Biophysical properties of membrane lipids of anammox bacteria: I. Ladderane phospholipids form highly organized fluid membranes

How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis

Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.

Potential Role of the Anammoxosome in the Adaptation of Anammox Bacteria to Salinity Stress

The underlying adaptative mechanisms of anammox bacteria to salt stress are still unclear. The potential role of the anammoxosome in modulating material and energy metabolism in response to salinity stress was investigated in this study. The results showed that anammox bacteria increased membrane fluidity and decreased mechanical properties by shortening the ladderane fatty acid chain length of anammoxosome in response to salinity shock, which led to the breakdown of the proton motive force driving ATP synthesis and retarded energy metabolism activity. Afterward, the fatty acid chain length and membrane properties were recovered to enhance the energy metabolic activity. The relative transmission electron microscopy (TEM) area proportion of anammoxosome decreased from 55.9 to 38.9% under salinity stress. The 3D imaging of the anammox bacteria based on Synchrotron soft X-ray tomography showed that the reduction in the relative volume proportion of the anammoxosome and the concave surfaces was induced by salinity stress, which led to the lower energy expenditure of the material transportation and provided more binding sites for enzymes. Therefore, anammox bacteria can modulate nitrogen and energy metabolism by changing the membrane properties and morphology of the anammoxosome in response to salinity stress. This study broadens the response mechanism of anammox bacteria to salinity stress.

Effect of temperature on the compositions of ladderane lipids in globally surveyed anammox populations

The adaptation of bacteria involved in anaerobic ammonium oxidation (anammox) to low temperatures will enable more efficient removal of nitrogen from sewage across seasons. At lower temperatures, bacteria typically tune the synthesis of their membrane lipids to promote membrane fluidity. However, such adaptation of anammox bacteria lipids, including unique ladderane phospholipids and especially shorter ladderanes with absent phosphatidyl headgroup, is yet to be described in detail. We investigated the membrane lipids composition (UPLC-HRMS/MS) and dominant anammox populations (16S rRNA gene amplicon sequencing, Fluorescence in situ hybridization) in 14 anammox enrichments cultivated at 10-37 °C. "Candidatus Brocadia" appeared to be the dominant organism in all but two laboratory enrichments of "Ca. Scalindua" and "Ca. Kuenenia". At lower temperatures, the membranes of all anammox populations were composed of shorter [5]-ladderane ester (reduced chain length demonstrated by decreased fraction of C20/(C18 + C20)). This confirmed the previous preliminary evidence on the prominent role of this ladderane fatty acid in low-temperature adaptation. "Ca. Scalindua" and "Ca. Kuenenia" had distinct profile of ladderane lipids compared to "Ca. Brocadia" biomasses with potential implications for adaptability to low temperatures. "Ca. Brocadia" membranes contained a much lower amount of C18 [5]-ladderane esters than reported in the literature for "Ca. Scalindua" at similar temperature and measured here, suggesting that this could be one of the reasons for the dominance of "Ca. Scalindua" in cold marine environments. Furthermore, we propose additional and yet unreported mechanisms for low-temperature adaptation of anammox bacteria, one of which involves ladderanes with absent phosphatidyl headgroup. In sum, we deepen the understanding of cold anammox physiology by providing for the first time a consistent comparison of anammox-based communities across multiple environments.

Ladderane Natural Products: From the Ground Up

The ladderane family of natural products are well known for their linearly concatenated cyclobutane skeletal structure. Owing to their unique carbocyclic framework, several chemical syntheses have been reported since their discovery in 2002. The focus of this review is to showcase the novel tactics that have been used to generate the ladderane core and the challenges that are associated with the synthesis of these unusual and complex natural products.

Absolute Configurations of Naturally Occurring [5]- and [3]-Ladderanoic Acids: Isolation, Chiroptical Spectroscopy, and Crystallography

We have isolated mixtures of [5]- and [3]-ladderanoic acids 1a and 2a from the biomass of an anammox bioreactor and have separated the acids and their phenacyl esters for the first time by HPLC. The absolute configurations of the naturally occurring acids and their phenacyl esters are assigned as R at the site of side-chain attachment by comparison of experimental specific rotations with corresponding values predicted using quantum chemical (QC) methods. The absolute configurations for 1a and 2a were independently verified by comparison of experimental Raman optical activity spectra with corresponding spectra predicted using QC methods. The configurational assignments of 1a and 2a and of the phenacyl ester of 1a were also confirmed by X-ray crystallography.

Trending topics and open questions in anaerobic ammonium oxidation

Anaerobic ammonium-oxidizing (anammox) bacteria are major players in the biological nitrogen cycle and can be applied in wastewater treatment for the removal of nitrogen compounds. Anammox bacteria anaerobically convert the substrates ammonium and nitrite into dinitrogen gas in a specialized intracellular compartment called the anammoxosome. The anammox cell biology, physiology and biochemistry is of exceptional interest but also difficult to study because of the lack of a pure culture, standard cultivation techniques and genetic tools. Here we review the most important recent developments regarding the cell structure - anammoxosome and cell envelope - and anammox energy metabolism - nitrite reductase, hydrazine synthase and energy conversion - including the trending topics electro-anammox, extracellular polymeric substances and ladderane lipids.

Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability

Ladderane lipids are unique to anaerobic ammonium-oxidizing (anammox) bacteria and are enriched in the membrane of the anammoxosome, an organelle thought to compartmentalize the anammox process, which involves the toxic intermediate hydrazine (N2H4). Due to the slow growth rate of anammox bacteria and difficulty of isolating pure ladderane lipids, experimental evidence of the biological function of ladderanes is lacking. We have synthesized two natural and one unnatural ladderane phosphatidylcholine lipids and compared their thermotropic properties in self-assembled bilayers to distinguish between [3]- and [5]-ladderane function. We developed a hydrazine transmembrane diffusion assay using a water-soluble derivative of a hydrazine sensor and determined that ladderane membranes are as permeable to hydrazine as straight-chain lipid bilayers. However, pH equilibration across ladderane membranes occurs 5-10 times more slowly than across straight-chain lipid membranes. Langmuir monolayer analysis and the rates of fluorescence recovery after photobleaching suggest that dense ladderane packing may preclude formation of proton/hydroxide-conducting water wires. These data support the hypothesis that ladderanes prevent the breakdown of the proton motive force rather than blocking hydrazine transmembrane diffusion in anammox bacteria.

Synthesis of ent-[3]-Ladderanol: Development and Application of Intramolecular Chirality Transfer [2+2] Cycloadditions of Allenic Ketones and Alkenes

An enantioselective synthesis of ent-[3]-ladderanol is presented. The ladderanes are an interesting class of molecules for their unique structure of fused cyclobutane rings as well as their perceived biological function of organism protection. The route hinges on the development and application of a chirality transfer [2+2] cycloaddition of an allenic ketone and alkene. Further stereocontrolled transformations allowed for completion of the synthesis. The scope of the chirality transfer [2+2] cycloaddition is also presented.

Chemical Synthesis and Self-Assembly of a Ladderane Phospholipid

Ladderane lipids produced by anammox bacteria constitute some of the most structurally fascinating yet poorly studied molecules among biological membrane lipids. Slow growth of the producing organism and the inherent difficulty of purifying complex lipid mixtures have prohibited isolation of useful amounts of natural ladderane lipids. We have devised a highly selective total synthesis of ladderane lipid tails and a full phosphatidylcholine to enable biophysical studies on chemically homogeneous samples of these molecules. Additionally, we report the first proof of absolute configuration of a natural ladderane.

Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans

Microbial decomposition of organic matter is an essential process in the global carbon cycle. The soil bacteria Pseudopedobacter saltans and Flavobacterium johnsoniae are both able to degrade complex organic molecules, but it is not fully known how their membrane structures are adapted to their environmental niche. The membrane lipids of these species were extracted and analyzed using high performance liquid chromatography-electrospray ionization/ion trap/mass spectrometry (HPLC-ESI/IT/MS) and high resolution accurate mass/mass spectrometry (HRAM/MS). Abundant unknown intact polar lipids (IPLs) from P. saltans were isolated and further characterized using amino acid analysis and two dimensional nuclear magnetic resonance (NMR) spectroscopy. Ornithine IPLs (OLs) with variable (hydroxy) fatty acid composition were observed in both bacterial species. Lysine-containing IPLs (LLs) were also detected in both species and were characterized here for the first time using HPLC-MS. Novel LLs containing hydroxy fatty acids and novel hydroxylysine lipids with variable (hydroxy) fatty acid composition were identified in P. saltans. The confirmation of OL and LL formation in F. johnsoniae and P. saltans and the presence of OlsF putative homologs in P. saltans suggest the OlsF gene coding protein is possibly involved in OL and LL biosynthesis in both species, however, potential pathways of OL and LL hydroxylation in P. saltans are still undetermined. Triplicate cultures of P. saltans were grown at three temperature/pH combinations: 30°C/pH 7, 15°C/pH 7, and 15°C/pH 9. The fractional abundance of total amino acid containing IPLs containing hydroxylated fatty acids was significantly higher at higher temperature, and the fractional abundance of lysine-containing IPLs was significantly higher at lower temperature and higher pH. These results suggest that these amino acid-containing IPLs, including the novel hydroxylysine lipids, could be involved in temperature and pH stress response of soil bacteria.

Biophysical implications of lipid bilayer rheometry for mechanosensitive channels

The lipid bilayer plays a crucial role in gating of mechanosensitive (MS) channels. Hence it is imperative to elucidate the rheological properties of lipid membranes. Herein we introduce a framework to characterize the mechanical properties of lipid bilayers by combining micropipette aspiration (MA) with theoretical modeling. Our results reveal that excised liposome patch fluorometry is superior to traditional cell-attached MA for measuring the intrinsic mechanical properties of lipid bilayers. The computational results also indicate that unlike the uniform bilayer tension estimated by Laplace's law, bilayer tension is not uniform across the membrane patch area. Instead, the highest tension is seen at the apex of the patch and the lowest tension is encountered near the pipette wall. More importantly, there is only a negligible difference between the stress profiles of the outer and inner monolayers in the cell-attached configuration, whereas a substantial difference (∼30%) is observed in the excised configuration. Our results have far-reaching consequences for the biophysical studies of MS channels and ion channels in general, using the patch-clamp technique, and begin to unravel the difference in activity seen between MS channels in different experimental paradigms.

Novel mono-, di-, and trimethylornithine membrane lipids in northern wetland planctomycetes

Northern peatlands represent a significant global carbon store and commonly originate from Sphagnum moss-dominated wetlands. These ombrotrophic ecosystems are rain fed, resulting in nutrient-poor, acidic conditions. Members of the bacterial phylum Planctomycetes are highly abundant and appear to play an important role in the decomposition of Sphagnum-derived litter in these ecosystems. High-performance liquid chromatography coupled to high-resolution accurate-mass mass spectrometry (HPLC-HRAM/MS) analysis of lipid extracts of four isolated planctomycetes from wetlands of European north Russia revealed novel ornithine membrane lipids (OLs) that are mono-, di-, and trimethylated at the ε-nitrogen position of the ornithine head group. Nuclear magnetic resonance (NMR) analysis of the isolated trimethylornithine lipid confirmed the structural identification. Similar fatty acid distributions between mono-, di-, and trimethylornithine lipids suggest that the three lipid classes are biosynthetically linked, as in the sequential methylation of the terminal nitrogen in phosphatidylethanolamine to produce phosphatidylcholine. The mono-, di-, and trimethylornithine lipids described here represent the first report of methylation of the ornithine head groups in biological membranes. Various bacteria are known to produce OLs under phosphorus limitation or fatty-acid-hydroxylated OLs under thermal or acid stress. The sequential methylation of OLs, leading to a charged choline-like moiety in the trimethylornithine lipid head group, may be an adaptation to provide membrane stability under acidic conditions without the use of scarce phosphate in nutrient-poor ombrotrophic wetlands.

Cell biology of unique anammox bacteria that contain an energy conserving prokaryotic organelle

Anammox bacteria obtain their energy for growth from the anaerobic oxidation of ammonium with nitrite to dinitrogen gas. This property has made anammox bacteria very valuable for industry where they are applied for the removal of nitrogen compounds from industrial and domestic wastewaters. Anammox bacteria are also important in nature where they contribute significantly to oceanic nitrogen loss. Further, anammox bacteria have similarities to both Archaea and Eukarya, making them extremely interesting from a cell biological perspective. The anammox cell does not conform to the typical prokaryotic cell plan: single bilayer membranes divide the anammox cell into three distinct cellular compartments that possibly also have distinct cellular functions. The innermost and largest compartment, the anammoxosome, is the location of the energy metabolism. The middle compartment, the riboplasm, contains the nucleoid and ribosomes and thus has a genetic, information processing function. Finally, the outermost compartment, the paryphoplasm, has an as yet unknown function. In addition, anammox bacteria are proposed to have an atypical cell wall devoid of both peptidoglycan and a typical outer membrane. Here, I review the current knowledge on the cell biology of this enigmatic group of bacteria.

How to make a living from anaerobic ammonium oxidation

Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.

Low-frequency ultrasound-induced transport across non-raft-forming ternary lipid bilayers

We examined the effect of bilayer composition on membrane sensitivity to low-frequency ultrasound (LFUS) in bilayers composed of ternary mixtures of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), dipalmitoyl-phosphocholine (DPPC), and cholesterol. The phase diagram of this system does not display macroscopic phase coexistence between liquid phases (although there are suggestions that there is coexistence between a liquid and a solid phase). Samples from across the composition space were exposed to 20 kHz, continuous wave ultrasound, and the response of the bilayer was quantified using steady-state fluorescence spectroscopy to measure the release of a self-quenching dye, calcein, from large unilamellar vesicles. Dynamic light scattering measurements indicate that, in this system, release proceeds primarily by transport through the vesicle bilayer. While vesicle destruction might account, at least in part, for the light scattering trends observed, evidence of destruction was not as obvious as in other lipid systems. Values for bilayer permeability are obtained by fitting release kinetics to a two-film theory mathematical model. The permeability due to LFUS is found to increase with increasing DPPC content, as the bilayer tends toward the solid-ordered phase. Permeability, and thus sensitivity to LFUS, decreases with either POPC or cholesterol mole fractions. In the liquid regime of this system, there is no recorded phase transition; thus cholesterol is the determining factor in release rates. However, the presence of domain boundaries between distinctly differing phases of liquid and solid is found to cause release rates to more than double. The correlation of permeability with phase behavior might prove useful in designing and developing therapies based on ultrasound and membrane interactions.

Anammox--growth physiology, cell biology, and metabolism

Anaerobic ammonium-oxidizing (anammox) bacteria are the last major addition to the nitrogen-cycle (N-cycle). Because of the presumed inert nature of ammonium under anoxic conditions, the organisms were deemed to be nonexistent until about 15 years ago. They, however, appear to be present in virtually any anoxic place where fixed nitrogen (ammonium, nitrate, nitrite) is found. In various mar`ine ecosystems, anammox bacteria are a major or even the only sink for fixed nitrogen. According to current estimates, about 50% of all nitrogen gas released into the atmosphere is made by these bacteria. Besides this, the microorganisms may be very well suited to be applied as an efficient, cost-effective, and environmental-friendly alternative to conventional wastewater treatment for the removal of nitrogen. So far, nine different anammox species divided over five genera have been enriched, but none of these are in pure culture. This number is only a modest reflection of a continuum of species that is suggested by 16S rRNA analyses of environmental samples. In their environments, anammox bacteria thrive not just by competition, but rather by delicate metabolic interactions with other N-cycle organisms. Anammox bacteria owe their position in the N-cycle to their unique property to oxidize ammonium in the absence of oxygen. Recent research established that they do so by activating the compound into hydrazine (N(2)H(4)), using the oxidizing power of nitric oxide (NO). NO is produced by the reduction of nitrite, the terminal electron acceptor of the process. The forging of the N-N bond in hydrazine is catalyzed by hydrazine synthase, a fairly slow enzyme and its low activity possibly explaining the slow growth rates and long doubling times of the organisms. The oxidation of hydrazine results in the formation of the end product (N(2)), and electrons that are invested both in electron-transport phosphorylation and in the regeneration of the catabolic intermediates (N(2)H(4), NO). Next to this, the electrons provide the reducing power for CO(2) fixation. The electron-transport phosphorylation machinery represents another unique characteristic, as it is most likely localized on a special cell organelle, the anammoxosome, which is surrounded by a glycerolipid bilayer of ladder-like ("ladderane") cyclobutane and cyclohexane ring structures. The use of ammonium and nitrite as sole substrates might suggest a simple metabolic system, but the contrary seems to be the case. Genome analysis and ongoing biochemical research reveal an only partly understood redundancy in respiratory systems, featuring an unprecedented collection of cytochrome c proteins. The presence of the respiratory systems lends anammox bacteria a metabolic versatility that we are just beginning to appreciate. A specialized use of substrates may provide different anammox species their ecological niche.

Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties

Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called "prokaryotic organelle" analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya.

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.

Analysis of intact ladderane phospholipids, originating from viable anammox bacteria, using RP-LC-ESI-MS

Since the discovery of the anaerobic ammonium oxidizing (anammox) bacteria, many attempts have been made in order to identify these environmentally important bacteria in natural environments. Anammox bacteria contain a unique class of lipids, called ladderane lipids and here we present a novel method to detect viable anammox bacteria in sediments and waste water treatment plants based on the use of a ladderane lipid biomarker. Intact ladderane phosphatidylcholine (PC) lipids are analyzed using reversed-phase liquid chromatography-electrospray ionization-mass spectrometry. Following extraction from the complex sediment matrix, reversed-phase LC is used to separate ladderane PC lipids based on their tail group hydrophobicity as well as their ether or ester link to the glycerol backbone in the sn-2 position. We investigate the presence of intact ladderane lipids in natural sediments displaying anammox activity and illustrate the use of a specific intact membrane forming PC lipid as a biomarker for viable anammox bacterial cells. The presented method can be used to elucidate the whereabouts of viable anammox bacteria, subsequently enabling an estimation of anammox activity. This will greatly increase the knowledge of anammox bacteria and their importance in the global nitrogen cycle.