmicb.2021.822229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 01/22/2023] Open
Abstract
Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.
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Affiliation(s)
- Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jorge H. Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, 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
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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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Naafs BDA, Bianchini G, Monteiro FM, Sánchez-Baracaldo P. The occurrence of 2-methylhopanoids in modern bacteria and the geological record. GEOBIOLOGY 2022; 20:41-59. [PMID: 34291867 DOI: 10.1111/gbi.12465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
The 2-methylhopanes (2-MeHops) are molecular fossils of 2-methylbacteriohopanepolyols (2-MeBHPs) and among the oldest biomarkers on Earth. However, these biomarkers' specific sources are currently unexplained, including whether they reflect an expansion of marine cyanobacteria. Here, we study the occurrence of 2-MeBHPs and the genes involved in their synthesis in modern bacteria and explore the occurrence of 2-MeHops in the geological record. We find that the gene responsible for 2-MeBHP synthesis (hpnP) is widespread in cyano- and ⍺-proteobacteria, but absent or very limited in other classes/phyla of bacteria. This result is consistent with the dominance of 2-MeBHP in cyano- and ⍺-proteobacterial cultures. The review of their geological occurrence indicates that 2-MeHops are found from the Paleoproterozoic onwards, although some Precambrian samples might be biased by drilling contamination. During the Phanerozoic, high 2-MeHops' relative abundances (index >15%) are associated with climatic and biogeochemical perturbations such as the Permo/Triassic boundary and the Oceanic Anoxic Events. We analyzed the modern habitat of all hpnP-containing bacteria and find that the only one species coming from an undisputed open marine habitat is an ⍺-proteobacterium acting upon the marine nitrogen cycle. Although organisms can change their habitat in response to environmental stress and evolutionary pressure, we speculate that the high sedimentary 2-MeHops' occurrence observed during the Phanerozoic reflect ⍺-proteobacteria expansion and marine N-cycle perturbations in response to climatic and environmental change.
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Affiliation(s)
- B D A Naafs
- Organic Geochemistry Unit, School of Chemistry and School of Earth Sciences, University of Bristol, Bristol, UK
| | - G Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, UK
| | - F M Monteiro
- School of Geographical Sciences, University of Bristol, Bristol, UK
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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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Sefah E, Mertz B. Bacterial Analogs to Cholesterol Affect Dimerization of Proteorhodopsin and Modulates Preferred Dimer Interface. J Chem Theory Comput 2021; 17:2502-2512. [PMID: 33788568 DOI: 10.1021/acs.jctc.0c01174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hopanoids, the bacterial analogues of sterols, are ubiquitous in bacteria and play a significant role in organismal survival under stressful environments. Unlike sterols, hopanoids have a high degree of variation in the size and chemical nature of the substituent attached to the ring moiety, leading to different effects on the structure and dynamics of biological membranes. While it is understood that hopanoids can indirectly tune membrane physical properties, little is known on the role that hopanoids may play in affecting the organization and behavior of bacterial membrane proteins. In this work we used coarse-grained molecular dynamics simulations to characterize the effects of two hopanoids, diploptene (DPT) and bacteriohopanetetrol (BHT), on the oligomerization of proteorhodopsin (PR) in a model membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phophoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-3-phosphoglycerol (POPG). PR is a bacterial membrane protein that functions as a light-activated proton pump. We chose PR based on its ability to adopt a distribution of oligomeric states in different membrane environments. Furthermore, the efficiency of proton pumping in PR is intimately linked to its organization into oligomers. Our results reveal that both BHT and DPT indirectly affect dimerization by tuning membrane properties in a fashion that is concentration-dependent. Variation in their interaction with PR in the membrane-embedded and the cytoplasmic regions leads to distinctly different effects on the plasticity of the dimer interface. BHT has the ability to intercalate between monomers in the dimeric interface, whereas DPT shifts dimerization interactions via packing of the interleaflet region of the membrane. Our results show a direct relationship between hopanoid structure and lateral organization of PR, providing a first glimpse at how these bacterial analogues to eukaryotic sterols produce very similar biophysical effects within the cell membrane.
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Affiliation(s)
- Eric Sefah
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States.,WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
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Vitamin B 12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification. Proc Natl Acad Sci U S A 2020; 117:32996-33004. [PMID: 33318211 DOI: 10.1073/pnas.2012357117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.
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Banta AB, Enright AL, Siletti C, Peters JM. A High-Efficacy CRISPR Interference System for Gene Function Discovery in Zymomonas mobilis. Appl Environ Microbiol 2020; 86:e01621-20. [PMID: 32978126 PMCID: PMC7657623 DOI: 10.1128/aem.01621-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/20/2020] [Indexed: 01/23/2023] Open
Abstract
Zymomonas mobilis is a promising biofuel producer due to its high alcohol tolerance and streamlined metabolism that efficiently converts sugar to ethanol. Z. mobilis genes are poorly characterized relative to those of model bacteria, hampering our ability to rationally engineer the genome with pathways capable of converting sugars from plant hydrolysates into valuable biofuels and bioproducts. Many of the unique properties that make Z. mobilis an attractive biofuel producer are controlled by essential genes; however, these genes cannot be manipulated using traditional genetic approaches (e.g., deletion or transposon insertion) because they are required for viability. CRISPR interference (CRISPRi) is a programmable gene knockdown system that can precisely control the timing and extent of gene repression, thus enabling targeting of essential genes. Here, we establish a stable, high-efficacy CRISPRi system in Z. mobilis that is capable of perturbing all genes-including essential genes. We show that Z. mobilis CRISPRi causes either strong knockdowns (>100-fold) using single guide RNA (sgRNA) spacers that perfectly match target genes or partial knockdowns using spacers with mismatches. We demonstrate the efficacy of Z. mobilis CRISPRi by targeting essential genes that are universally conserved in bacteria, are key to the efficient metabolism of Z. mobilis, or underlie alcohol tolerance. Our Z. mobilis CRISPRi system will enable comprehensive gene function discovery, opening a path to rational design of biofuel production strains with improved yields.IMPORTANCE Biofuels produced by microbial fermentation of plant feedstocks provide renewable and sustainable energy sources that have the potential to mitigate climate change and improve energy security. Engineered strains of the bacterium Z. mobilis can convert sugars extracted from plant feedstocks into next-generation biofuels like isobutanol; however, conversion by these strains remains inefficient due to key gaps in our knowledge about genes involved in metabolism and stress responses such as alcohol tolerance. Here, we develop CRISPRi as a tool to explore gene function in Z. mobilis We characterize genes that are essential for growth, required to ferment sugar to ethanol, and involved in resistance to isobutanol. Our Z. mobilis CRISPRi system makes it straightforward to define gene function and can be applied to improve strain engineering and increase biofuel yields.
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Affiliation(s)
- Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy L Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cheta Siletti
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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14
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Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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15
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Mangiarotti A, Genovese DM, Naumann CA, Monti MR, Wilke N. Hopanoids, like sterols, modulate dynamics, compaction, phase segregation and permeability of membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183060. [DOI: 10.1016/j.bbamem.2019.183060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/06/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022]
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16
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Belin BJ, Tookmanian EM, de Anda J, Wong GCL, Newman DK. Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1415-1428. [PMID: 31170026 PMCID: PMC7583662 DOI: 10.1094/mpmi-04-19-0111-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here, we demonstrate that the nitrogen-fixation defect conferred by extended hopanoid loss can be fully explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen-fixation levels. Using a single-nodule tracking approach to quantify A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and the presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
| | - Elise M. Tookmanian
- Division of Chemistry & Chemical Engineering, California Institute of Technology
| | - Jaime de Anda
- Department of Bioengineering, Department of Chemistry and Biochemistry, and California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, U.S.A
| | - Gerard C. L. Wong
- Division of Geological & Planetary Sciences, California Institute of Technology
| | - Dianne K. Newman
- Division of Biology & Bioengineering, California Institute of Technology, Pasadena, CA, U.S.A
- Division of Geological & Planetary Sciences, California Institute of Technology
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17
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Bohutskyi P, McClure RS, Hill EA, Nelson WC, Chrisler WB, Nuñez JR, Renslow RS, Charania MA, Lindemann SR, Beliaev AS. Metabolic effects of vitamin B12 on physiology, stress resistance, growth rate and biomass productivity of Cyanobacterium stanieri planktonic and biofilm cultures. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Belin BJ, Busset N, Giraud E, Molinaro A, Silipo A, Newman DK. Hopanoid lipids: from membranes to plant-bacteria interactions. Nat Rev Microbiol 2018; 16:304-315. [PMID: 29456243 PMCID: PMC6087623 DOI: 10.1038/nrmicro.2017.173] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Busset
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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19
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Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress. Appl Environ Microbiol 2017; 83:AEM.00777-17. [PMID: 28455341 DOI: 10.1128/aem.00777-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S-adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting ΔhpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the ΔhpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and ΔhpnP mutant strains were similar to those of vegetative cell-dominated cultures. However, the ΔhpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the ΔhpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions.IMPORTANCE As the first group of organisms to develop oxygenic photosynthesis, Cyanobacteria are central to the evolutionary history of life on Earth and the subsequent oxygenation of the atmosphere. To investigate the origin of cyanobacteria and the emergence of oxygenic photosynthesis, geobiologists use biomarkers, the remnants of lipids produced by different organisms that are found in geologic sediments. 2-Methylhopanes have been considered indicative of cyanobacteria in some environmental settings, with the parent lipids 2-methylhopanoids being present in many contemporary cyanobacteria. We have created a Nostoc punctiforme ΔhpnP mutant strain that does not produce 2-methylhopanoids to assess the influence of 2-methylhopanoids on stress tolerance. Increased metabolic activity in the mutant under stress indicates compensatory alterations in metabolism in the absence of 2-methylhopanoids.
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20
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Bradley AS, Swanson PK, Muller EEL, Bringel F, Caroll SM, Pearson A, Vuilleumier S, Marx CJ. Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment. PLoS One 2017; 12:e0173323. [PMID: 28319163 PMCID: PMC5358736 DOI: 10.1371/journal.pone.0173323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/17/2017] [Indexed: 01/27/2023] Open
Abstract
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane.
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Affiliation(s)
- Alexander S. Bradley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Earth and Planetary Sciences, Washington University in St Louis, St Louis, MO, United States of America
| | - Paige K. Swanson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Emilie E. L. Muller
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Sean M. Caroll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States of America
| | - Stéphane Vuilleumier
- Equipe Adaptations et interactions microbiennes, Université de Strasbourg, UMR 7156 UNISTRA–CNRS Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States of America
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States of America
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21
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Ricci JN, Morton R, Kulkarni G, Summers ML, Newman DK. Hopanoids play a role in stress tolerance and nutrient storage in the cyanobacterium Nostoc punctiforme. GEOBIOLOGY 2017; 15:173-183. [PMID: 27527874 DOI: 10.1111/gbi.12204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Hopanes are abundant in ancient sedimentary rocks at discrete intervals in Earth history, yet interpreting their significance in the geologic record is complicated by our incomplete knowledge of what their progenitors, hopanoids, do in modern cells. To date, few studies have addressed the breadth of diversity of physiological functions of these lipids and whether those functions are conserved across the hopanoid-producing bacterial phyla. Here, we generated mutants in the filamentous cyanobacterium, Nostoc punctiforme, that are unable to make all hopanoids (shc) or 2-methylhopanoids (hpnP). While the absence of hopanoids impedes growth of vegetative cells at high temperature, the shc mutant grows faster at low temperature. This finding is consistent with hopanoids acting as membrane rigidifiers, a function shared by other hopanoid-producing phyla. Apart from impacting fitness under temperature stress, hopanoids are dispensable for vegetative cells under other stress conditions. However, hopanoids are required for stress tolerance in akinetes, a resting survival cell type. While 2-methylated hopanoids do not appear to contribute to any stress phenotype, total hopanoids and to a lesser extent 2-methylhopanoids were found to promote the formation of cyanophycin granules in akinetes. Finally, although hopanoids support symbiotic interactions between Alphaproteobacteria and plants, they do not appear to facilitate symbiosis between N. punctiforme and the hornwort Anthoceros punctatus. Collectively, these findings support interpreting hopanes as general environmental stress biomarkers. If hopanoid-mediated enhancement of nitrogen-rich storage products turns out to be a conserved phenomenon in other organisms, a better understanding of this relationship may help us parse the enrichment of 2-methylhopanes in the rock record during episodes of disrupted nutrient cycling.
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Affiliation(s)
- J N Ricci
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R Morton
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - G Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - M L Summers
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - D K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, Pasadena, CA, USA
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22
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Kulkarni G, Busset N, Molinaro A, Gargani D, Chaintreuil C, Silipo A, Giraud E, Newman DK. Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens. mBio 2015. [PMID: 26489859 DOI: 10.1128/mbio.01251-1215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
UNLABELLED A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage. IMPORTANCE Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.
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Affiliation(s)
- Gargi Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | | | - Clemence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA Howard Hughes Medical Institute, Pasadena, California, USA Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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23
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Kulkarni G, Busset N, Molinaro A, Gargani D, Chaintreuil C, Silipo A, Giraud E, Newman DK. Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens. mBio 2015; 6:e01251-15. [PMID: 26489859 PMCID: PMC4620461 DOI: 10.1128/mbio.01251-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage. IMPORTANCE Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.
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Affiliation(s)
- Gargi Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | | | - Clemence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA Howard Hughes Medical Institute, Pasadena, California, USA Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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24
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Abstract
The functionality of cellular membranes relies on the molecular order imparted by lipids. In eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. The structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. We present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly ordered bilayer in a manner analogous to the interaction of sterols with sphingolipids in eukaryotic plasma membranes. Furthermore, multidrug transport is impaired in a hopanoid-deficient mutant of the gram-negative Methylobacterium extorquens, which introduces a link between membrane order and an energy-dependent, membrane-associated function in prokaryotes. Thus, we reveal a convergence in the architecture of bacterial and eukaryotic membranes and implicate the biosynthetic pathways of hopanoids and other order-modulating lipids as potential targets to fight pathogenic multidrug resistance.
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Neubauer C, Dalleska NF, Cowley ES, Shikuma NJ, Wu CH, Sessions AL, Newman DK. Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation. GEOBIOLOGY 2015; 13:443-53. [PMID: 25923996 DOI: 10.1111/gbi.12143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/23/2015] [Indexed: 05/17/2023]
Abstract
The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80%). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.
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Affiliation(s)
- C Neubauer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N F Dalleska
- Environmental Analysis Center, California Institute of Technology, Pasadena, CA, USA
| | - E S Cowley
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - N J Shikuma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - C-H Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - A L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - D K Newman
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Environmental Analysis Center, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, Pasadena, CA, USA
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Ricci JN, Michel AJ, Newman DK. Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria. GEOBIOLOGY 2015; 13:267-277. [PMID: 25630231 DOI: 10.1111/gbi.12129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/10/2015] [Indexed: 06/04/2023]
Abstract
Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record-the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.
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Affiliation(s)
- J N Ricci
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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