Microbial Eukaryotes that Lack Sterols

It is widely held that sterols are key cyclic triterpenoid lipids in eukaryotic cell membranes and are synthesized through oxygen‐dependent multienzyme pathways. However, there are known exceptions―ciliated protozoans, such as Tetrahymena, along with diverse low‐oxygen‐adapted eukaryotes produce, instead of sterols, the cyclic triterpenoid lipid tetrahymanol that does not require molecular oxygen for its biosynthesis. Here, we report that a number of anaerobic microbial eukaryotes (protists) utilize neither sterols nor tetrahymanol in their membranes. The lack of detectable sterol‐like compounds in their membranes may provide an opportunity to reconsider the physiological function of sterols and sterol‐like lipids in eukaryotes.     

Origin and evolution of the light-dependent protochlorophyllide oxidoreductase (LPOR) genes

Abstract: Light‐dependent NADPH‐protochlorophyllide oxidoreductase (LPOR) is a nuclear‐encoded chloroplast protein in green algae and higher plants which catalyzes the light‐dependent reduction of protochlorophyllide to chlorophyllide. Light‐dependent chlorophyll biosynthesis occurs in all oxygenic photosynthetic organisms. With the exception of angiosperms, this pathway coexists with a separate light‐independent chlorophyll biosynthetic pathway, which is catalyzed by light‐independent protochlorophyllide reductase (DPOR) in the dark. In contrast, the light‐dependent function of chlorophyll biosynthesis is absent from anoxygenic photosynthetic bacteria. Consequently, the question is whether cyanobacteria are the ancestors of all organisms that conduct light‐dependent chlorophyll biosynthesis. If so, how did photosynthetic eukaryotes acquire the homologous genes of LPOR in their nuclear genomes? The large number of complete genome sequences now available allow us to detect the evolutionary history of LPOR genes by conducting a genome‐wide sequence comparison and phylogenetic analysis. Here, we show the results of a detailed phylogenetic analysis of LPOR and other functionally related enzymes in the short chain dehydrogenase/reductase (SDR) family. We propose that the LPOR gene originated in the cyanobacterial genome before the divergence of eukaryotic photosynthetic organisms. We postulated that the photosynthetic eukaryotes obtained their LPOR homologues through endosymbiotic gene transfer.     

Comparative genomics and evolution of eukaryotic phospholipid biosynthesis

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.     

Protein glycosylation in bacterial mucosal pathogens

In eukaryotes, glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces. Their oligosaccharide moieties are implicated in a wide range of cell-cell and cell-matrix recognition events that are required for biological processes ranging from immune recognition to cancer development. Glycosylation was previously considered to be restricted to eukaryotes; however, through advances in analytical methods and genome sequencing, there have been increasing reports of both O-linked and N-linked protein glycosylation pathways in bacteria, particularly amongst mucosal-associated pathogens. Studying glycosylation in relatively less-complicated bacterial systems provides the opportunity to elucidate and exploit glycoprotein biosynthetic pathways. We will review the genetic organization, glycan structures and function of glycosylation systems in mucosal bacterial pathogens, and speculate on how this knowledge may help us to understand glycosylation processes in more complex eukaryotic systems and how it can be used for glycoengineering.     

Versatility of hydrocarbon production in cyanobacteria

Cyanobacteria are photosynthetic microorganisms using solar energy, H₂O, and CO₂ as the primary inputs. Compared to plants and eukaryotic microalgae, cyanobacteria are easier to be genetically engineered and possess higher growth rate. Extensive genomic information and well-established genetic platform make cyanobacteria good candidates to build efficient biosynthetic pathways for biofuels and chemicals by genetic engineering. Hydrocarbons are a family of compounds consisting entirely of hydrogen and carbon. Structural diversity of the hydrocarbon family is enabled by variation in chain length, degree of saturation, and rearrangements of the carbon skeleton. The diversified hydrocarbons can be used as valuable chemicals in the field of food, fuels, pharmaceuticals, nutrition, and cosmetics. Hydrocarbon biosynthesis is ubiquitous in bacteria, yeasts, fungi, plants, and insects. A wide variety of pathways for the hydrocarbon biosynthesis have been identified in recent years. Cyanobacteria may be superior chassis for hydrocabon production in a photosynthetic manner. A diversity of hydrocarbons including ethylene, alkanes, alkenes, and terpenes can be produced by cyanobacteria. Metabolic engineering and synthetic biology strategies can be employed to improve hydrocarbon production in cyanobacteria. This review mainly summarizes versatility and perspectives of hydrocarbon production in cyanobacteria.

     

Steroid biosynthesis in prokaryotes: identification of myxobacterial steroids and cloning of the first bacterial 2,3(S)-oxidosqualene cyclase from the myxobacterium Stigmatella aurantiaca

Steroids, such as cholesterol, are synthesized in almost all eukaryotic cells, which use these triterpenoid lipids to control the fluidity and flexibility of their cell membranes. Bacteria rarely synthesize such tetracyclic compounds but frequently replace them with a different class of triterpenoids, the pentacyclic hopanoids. The intriguing mechanisms involved in triterpene biosynthesis have attracted much attention, resulting in extensive studies of squalene-hopene cyclase in bacteria and (S)-2,3-oxidosqualene cyclases in eukarya. Nevertheless, almost nothing is known about steroid biosynthesis in bacteria. Only three steroid-synthesizing bacterial species have been identified before this study. Here, we report on a variety of sterol-producing myxobacteria. Stigmatella aurantiaca is shown to produce cycloartenol, the well-known first cyclization product of steroid biosynthesis in plants and algae. Additionally, we describe the cloning of the first bacterial steroid biosynthesis gene, cas, encoding the cycloartenol synthase (Cas) of S. aurantiaca. Mutants of cas generated via site-directed mutagenesis do not produce the compound. They show neither growth retardation in comparison with wild type nor any increase in ethanol sensitivity. The protein encoded by cas is most similar to the Cas proteins from several plant species, indicating a close evolutionary relationship between myxobacterial and eukaryotic steroid biosynthesis.     

Hypotheses for the origin and early evolution of triterpenoid cyclases

Hopanes and steranes are found almost universally in the sedimentary rock record where they often are used as proxies for aerobic organisms, metabolisms, and environments. In order to interpret ancient lipid signatures confidently we require a complementary understanding of how these modern biochemical pathways evolved since their conception. For example, generally it has been assumed that hopanoid biosynthesis was an evolutionary predecessor to steroid biosynthesis. Here we re‐evaluate this assumption. Using a combined phylogenetic and biochemical perspective, we address the evolution of polycyclic triterpenoid biosynthesis and suggest several constraints on using these molecules as aerobic biomarkers. Amino acid sequence data show that the enzymes responsible for polycyclic triterpenoid biosynthesis (i.e. squalene and 2,3‐oxidosqualene cyclases) are homologous. Numerous conserved domains correspond to active sites in the enzymes that are required to complete the complex cyclization reaction. From these sites we develop an evolutionary analysis of three independent characters to explain the evolution of the major classes of polycyclic triterpenoids. These characters are: (i) the number of unfavourable anti‐Markovnikov ring closures, (ii) all‐chair (CCC) or chair‐boat‐chair (CBC) substrate conformation, and (iii) the choice between squalene and 2,3‐oxidosqualene as the substrate. We use these characters to construct four competing phylogenies to describe the evolution of polycyclic triterpenoid biosynthesis. The analysis suggests that malabaricanoids would be the most ancient polycyclic triterpenoids. The two most parsimonious evolutionary trees are the ones in which hopanoid and steroid cyclases diverged from a common ancestor. The transition from a CCC‐ to CBC‐fold marks the major divergence in the evolution of these pathways, and it is diagnosable in the geological record. However, this transition does not require the simultaneous adoption of the aerobic substrate, 2,3‐oxidosqualene, because these characters are controlled by independent parts of the enzyme.     

Structural requirements for substrate recognition of Mycobacterium tuberculosis 14 alpha-demethylase: implications for sterol biosynthesis

Sterol 14 alpha-demethylase (14DM) is a cytochrome P-450 involved in sterol biosynthesis in eukaryotes. It was reported that Mycobacterium smegmatis also makes cholesterol and that cholesterol is essential to Mycobacterium tuberculosis (MT) infection, although the origin of the cholesterol is unknown. A protein product from MT having about 30% sequence identity with eukaryotic 14 alpha-demethylases has been found to convert sterols to their 14-demethyl products indicating that a sterol pathway might exist in MT. To determine the optimal sterol structure recognized by MT 14DM, binding of 28 sterol and sterol-like (triterpenoids) molecules to the purified recombinant 14 alpha-demethylase was examined. Like eukaryotic forms, a 3 beta-hydroxy group and a 14 alpha-methyl group are essential for substrate acceptability by the bacterial 14 alpha-demethylase. The high affinity binding of 31-norcycloartenol without detectable activity indicates that the Delta(8)-bond is required for activity but not for binding. As for plant 14 alpha-demethylases, 31-nor-sterols show a binding preference for MT 14DM. Similar to enzymes from mammals and yeast, a C24-alkyl group is not required for MT 14DM binding and activity, whereas it is for plant 14 alpha-demethylases.Thus, substrate binding to MT 14DM seems to share common features with all eukaryotic 14 alpha-demethylases, the MT form seemingly having the broadest substrate recognition of all forms of 14 alpha-demethylase studied so far. - Bellamine, A., A. T. Mangla, A. L. Dennis, W. D. Nes, and M. R. Waterman. Structural requirements for substrate recognition of Mycobacterium tuberculosis 14 alpha-demethylase: implications for sterol biosynthesis. J. Lipid Res. 2001. 42: 128;-136.     

Total biosynthesis of hydrocortisone from a simple carbon source in yeast

We report on the production of hydrocortisone, the major adrenal glucocorticoid of mammals and an important intermediate of steroidal drug synthesis, from a simple carbon source by recombinant Saccharomyces cerevisiae strains. An artificial and fully self-sufficient biosynthetic pathway involving 13 engineered genes was assembled and expressed in a single yeast strain. Endogenous sterol biosynthesis was rerouted to produce compatible sterols to serve as substrates for the heterologous part of the pathway. Biosynthesis involves eight mammalian proteins (mature forms of CYP11A1, adrenodoxin (ADX), and adrenodoxin reductase (ADR); mitochondrial forms of ADX and CYP11B1; 3beta-HSD, CYP17A1, and CYP21A1). Optimization involved modulating the two mitochondrial systems and disrupting of unwanted side reactions associated with ATF2, GCY1, and YPR1 gene products. Hydrocortisone was the major steroid produced. This work demonstrates the feasibility of transfering a complex biosynthetic pathway from higher eukaryotes into microorganisms.     

Distribution and Functions of Sterols and Sphingolipids

Sterols and sphingolipids are considered mainly eukaryotic lipids even though both are present in some prokaryotes, with sphingolipids being more widespread than sterols. Both sterols and sphingolipids differ in their structural features in vertebrates, plants, and fungi. Interestingly, some invertebrates cannot synthesize sterols de novo and seem to have a reduced dependence on sterols. Sphingolipids and sterols are found in the plasma membrane, but we do not have a clear picture of their precise intracellular localization. Advances in lipidomics and subcellular fractionation should help to improve this situation. Genetic approaches have provided insights into the diversity of sterol and sphingolipid functions in eukaryotes providing evidence that these two lipid classes function together. Intermediates in sphingolipid biosynthesis and degradation are involved in signaling pathways, whereas sterol structures are converted to hormones. Both lipids have been implicated in regulating membrane trafficking.Typical examples of eukaryotic lipids, sterols, and sphingolipids can both be found in membranes from simple unicellular fungi and protists to multicellular animals and plants. Their versatile use as structural elements but also as signaling molecules has probably played an important role during the evolution of this large and diverse group of organisms. There are also many eukaryotes that have lost the ability to synthesize sterols de novo including nematodes, insects, and marine invertebrates, which have to take up sterols with their diet. Sterol biosynthesis has also been reported in a number of bacteria. Sphingolipids are more widely spread among prokaryotes than sterols and also show a greater variety of structures among the different eukaryotes.In this short review we will first give an overview about the diversity of sterol and sphingolipid structures and their distribution in nature. Then we will discuss their subcellular distribution. A brief technical section will add some information on the separation and detection of these lipid molecules. Subsequently, we will summarize different genetic approaches to study the functions of sterols and sphingolipids, and finally, we will discuss the functional and possible physical interactions of the two lipid classes within the cell. Far from being comprehensive, we will focus only on a few interesting aspects and try to give new view points, which are less frequently discussed.     

细菌中倍半萜生物合成的研究进展

萜类化合物是一大类小分子天然产物,在生物体内扮演重要的角色。植物和真菌中萜类化合物的生物合成已被广泛研究,但是在真核生物中克隆或改造萜类化合物生物合成途径还有较大难度。许多细菌同样可以产生萜类化合物。在过去十多年间细菌萜类合酶的研究进展为我们对萜类化合物生物合成的理解做出了显著的贡献。这里我们主要关注细菌中合成的倍半萜化合物,概述其化学结构、倍半萜合酶对法尼基焦磷酸环化的机制、后修饰酶特别是氧化还原酶所参与的后修饰、代谢调控以及合成途径中尚未解决的问题等。     

Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attack

Sterols are an essential class of lipids in eukaryotes, where they serve as structural components of membranes and play important roles as signaling molecules. Sterols are also of high pharmacological significance: cholesterol-lowering drugs are blockbusters in human health, and inhibitors of ergosterol biosynthesis are widely used as antifungals. Inhibitors of ergosterol synthesis are also being developed for Chagas’s disease, caused by Trypanosoma cruzi. Here we develop an in silico pipeline to globally evaluate sterol metabolism and perform comparative genomics. We generate a library of hidden Markov model-based profiles for 42 sterol biosynthetic enzymes, which allows expressing the genomic makeup of a given species as a numerical vector. Hierarchical clustering of these vectors functionally groups eukaryote proteomes and reveals convergent evolution, in particular metabolic reduction in obligate endoparasites. We experimentally explore sterol metabolism by testing a set of sterol biosynthesis inhibitors against trypanosomatids, Plasmodium falciparum, Giardia, and mammalian cells, and by quantifying the expression levels of sterol biosynthetic genes during the different life stages of T. cruzi and Trypanosoma brucei. The phenotypic data correlate with genomic makeup for simvastatin, which showed activity against trypanosomatids. Other findings, such as the activity of terbinafine against Giardia, are not in agreement with the genotypic profile.     

Trichothecene biosynthesis in Fusarium species: chemistry, genetics, and significance.

Several species of the genus Fusarium and related fungi produce trichothecenes which are sesquiterpenoid epoxides that act as potent inhibitors of eukaryotic protein synthesis. Interest in the trichothecenes is due primarily to their widespread contamination of agricultural commodities and their adverse effects on human and animal health. In this review, we describe the trichothecene biosynthetic pathway in Fusarium species and discuss genetic evidence that several trichothecene biosynthetic genes are organized in a gene cluster. Trichothecenes are highly toxic to a wide range of eukaryotes, but their specific function, if any, in the survival of the fungi that produce them is not obvious. Trichothecene gene disruption experiments indicate that production of trichothecenes can enhance the severity of disease caused by Fusarium species on some plant hosts. Understanding the regulation and function of trichothecene biosynthesis may aid in development of new strategies for controlling their production in food and feed products.     

Sterol biosynthesis and prokaryotes-to-eukaryotes evolution

It has been widely accepted that there exists a correlation between prokaryotes-to-eukaryotes evolution and atmospheric oxygen rise. However, it is a great challenge to elucidate the mechanisms underlying the correlation. Considering the facts that cellular communication of eukaryotes depends largely on membrane functions (e.g., endo- and exocytosis) and sterols play a key role in fulfilling these functions, we propose that the biosynthesis of sterols represents a critical step in the prokaryotes-to-eukaryotes evolution. Indeed, sterol biosynthesis is nearly ubiquitous among eukaryotes, but is generally excluded by prokaryotes. More importantly, during the biosynthesis of sterols, oxygen is absolutely required. Therefore, the missing link between prokaryotes-to-eukaryotes evolution and atmospheric oxygen rise is likely to reside in, at least in part, sterol biosynthesis, i.e., high atmospheric oxygen concentration facilitates the generation of sterols and thus benefits the birth of complex organisms.     

Interactions between sterol biosynthesis genes in embryonic development of Arabidopsis

The sterol biosynthesis pathway of Arabidopsis produces a large set of structurally related phytosterols including sitosterol and campesterol, the latter being the precursor of the brassinosteroids (BRs). While BRs are implicated as phytohormones in post-embryonic growth, the functions of other types of steroid molecules are not clear. Characterization of the fackel (fk) mutants provided the first hint that sterols play a role in plant embryogenesis. FK encodes a sterol C-14 reductase that acts upstream of all known enzymatic steps corresponding to BR biosynthesis mutants. Here we report that genetic screens for fk-like seedling and embryonic phenotypes have identified two additional genes coding for sterol biosynthesis enzymes: CEPHALOPOD (CPH), a C-24 sterol methyl transferase, and HYDRA1 (HYD1), a sterol C-8,7 isomerase. We describe genetic interactions between cph, hyd1 and fk, and studies with 15-azasterol, an inhibitor of sterol C-14 reductase. Our experiments reveal that FK and HYD1 act sequentially, whereas CPH acts independently of these genes to produce essential sterols. Similar experiments indicate that the BR biosynthesis gene DWF1 acts independently of FK, whereas BR receptor gene BRI1 acts downstream of FK to promote post-embryonic growth. We found embryonic patterning defects in cph mutants and describe a GC-MS analysis of cph tissues which suggests that steroid molecules in addition to BRs play critical roles during plant embryogenesis. Taken together, our results imply that the sterol biosynthesis pathway is not a simple linear pathway but a complex network of enzymes that produce essential steroid molecules for plant growth and development.     

The expression of antibiotic resistance genes in antibiotic‐producing bacteria

Antibiotic‐producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. In many cases, the expression of resistance genes is tightly linked to that of antibiotic biosynthetic genes. In others, the resistance genes can be induced by their cognate antibiotics or by intermediate molecules from their biosynthetic pathways. The regulatory mechanisms that couple resistance to antibiotic biosynthesis are mechanistically diverse and potentially relevant to the origins of clinical antibiotic resistance.     

Different polyketide folding modes converge to an identical molecular architecture

Metabolic diversity is being studied intensively by evolutionary biologists, but so far there has been no comparison of biosynthetic pathways leading to a particular secondary metabolite in both prokaryotes and eukaryotes. We have detected the bioactive anthraquinone chrysophanol, which serves as a chemical defense in diverse eukaryotic organisms, in a bacterial Nocardia strain, thereby permitting the first comparative biosynthetic study. Two basic modes of folding a polyketide chain to fused-ring aromatic structures have so far been described: mode F (referring to fungi) and mode S (from Streptomyces). We have demonstrated that in eukaryotes (fungi, higher plants and insects), chrysophanol is formed via folding mode F. In actinomycetes, by contrast, the cyclization follows mode S. Thus, chrysophanol is the first polyketide synthase product that is built up by more than one polyketide folding mode.     

Boosting crop yields with plant steroids

Plant sterols and steroid hormones, the brassinosteroids (BRs), are compounds that exert a wide range of biological activities. They are essential for plant growth, reproduction, and responses to various abiotic and biotic stresses. Given the importance of sterols and BRs in these processes, engineering their biosynthetic and signaling pathways offers exciting potentials for enhancing crop yield. In this review, we focus on how alterations in components of sterol and BR metabolism and signaling or application of exogenous steroids and steroid inhibitors affect traits of agronomic importance. We also discuss areas for future research and identify the fine-tuning modulation of endogenous BR content as a promising strategy for crop improvement.     

Development of structural organization of protein-synthesizing machinery from prokaryotes to eukaryotes

Though the mechanisms of protein biosynthesis are similar in the cells of prokaryotes and eukaryotes, the eukaryotic translational machinery in the cell is arranged more intricately. One of the most striking characteristic features of the eukaryotic translational machinery is that the eukaryotic proteins involved in the translational process, such as initiation factors, elongation factors and aminoacyl-tRNA synthetases, in contrast to their prokaryotic analogs, possess a non-specific affinity for RNA. Due to the RNA-binding ability, these eukaryotic proteins can be compartmentalized on polyribosomes. In addition to the proteins of the translational apparatus, several other eukaryotic RNA-binding proteins can be also compartmentalized on polyribosomes; these proteins include glycolytic enzymes, steroid hormone receptors and intermediate filament proteins. Thus, the eukaryotic polyribosome is an element of the cytoplasmic labile structure on which various proteins can be compartmentalized and, consequently, different biochemical pathways can be integrated.