Hopanoid lipids in Bradyrhizobium and other plant-associated bacteria and cloning of the Bradyrhizobium japonicum squalene-hopene cyclase gene

Hopanoid lipids have been discovered recently in a number of nitrogen-fixing soil bacteria and in Bradyrhizobium bacteria which fix nitrogen in association with legume plants. We report here an investigation of the hopanoid content in an additional number of soil bacteria capable of living in close association with plants. Of the strains investigated, hopanoids were discovered in phototrophic, nitrogen-fixing bacteria and in an extended number of Bradyrhizobium strains. Strains in which hopanoids so far have not been found belong to the following genera: Rhizobium, Sinorhizobium, Phyllobacterium, Agrobacterium, and Azoarcus. To address the function of hopanoids in Bradyrhizobium, we cloned the gene coding for a key enzyme of hopanoid biosynthesis, the squalene-hopene cyclase, and expressed the gene in E. coli. The recombinant enzyme catalyzed in vitro the cyclization of squalene to hopanoid derivatives.Abbreviations SHC squalene-hopene cyclase - shc squalene-hopene cyclase gene     

Phylogenetic analysis of HpnP reveals the origin of 2‐methylhopanoid production in Alphaproteobacteria

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.     

Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis

Hopanoids are a class of membrane lipids found in diverse bacterial lineages, but their physiological roles are not well understood. The ethanol fermenter Zymomonas mobilis features the highest measured concentration of hopanoids, leading to the hypothesis that these lipids can protect against the solvent toxicity. However, the lack of genetic tools for manipulating hopanoid composition in this bacterium has limited their further functional analysis. Due to the polyploidy (>50 genome copies per cell) of Z. mobilis, we found that disruptions of essential hopanoid biosynthesis (hpn) genes act as genetic knockdowns, reliably modulating the abundance of different hopanoid species. Using a set of hpn transposon mutants, we demonstrate that both reduced hopanoid content and modified hopanoid polar head group composition mediate growth and survival in ethanol. In contrast, the amount of hopanoids, but not their head group composition, contributes to fitness at low pH. Spectroscopic analysis of bacterial‐derived liposomes showed that hopanoids protect against several ethanol‐driven phase transitions in membrane structure, including lipid interdigitation and bilayer dissolution. We propose that hopanoids act through a combination of hydrophobic and inter‐lipid hydrogen bonding interactions to stabilize bacterial membranes during solvent stress.     

2-Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications

2-Methylhopanes, molecular fossils of 2-methylbacteriohopanepolyol (2-MeBHP) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. However, the robustness of this interpretation is unclear, as 2-methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. As a first step toward understanding the role of 2-MeBHP in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the three cell types of Nostoc punctiforme : vegetative cells, akinetes, and heterocysts. Cultures in which N. punctiforme had differentiated into akinetes contained approximately 10-fold higher concentrations of 2-methylhopanoids than did cultures that contained only vegetative cells. In contrast, 2-methylhopanoids were only present at very low concentrations in heterocysts. Hopanoid production initially increased threefold in cells starved of nitrogen but returned to levels consistent with vegetative cells within 2 weeks. Vegetative and akinete cell types were separated into cytoplasmic, thylakoid, and outer membrane fractions; the increase in hopanoid expression observed in akinetes was due to a 34-fold enrichment of hopanoid content in their outer membrane relative to vegetative cells. Akinetes formed in response either to low light or phosphorus limitation, exhibited the same 2-methylhopanoid localization and concentration, demonstrating that 2-methylhopanoids are associated with the akinete cell type per se . Because akinetes are resting cells that are not photosynthetically active, 2-methylhopanoids cannot be functionally linked to oxygenic photosynthesis in N.   punctiforme .     

Hopanoids in marine cyanobacteria: probing their phylogenetic distribution and biological role

Cyanobacteria are key players in the global carbon and nitrogen cycles and are thought to have been responsible for the initial rise of atmospheric oxygen during the Neoarchean. There is evidence that a class of membrane lipids known as hopanoids serve as biomarkers for bacteria, including many cyanobacteria, in the environment and in the geologic record. However, the taxonomic distributions and physiological roles of hopanoids in marine cyanobacteria remain unclear. We examined the distribution of bacteriohopanepolyols (BHPs) in a collection of marine cyanobacterial enrichment and pure cultures and investigated the relationship between the cellular abundance of BHPs and nitrogen limitation in Crocosphaera watsonii, a globally significant nitrogen‐fixing cyanobacterium. In pure culture, BHPs were only detected in species capable of nitrogen fixation, implicating hopanoids as potential markers for diazotrophy in the oceans. The enrichment cultures we examined exhibited a higher degree of BHP diversity, demonstrating that there are presently unaccounted for marine bacteria, possibly cyanobacteria, associated with the production of a range of BHP structures. Crocosphaera watsonii exhibited high membrane hopanoid content consistent with the idea that hopanoids have an important effect on the bulk physical properties of the membrane. However, the abundance of BHPs in C. watsonii did not vary considerably when grown under nitrogen‐limiting and nitrogen‐replete conditions, suggesting that the role of hopanoids in this organism is not directly related to the physiology of nitrogen fixation. Alternatively, we propose that high hopanoid content in C. watsonii may serve to reduce membrane permeability to antimicrobial toxins in the environment.     

Diversity of hopanoids and squalene-hopene cyclases across a tropical land-sea gradient

Bacterial hopanoids are ubiquitous in Earth surface environments. They hold promise as environmental and ecological biomarkers, if the phylogeny and physiological drivers of hopanoid biosynthesis can be linked with the distribution of hopanoids observed across a breadth of samples. Here we survey the diversity of hopanoid cyclases from a land‐sea gradient across the island of San Salvador, in the easternmost part of the Bahamas. The distribution of lipids was determined for the same sites, for the first time overlaying quantification of bacteriohopanepolyols with sqhC phylogeny. The results are similar to previous reports: environmental sqhCs average < 65% translated amino acid identity to their closest named relatives, and sequences from putative Proteobacteria dominate. Additionally, a new and apparently ubiquitous group of marine hopanoid producers is identified; it has no identifiable close relatives. The greatest diversity of hopanoid lipids occurs in soil, but hopanoids represent a minor fraction of total soil‐derived lipids. Marine samples contain fewer identifiable hopanoids, but they are more abundant as a fraction of the total extractable lipids. In soil, the dominant compounds are 35‐aminobacteriohopane‐32,33,34‐triol and adenosylhopane. In an upper estuarine sample, bacteriohopanetetrol and 32,35‐anhydrobacteriohopanetetrol dominate; while in lower estuarine and open marine samples, the most abundant are bacteriohopanetetrol and bacteriohopaneribonolactone. Cyclitol ethers are trace components in the soil, absent in the estuary, and of moderate abundance in the open marine setting, suggesting a dominant marine source. Conversely, aminotriol and aminotetrol decrease in abundance or disappear completely from land to ocean, while 2‐methyldiplopterol shows the opposite trend. Small quantities of 2‐methylbacteriohopanepolyols are detectable in all samples. The overall hopanoid distributions may correlate to the major phylogenetic families of hopanoid producers or to the environments in which they are found.     

Elucidation of the Burkholderia cenocepacia hopanoid biosynthesis pathway uncovers functions for conserved proteins in hopanoid‐producing bacteria

Hopanoids are bacterial surrogates of eukaryotic membrane sterols and among earth's most abundant natural products. Their molecular fossils remain in sediments spanning more than a billion years. However, hopanoid metabolism and function are not fully understood. Burkholderia species are environmental opportunistic pathogens that produce hopanoids and also occupy diverse ecological niches. We investigated hopanoids biosynthesis in Burkholderia cenocepacia by deletion mutagenesis and structural characterization of the hopanoids produced by the mutants. The enzymes encoded by hpnH and hpnG were essential for production of all C₃₅ extended hopanoids, including bacteriohopanetetrol (BHT), BHT glucosamine and BHT cyclitol ether. Deletion of hpnI resulted in BHT production, while ΔhpnJ produced only BHT glucosamine. Thus, HpnI is required for BHT glucosamine production while HpnJ is responsible for its conversion to the cyclitol ether. The ΔhpnH and ΔhpnG mutants could not grow under any stress condition tested, whereas ΔhpnI, ΔhpnJ and ΔhpnK displayed wild‐type growth rates when exposed to detergent, but varying levels of sensitivity to low pH and polymyxin B. This study not only elucidates the biosynthetic pathway of hopanoids in B. cenocepacia, but also uncovers a biosynthetic role for the conserved proteins HpnI, HpnJ and HpnK in other hopanoid‐producing bacteria.     

Targeted genomic detection of biosynthetic pathways: anaerobic production of hopanoid biomarkers by a common sedimentary microbe

The lipid biomarker principle requires that preservable molecules (molecular fossils) carry specific taxonomic, metabolic, or environmental information. Historically, an empirical approach was used to link specific taxa with the compounds they produce. The lipids extracted from numerous, but randomly cultured species provided the basis for the interpretation of biomarkers in both modern environments and in the geological record. Now, with the rapid sequencing of hundreds of microbial genomes, a more focused genomic approach can be taken to test phylogenetic patterns and hypotheses about the origins of biomarkers. Candidate organisms can be selected for study on the basis of genes that encode proteins fundamental to the synthesis of biomarker compounds. Hopanoids, a class of pentacyclic triterpenoid lipid biomarkers, provide an illustrative example. For many years, interpretations of biomarker data were made with the assumption that hopanoids are produced only by aerobic organisms. However, the recent discovery of ¹³C‐depleted hopanoids in environments undergoing anaerobic methane oxidation and in enrichment cultures of anammox planctomycetes indicates that some hopanoids are produced anaerobically. To further examine the potential distribution of hopanoid biosynthesis by anaerobes, we searched publicly available genomic databases for the presence of squalene‐hopene cyclase genes in known obligate or facultative anaerobes. Here we present evidence that Geobacter sulfurreducens, Geobacter metallireducens, and Magnetospirillum magnetotacticum, all bacteria common in anoxic environments, have the appropriate genes for hopanoid biosynthesis. We further show that these data accurately predict that G. sulfurreducens does produce a variety of complex hopanoids under strictly anaerobic conditions in pure culture.     

Lipid remodeling in Rhodopseudomonas palustris TIE‐1 upon loss of hopanoids and hopanoid methylation

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.     

Potassium deficiency triggers the development of dormant cells (akinetes) in Aphanizomenon ovalisporum (Nostocales,Cyanoprokaryota)1

Akinetes are spore‐like nonmotile cells that differentiate from vegetative cells of filamentous cyanobacteria from the order Nostocales. They play a key role in the survival and distribution of these species and contribute to their perennial blooms. Various environmental factors were reported to trigger the differentiation of akinetes including light intensity and quality, temperature, and nutrient deficiency. Here, we report that deprivation of potassium ion (K⁺) triggers akinete development in the cyanobacterium Aphanizomenon ovalisporum. Akinetes formation is initiated 3 d–7 d after an induction by K⁺ depletion, followed by 2–3 weeks of a maturation process. Akinete formation occurs within a restricted matrix of environmental conditions such as temperature, light intensity or photon flux. Phosphate is essential for akinete maturation and P‐limitation restricts the number of mature akinetes. DNA replication is essential for akinete maturation and akinete development is limited in the presence of Nalidixic acid. While our results unequivocally demonstrated the effect of K⁺ deficiency on akinete formation in laboratory cultures of A. ovalisporum, this trigger did not cause Cylindrospermopsis raciborskii to produce akinetes. Anabaena crassa however, produced akinetes upon potassium deficiency, but the highest akinete concentration was achieved at conditions that supported vegetative growth. It is speculated that an unknown internal signal is associated with the cellular response to K⁺ deficiency to induce the differentiation of a certain vegetative cell in a trichome into an akinete. A universal stress protein that functions as mediator in K⁺ deficiency signal transduction cascade, may communicate between the lack of K⁺ and akinete induction.     

PHOTOSYNTHETIC CHARACTERIZATION OF DEVELOPING AND MATURE AKINETES OF APHANIZOMENON OVALISPORUM (CYANOPROKARYOTA)1

Akinetes, differentiated resting cells produced by many species of filamentous, heterocystous cyanobacteria, enable the organism to survive adverse conditions, such as cold winters and dry seasons, and to maintain germination capabilities until the onset of suitable conditions for vegetative growth. Mature akinetes maintain a limited level of metabolic activities, including photosynthesis. In the present study, we have characterized changes in the photosynthetic apparatus of vegetative cells and akinetes of the cyanobacterium Aphanizomenon ovalisporum Forti (Nostocales) during their development and maturation. Photosynthetic variable fluorescence was measured by microscope‐PAM (pulse‐amplitude‐modulated) fluorometry, and the fundamental composition of the photosynthetic apparatus was evaluated by fluorescence and immunological techniques. Vegetative cells and akinetes from samples of Aphanizomenon trichomes from akinete‐induced cultures at various ages demonstrated a gradual reduction, with age, in the maximal photosynthetic quantum yield in both cell types. However, the maximal quantum yield of akinetes declined slightly faster than that of their adjacent vegetative cells. Mature akinetes isolated from 6‐ to 8‐week‐old akinete‐induced cultures maintained only residual photosynthetic activity, as indicated by very low values of maximal photosynthetic quantum yields. Based on 77 K fluorescence emission data and immunodetection of PSI and PSII polypeptides, we concluded that the ratio of PSI to PSII reaction centers in mature akinetes is slightly higher than the ratio estimated for exponentially grown vegetative cells. Furthermore, the cellular abundance of these protein complexes substantially increased in akinetes relative to exponentially grown vegetative cells, presumably due to considerable increase in the biovolume of akinetes.     

Interaction of hopanoids with phosphatidylcholines containing oleic and ω-cyclohexyldodecanoic acid in lipid bilayer membranes

Lipid bilayer membranes were made from hopanoid phosphatidylcholine mixtures dissolved in decane. The specific capacity of the mixed membranes was found to increase with increasing hopanoid content. This indicates an interaction between hopanoids and lipids which leads to a reduction of the chemical potential of the solvent in the membranes.The structural properties of mixtures of hopanoids and phosphatidylcholines were investigated using charged probe molecules, the negatively charged lipophilic ions dipicrylamine (DPA) and tetraphenylborate (TØB) and the positively charged potassium complex PV-K⁺ (PV, cyclo (D-Val-L-Pro-L-Val-D-Pro)₃). The transport properties of the lipophilic ions in the mixed membranes indicate that the electrical properties like dipolar potential and surface potentials of phosphatidylcholine membranes are not changed by the insertion of the hopanoids. The translocation rate constant K of the PV-K⁺ complex is drastically reduced in the hopanoid phosphatidylcholine membranes with increasing hopanoid content. This effect is discussed on the basis of an alteration of the microviscosity in the mixed membranes. There exists a close analogy between the action of cholesterol and hopanoids in bilayer membranes from phosphatidylcholines.A bilayer membrane composed of di-ω-cyclohexyldodecanoyl-phosphatidylcholine (DCPC) was found to possess a higher specific capacity as compared to other phosphatidylcholines. Also a lower translocation rate constant for PV-K⁺ was observed which may be caused by the relative high microviscosity of this lipid even above the phase transition temperature.     

Hopanoids are formed during transition from substrate to aerial hyphae in Streptomyces coelicolor A3(2)

Streptomyces coelicolor A3(2) contains a cluster of putative isoprenoid and hopanoid biosynthetic genes. The strain does not produce the pentacyclic hopanoids in liquid culture but produces them on solid medium when sporulating. Mutants defective in the formation of aerial mycelium and spores (bld), with the exception of bldB, do not synthesize hopanoids, whereas mutants, which form aerial mycelium but no spores (whi), do. The membrane condensing hopanoids possibly may alleviate stress in aerial mycelium by diminishing water permeability across the membrane.     

Effect of alcohols and temperature on the hopanoid content of Zymomonas mobilis

Summary The influence of different culture conditions on the hopanoid content of Zymomonas mobilis was investigated in batch cultures. With a gas-liquid chromatographic method it could be shown that the content of 1,2,3,4-tetrahydroxypentane-29-hopane (THBH) reached a maximum value in the stationary phase due to the high level of ethanol accumulated in the medium. The hopanoid content increased sharply with the addition of ethanol to the culture. Ethanol was shown to be the most effective of the alcohols tested in causing an increase of the hopanoid content. Furthermore, an alteration of the incubation temperature from 14° to 37°C also caused an increase of the amount of hopanoids.Abbreviations THBH 1,2,3,4-tetrahydroxy-pentane-29-hopane - HMG-CoA reductase 3-hydroxy-3-methylglutaryl coenzyme A reductase     

Vegetative survival, akinete formation and germination in three blue-green algae and one green alga in relation to light intensity, temperature, heat shock and UV exposure

The mere vegetative survival was not sufficient but suitable growth conditions were required for akinete formation to occur in the blue-green algaeAnabœna iyengarii, Westiellopsis prolifica, Nostochopsis lobatus and in the green algaPithophora oedogonia. In all algae, akinetes were neither formed nor germinated in darkness, and while dim light of 300 lx was sufficient for most of akinetes to germinate and also to maintain vegetative survival, it was not adequate for optinum akinete formation. Although akinetes of all algae could germinate at 35°C, both the vegetative survival and akinete formation were markedly suppressed at this temperature. Heat or UV shock of any level, whether ineffective or effecting vegetative survival, did not promote akinete formation or germination in any alga tested. Akinetes of all algae under study were relatively tolerant to heat and also to some extent to UV. Both wet and dried akinetes of all algae were equally UV tolerant. In all algae, the viability of both wet and dried akinetes decreased more or less equally with storage time, but the decrease was more drastic when storage temperature was progressively lowered from 20 to 0°C. Hence the akinetes can tolerate dryness but not frost.     

Seasonal dynamics of akinetes of Anabaena flos-aquae in bottom sediments and water column of small Siberian reservoir

Seasonal dynamics of Anabaena flos-aquae (Lyngb.) Breb., including vegetative cells, akinetes and akinete envelopes, in bottom sediments and water column at both littoral and deeper central stations of a small Siberian reservoir was studied. Two types of akinetes were observed: in the first half of summer Anabaena formed akinetes, which served for vegetative reproduction and germinated in water column soon after differentiation, while in the second half of summer the akinetes produced served as a resting stages, which were deposited to bottom sediments. Canonical correlation analyses revealed that decrease of water temperature was the main environmental factor that stimulated the akinete formation. In contrast to the general opinion, concentration of inorganic phosphorus slightly, but positively influenced the akinete formation. Thus, akinetes formed in response to the temperature decrease, needs a certain level of this nutrient. At littoral and open-water stations abundance and seasonal dynamics of akinetes in water column and their sinking pattern were very similar. However, seasonal dynamics of abundance of akinetes in sediments in these two reservoir locations differed: whereas the abundance of akinetes in open water increased permanently during the summer, that in the littoral decreased soon after their sedimentation. The cause for decrease in abundance of akinetes in bottom sediments in winter is unknown.     

Oxidation of Fe(II) leads to increased C‐2 methylation of pentacyclic triterpenoids in the anoxygenic phototrophic bacterium Rhodopseudomonas palustris strain TIE‐1

Hopanoids are among the most widespread biomarkers of bacteria that are used as indicators for past and present bacterial activity. Our understanding of the production, function, and distribution of hopanoids in bacteria has improved greatly, partly due to genetic, culture‐independent studies. Culture‐based studies are important to determine hopanoid function and the environmental conditions under which these compounds are produced. This study compares the lipid inventory of Rhodopseudomonas palustris strain TIE‐1 under anoxic photoautotrophic conditions using either H₂ or Fe(II) as electron donor. The high amount to which adenosylhopane is produced irrespective of the used electron donor suggests a specific function of this compound rather than its exclusive role as an intermediate in bacteriohopanepolyol biosynthesis. C‐2 methylated hopanoids and tetrahymanol account for as much as 59% of the respective C‐2 methylated/non‐methylated homologs during growth with Fe(II) as electron donor, as compared with 24% C‐2 methylation for growth with H₂. This observation reveals that C‐2 methylated hopanoids have a specific function and are preferentially synthesized in response to elevated Fe(II) concentrations. The presence of C‐2 methylated pentacyclic triterpenoids has commonly been used as a biosignature for the interpretation of paleoenvironments. These new findings suggest that increased C‐2 methylation may indicate anoxic ferrous conditions, in addition to other environmental stressors that have been previously reported.