Distribution, metabolism and function of dolichol and polyprenols

GrcC1 mediates low-level resistance to multiple drugs in M. marinum, M. abscessus, and M. smegmatis

The escalating threat of mycobacterial infectious diseases, particularly those caused by nontuberculous mycobacteria (NTM), poses a serious challenge to public health. Linezolid (LZD), an oxazolidinone antimicrobial, exhibits potent activity against Mycobacterium tuberculosis and NTM. Generally, mutations in the rrl and rplC genes are widely associated with resistance to LZD. However, in this study, we screened Mycobacterium marinum strains lacking such mutations, indicating the presence of an alternative resistance mechanism. Notably, through whole-genome sequencing, we identified a novel mutation C395T in the MMAR_0911 (grcC1) gene that has never been linked to drug resistance. This mutation leads to an A132V substitution in the encoded protein, a polyprenyl diphosphate synthase potentially involved in the synthesis of cell wall components and menaquinones. We found that the overexpression of grcC1 caused resistance to multiple drugs including LZD, clarithromycin (CLR), vancomycin (VAN), clofazimine (CFZ), rifampicin (RIF), cefoxitin (CEF), levofloxacin (LEV), and moxifloxacin (MXF) and reduced cell wall permeability, while the silence and knockout of grcC1 showed increased cell wall permeability and susceptibility to these drugs. Using CRISPR/Cpf1-assisted gene editing, we confirmed that the A132V mutation conferred low-level resistance to the aforementioned drugs in Mycobacterium abscessus and Mycobacterium smegmatis. Furthermore, thin-layer chromatography analysis indicated reduced glycolipid polarity in the grcC1 mutant strains, suggesting an impact on the cell envelope integrity. Our findings suggest that GrcC1 contributes to low-level drug resistance in mycobacteria by potentially reducing cell wall permeability, highlighting its potential as a novel target for antimicrobial agents and as a diagnostic marker.IMPORTANCEOur study uncovers a novel drug resistance mechanism in mycobacteria, focusing on the previously uncharacterized grcC1 gene. We identified a new mutation, A132V, in GrcC1, which is involved in cell wall component synthesis and menaquinone production. This mutation contributes to low-level resistance not only to linezolid but also to a broad range of drugs, including clarithromycin, vancomycin, and rifampicin. Through advanced techniques like CRISPR interference and gene editing, we demonstrated that GrcC1 plays a critical role in drug susceptibility and cell wall permeability across multiple Mycobacterium species. These findings represent the first connection between GrcC1 and drug resistance, offering new insights into combating infections caused by nontuberculous mycobacteria (NTM). Our work highlights the potential of GrcC1 as a target for novel therapeutic approaches and as a diagnostic marker for drug-resistant NTM infections.

Synthesis of natural polyprenols for the production of biological prenylquinones and tocochromanols

We elaborate the chemical synthesis of polyprenols by chain lengthening, which is considerably less time-consuming than the other previously described methods. Our method eliminates critical steps requiring low temperature and toxic chemicals, which are difficult to perform in ordinary laboratories. The critical step of acetylene addition in liquid ammonia was replaced by a new approach, namely, the use of sodium acetylide in dimethoxyethane at room temperature, where the reaction is completed within one hour. This method is of general significance as it can also be applied to the synthesis of any other acetylides. Our method provides reasonable yields and can be scaled depending on the requirements. All the reactions were followed by high-performance liquid chromatography, allowing the formation of undesired isomers and other side-products to be controlled. The resulting polyprenols were further used in the synthesis of plastoquinones, although a variety of biological prenylquinones can be synthesized this way. Moreover, we found a new method for the direct formation of tocochromanols (plastochromanols, tocochromanols) from polyprenols and aromatic head groups.

Abnormal expression of lysosomal glycoproteins in patients with congenital disorders of glycosylation

OBJECTIVE

The study of the impact of some inherited defects in glycosylation on the biosynthesis of some lysosomal glycoproteins. Results description: Whole-exome sequencing revealed a homozygous variant; 428G > A; p. (R143K) in SRD5A3 in one patient and a heterozygous one c.46G > A p. (Gly16Arg) in SLC35A2 in the other patient. Both variants were predicted to be likely pathogenic. Lysosome-associated membrane glycoprotein 2 (LAMP2) immunodetection in both cases showed a truncated form of the protein. Cystinosin (CTN) protein appeared as normal and truncated forms in both patients in ratios of the mature to truncated forms of CTN were lower than the control. The levels of the truncated forms of both cellular proteins were higher in the SRD5A3-CDG case compared to the SLC35A2-CDG case. The tetrameric form of cathepsin C (CTSC) was expressed at low levels in both cases with congenital disorder of glycosylation (CDG). SLC35A2-CDG patient had one extra-unknown band while SRD5A3-CDG patient had a missing band of CTSC forms. The expression patterns of lysosomal glycoproteins could be different between different types of CDG.

Structural Identification of Lipid-α: A Glycosyl Lipid Involved in Oligo- And Polysaccharides Metabolism in Streptococcus agalactiae (Group B Streptococcus)

Streptococcus agalactiae (group B Streptococcus, GBS) is a gram-positive bacterium that is an asymptomatic colonizer commonly found in the gastrointestinal and genitourinary tract of healthy adults. GBS is also the most common cause of life-threatening bacterial infections in newborns and is emerging as a pathogen in immunocompromised and diabetic adults. The GBS cell wall and covalently linked capsular polysaccharides (CPS) are vital to the protection of the bacterial cell and act as virulence factors. GBS-CPS have been successfully used to produce conjugate vaccines for all currently identified GBS serotypes. However, the mechanisms of biosynthesis and assembly of CPS and the other cell wall components remain poorly defined due to their complex surface structures. In this biosynthetic study of the GBS cell wall-CPS complex, glycolipids with varying lengths of glycosyl-chains were discovered. Among those, one of the smallest glycolipids (named GBS Lipid-α) was structurally characterized. Lipid-α is involved in GBS saccharide metabolism and presumably acts as a glycosyl acceptor to elongate the glycosyl chain. GBS Lipid-α was determined to be a 3-monosaccharide 1,2 acyl glycerol with a molecular mass in the range of m/z = 724-808. GBS Lipid-α is highly heterogenic with various acyl groups and glycosyl moieties. This knowledge will pave the way for future studies to elucidate the entire metabolic pathway and genes involved. The Lipid-α pathway may also exist in other bacterial species and has the potential to be a biomarker for future drug development.

Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase

Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAc₂Man₉Glc₃, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc₃) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites.

Glycoconjugate journal special issue on: the glycobiology of Parkinson's disease

Parkinson's disease (PD) is a neurodegenerative disorder that affects over 10 million aging people worldwide. This condition is characterized by the degeneration of dopaminergic neurons in the pars compacta region of the substantia nigra (SNpc) and by aggregation of proteins, commonly α-synuclein (SNCA). The formation of Lewy bodies that encapsulate aggregated proteins in lipid vesicles is a hallmark of PD. Glycosylation of proteins and neuroinflammation are involved in the pathogenesis. SNCA has many posttranslational modifications and interacts with components of membranes that affect aggregation. The large membrane lipid dolichol accumulates in the brain upon age and has a significant effect on membrane structure. The replacement of dopamine and dopaminergic neurons are at the forefront of therapeutic development. This review examines the role of membrane lipids, glycolipids, glycoproteins and dopamine in the aggregation of SNCA and development of PD. We discuss the SNCA-dopamine-neuromelanin-dolichol axis and the role of membranes in neuronal stem cells that could be a regenerative therapy for PD patients.

Research advances on neurite outgrowth inhibitor B receptor

Neurite outgrowth inhibitor‐B (Nogo‐B) is a membrane protein which is extensively expressed in multiple organs, especially in endothelial cells and vascular smooth muscle cells of blood vessels and belongs to the reticulon protein family. Notably, its specific receptor, Nogo‐B receptor (NgBR), encoded by NUS1, has been implicated in many crucial cellular processes, such as cholesterol trafficking, lipid metabolism, dolichol synthesis, protein N‐glycosylation, vascular remodelling, angiogenesis, tumorigenesis and neurodevelopment. In recent years, accumulating studies have demonstrated the statistically significant changes of NgBR expression levels in human diseases, including Niemann‐Pick type C disease, fatty liver, congenital disorders of glycosylation, persistent pulmonary hypertension of the newborn, invasive ductal breast carcinoma, malignant melanoma, non‐small cell lung carcinoma, paediatric epilepsy and Parkinson's disease. Besides, both the in vitro and in vivo studies have shown that NgBR overexpression or knockdown contribute to the alteration of various pathophysiological processes. Thus, there is a broad development potential in therapeutic strategies by modifying the expression levels of NgBR.

Synthesis and biological activity of polyprenols

The polyprenols and their derivatives are highlighted in this study. These lipid linear polymers of isoprenoid residues are widespread in nature from bacteria to human cells. This review primarily presents the synthesis and biological activities of polyprenyl derivatives. Attention is focused on the synthesis and biological activity of dolichols, polyprenyl ester derivatives and polyprenyl amines. Other polyprenyl derivatives, such as oxides of polyprenols, aromatic polyprenols, polyprenyl bromide and polyprenyl sulphates, are mentioned. It is noted that polyprenyl phosphates and polyprenyl-linked glycosylation have better antibacterial, gene therapy and immunomodulating performance, whereas polyprenyl amines have better for antibacterial and antithrombotic activity. Dolichols, polyprenyl acetic esters, polyprenyl phosphates and polyprenyl-linked glycosylation have pharmacological anti-tumour effects. Finally, the postulated prospect of polyprenols and their derivatives are discussed. Further in vivo studies on the above derivatives are needed. The compatibility of polyprenols and their derivatives with other drugs should be studied, and new preparations of polyprenyl derivatives, such as hydrogel glue and release-controlled drugs, are suggested for future research and development.

Novel Citronellyl-Based Photoprobes Designed to Identify ER Proteins Interacting with Dolichyl Phosphate in Yeast and Mammalian Cells

BACKGROUND

Dolichyl phosphate-linked mono- and oligosaccharides (DLO) are essential intermediates in protein N-glycosylation, C- and O-mannosylation and GPI anchor biosynthesis. While many membrane proteins in the endoplasmic reticulum (ER) involved in the assembly of DLOs are known, essential proteins believed to be required for the transbilayer movement (flip-flopping) and proteins potentially involved in the regulation of DLO synthesis remain to be identified.

METHODS

The synthesis of a series of Dol-P derivatives composed of citronellyl-based photoprobes with benzophenone groups equipped with alkyne moieties for Huisgen "click" chemistry is now described to utilize as tools for identifying ER proteins involved in regulating the biosynthesis and transbilayer movement of lipid intermediates. In vitro enzymatic assays were used to establish that the photoprobes contain the critical structural features recognized by pertinent enzymes in the dolichol pathway. ER proteins that photoreacted with the novel probes were identified by MS.

RESULTS

The potential of the newly designed photoprobes, m-PAL-Cit-P and p-PAL-Cit-P, for identifying previously unidentified Dol-P-interacting proteins is supported by the observation that they are enzymatically mannosylated by Man-P-Dol synthase (MPDS) from Chinese Hamster Ovary (CHO) cells at an enzymatic rate similar to that for Dol-P. MS analyses reveal that DPM1, ALG14 and several other yeast ER proteins involved in DLO biosynthesis and lipid-mediated protein O-mannosylation photoreacted with the novel probes.

CONCLUSION

The newly-designed photoprobes described in this paper provide promising new tools for the identification of yet to be identified Dol-P interacting ER proteins in yeast and mammalian cells, including the Dol-P flippase required for the "re-cycling" of the glycosyl carrier lipid from the lumenal monolayer of the ER to the cytoplasmic leaflet for new rounds of DLO synthesis.

Genetic defects in dolichol metabolism

Congenital disorders of glycosylation (CDG) comprise a group of inborn errors of metabolism with abnormal glycosylation of proteins and lipids. Patients with defective protein N-glycosylation are identified in routine metabolic screening via analysis of serum transferrin glycosylation. Defects in the assembly of the dolichol linked Glc(3)Man(9)GlcNAc(2) glycan and its transfer to proteins lead to the (partial) absence of complete glycans on proteins. These defects are called CDG-I and are located in the endoplasmic reticulum (ER) or cytoplasm. Defects in the subsequent processing of protein bound glycans result in the presence of truncated glycans on proteins. These defects are called CDG-II and the enzymes involved are located mainly in the Golgi apparatus. In recent years, human defects have been identified in dolichol biosynthesis genes within the group of CDG-I patients. This has increased interest in dolichol metabolism, has resulted in specific recognizable clinical symptoms in CDG-I and has offered new mechanistic insights in dolichol biosynthesis. We here review its biosynthetic pathways, the clinical and biochemical phenotypes in dolichol-related CDG defects, up to the formation of dolichyl-P-mannose (Dol-P-Man), and discuss existing evidence of regulatory networks in dolichol metabolism to provide an outlook on therapeutic strategies.

Comparative Analysis of Protein Glycosylation Pathways in Humans and the Fungal Pathogen Candida albicans

Protein glycosylation pathways are present in all kingdoms of life and are metabolic pathways found in all the life kingdoms. Despite sharing commonalities in their synthesis, glycans attached to glycoproteins have species-specific structures generated by the presence of different sets of enzymes and acceptor substrates in each organism. In this review, we present a comparative analysis of the main glycosylation pathways shared by humans and the fungal pathogen Candida albicans: N-linked glycosylation, O-linked mannosylation and glycosylphosphatidylinositol-anchorage. The knowledge of similarities and divergences between these metabolic pathways could help find new pharmacological targets for C. albicans infection.

Knock-down DHDDS expression induces photoreceptor degeneration in zebrafish

A mutation in the dehydrodolichol diphosphate synthase (DHDDS) was recently identified as the cause of a subtype of recessive retinitis pigmentosa (RP). Molecular modeling indicates that this mutation could result in low enzymatic efficiency of DHDDS. To investigate the possible link between insufficient DHDDS activity and photoreceptor degeneration, the expression of DHDDS was knocked down by morpholino oligonucleotides (MO) injected into zebrafish one cell embryos. The general appearance and behavior of 4-day-old MO-injected fish were normal, but they failed to respond to light-off, suggesting loss of visual function. Morphological analysis showed that photoreceptor outer segments in retinas of MO-injected fish are very short and in many cases completely missing. Peanut agglutinin (PNA) staining confirmed the absence of cone outer segments. These results demonstrate that suppression of DHDDS expression in zebrafish leads to the loss of photoreceptor outer segments and visual function. These results support the hypothesis that insufficient DHDDS function leads to retinal degeneration.

'Ashvagandharishta' prepared using yeast consortium from Woodfordia fruticosa flowers exhibit hepatoprotective effect on CCl4 induced liver damage in Wistar rats

ETHNOPHARMACOLOGICAL RELEVANCE

[corrected] Consortium of yeasts sourced from traditionally used Woodfordia fruticosa flowers proved to be beneficial for fermenting Ashvagandharishta. It resulted in faster fermentation, acceptable organoleptic properties and demonstrable hepatoprotective potential in CCl4 induced hepatotoxicity. To formulate Ashvagandharishta using consortium of yeasts and to investigate its physiochemical parameters. Standardize the formulation with the help of standard withaferin-A and withanolide-A and to evaluate its hepatoprotective potential in CCl4 induced hepatotoxicity in the rat model.

MATERIAL AND METHODS

Ashvagandharishta was prepared using a 5% consortium of yeasts and ascertained its quality through physiochemical and phytochemical investigation. Withaferin-A and withanolide-A was simultaneously estimated by HPLC for standardization. Hepatoprotective potential was evaluated by administering 2.31 and 1.15 ml/kg doses while considering biochemical parameters like serum AST, ALT, ALP and lipid profile. Gene expression study was carried out for the expression of antioxidant and inflammatory genes such as CAT, GPx and proinflammatory gene IL-6. Histopathology of liver was also studied with the help of H&E staining.

RESULTS

Ashvagandharishta was found organolepticaly acceptable with optimized physiochemical parameters. Withaferin-A and withanolide-A in Ashvagandharishta estimated as 0.3711, 0.7426 (%w/v), respectively. In the CCl4 induced hepato-toxicity model, Ashvagandharishta-2.31ml/kg dose showed significant decrease in elevated hepatic level of AST(p<0.001), ALT(p<0.01) and ALP(p<0.001). Both doses of Ashvagandharishta showed significant reduction of TG, Cholesterol, VLDL and LDL in serum, with corresponding reduction of (p<0.001) serum-HDL. Ashvagandharishta also showed increased serum protein (p<0.05) and albumin (p<0.01) with decrease in bilirubin (p<0.01). Additionally, Ashvagandharishta administration revealed up-regulation in antioxidant genes such as CAT and GPx in liver with concomitant down-regulation in proinflammatory IL-6gene (p<0.01). Histopathological parameters revealed restoration of normal tissue architecture by both doses of Ashvagandharishta.

CONCLUSIONS

Consortium of yeasts from Woodfordia fruticosa flowers showed better fermentation pattern for Ashvagandharishta produced with acceptable organoleptic properties. Hepatoprotection shown by Ashvagandharishta was mainly through prevention of oxidative damage. Up-regulation of CAT and GPx genes and corresponding down regulation of proinflammatory IL6 gene was revealed as possible mechanism of its action.

Aberrant dolichol chain lengths as biomarkers for retinitis pigmentosa caused by impaired dolichol biosynthesis

We observed a characteristic shortening of plasma and urinary dolichols in retinitis pigmentosa (RP) patients carrying K42E and T206A mutations in the dehydrodolichol diphosphate synthase (DHDDS) gene, using liquid chromatography-mass spectrometry. Dolichol-18 (D18) became the dominant dolichol species in patients instead of dolichol-19 (D19) in normal individuals. The D18/D19 ratio was calculated and used as an index of dolichol length distribution. K42E/K42E and K42E/T206A patients have significantly higher plasma and urinary D18/D19 ratios than K42E and T206A carriers. The ratios of carriers are significantly higher than normal individuals. Receiver operating characteristic (ROC) analysis shows that plasma and urinary D18/D19 ratios can unambiguously discriminate patients from carriers, and carriers from normal individuals. Dolichol analysis also provides evidence that the T206A mutation is RP-causative. The methodologies and procedures used for dolichol profiling are reliable, high throughput, and cost effective. Dolichol profiling, complementary to genotyping, can be readily adapted as a test in the clinic not only for the diagnosis of patients but also for identification of carriers with DHDDS or other genetic mutations that may impair dolichol biosynthesis.

N-linked protein glycosylation in the endoplasmic reticulum

The attachment of glycans to asparagine residues of proteins is an abundant and highly conserved essential modification in eukaryotes. The N-glycosylation process includes two principal phases: the assembly of a lipid-linked oligosaccharide (LLO) and the transfer of the oligosaccharide to selected asparagine residues of polypeptide chains. Biosynthesis of the LLO takes place at both sides of the endoplasmic reticulum (ER) membrane and it involves a series of specific glycosyltransferases that catalyze the assembly of the branched oligosaccharide in a highly defined way. Oligosaccharyltransferase (OST) selects the Asn-X-Ser/Thr consensus sequence on polypeptide chains and generates the N-glycosidic linkage between the side-chain amide of asparagine and the oligosaccharide. This ER-localized pathway results in a systemic modification of the proteome, the basis for the Golgi-catalyzed modification of the N-linked glycans, generating the large diversity of N-glycoproteome in eukaryotic cells. This article focuses on the processes in the ER. Based on the highly conserved nature of this pathway we concentrate on the mechanisms in the eukaryotic model organism Saccharomyces cerevisiae.

From discrete dilated cardiomyopathy to successful cardiac transplantation in congenital disorders of glycosylation due to dolichol kinase deficiency (DK1-CDG)

Congenital disorders of glycosylation are a growing group of inborn errors of protein glycosylation. Cardiac involvement is frequently observed in the most common form, PMM2-CDG, especially hypertrophic cardiomyopathy. Dilated cardiomyopathy, however, has been only observed in a few CDG subtypes, usually with a lethal outcome. We report on cardiac pathology in nine patients from three unrelated Israeli families, diagnosed with dolichol kinase deficiency, due to novel, homozygous DK1 gene mutations. The cardiac symptoms varied from discrete, mild dilation to overt heart failure with death. Two children died unexpectedly with acute symptoms of heart failure before the diagnosis of DK1-CDG and heart transplantation could take place. Three other affected children with mild dilated cardiomyopathy at the time of the diagnosis deteriorated rapidly, two of them within days after an acute infection. They all went through successful heart transplantation; one died unexpectedly and 2 others are currently (after 1-5 years) clinically stable. The other 4 children diagnosed with mild dilated cardiomyopathy are doing well on supportive heart failure therapy. In most cases, the cardiac findings dominated the clinical picture, without central nervous system or multisystem involvement, which is unique in CDG syndrome. We suggest to test for DK1-CDG in patients with dilated cardiomyopathy. Patients with discrete cardiomyopathy may remain stable on supportive treatment while others deteriorate rapidly. Our paper is the first comprehensive study on the phenotype of DK1-CDG and the first successful organ transplantation in CDG syndrome.

A predicted geranylgeranyl reductase reduces the ω-position isoprene of dolichol phosphate in the halophilic archaeon, Haloferax volcanii

In N-glycosylation in both Eukarya and Archaea, N-linked oligosaccharides are assembled on dolichol phosphate prior to transfer of the glycan to the protein target. However, whereas only the α-position isoprene subunit is saturated in eukaryal dolichol phosphate, both the α- and ω-position isoprene subunits are reduced in the archaeal lipid. The agents responsible for dolichol phosphate saturation remain largely unknown. The present study sought to identify dolichol phosphate reductases in the halophilic archaeon, Haloferax volcanii. Homology-based searches recognize HVO_1799 as a geranylgeranyl reductase. Mass spectrometry revealed that cells deleted of HVO_1799 fail to fully reduce the isoprene chains of H. volcanii membrane phospholipids and glycolipids. Likewise, the absence of HVO_1799 led to a loss of saturation of the ω-position isoprene subunit of C(55) and C(60) dolichol phosphate, with the effect of HVO_1799 deletion being more pronounced with C(60) dolichol phosphate than with C(55) dolichol phosphate. Glycosylation of dolichol phosphate in the deletion strain occurred preferentially on that version of the lipid saturated at both the α- and ω-position isoprene subunits.

Chemical synthesis of polyprenyl sialyl phosphate, a probable biosynthetic intermediate of bacterial polysialic acid

Using reaction of moraprenyl phosphate with the known N-acetylsialyl chloride and the novel N,N-diacetylsialyl (Neu5Ac(2)) chloride α- and β-anomers of polyprenyl sialyl phosphate were synthesized for the first time. The α-selectivity dramatically increased when Neu5Ac(2) chloride was used as the glycosyl donor.

From glycosylation disorders to dolichol biosynthesis defects: a new class of metabolic diseases

Polyisoprenoid alcohols are membrane lipids that are present in every cell, conserved from archaea to higher eukaryotes. The most common form, alpha-saturated polyprenol or dolichol is present in all tissues and most organelle membranes of eukaryotic cells. Dolichol has a well defined role as a lipid carrier for the glycan precursor in the early stages of N-linked protein glycosylation, which is assembled in the endoplasmic reticulum of all eukaryotic cells. Other glycosylation processes including C- and O-mannosylation, GPI-anchor biosynthesis and O-glucosylation also depend on dolichol biosynthesis via the availability of dolichol-P-mannose and dolichol-P-glucose in the ER. The ubiquity of dolichol in cellular compartments that are not involved in glycosylation raises the possibility of additional functions independent of these protein post-translational modifications. The molecular basis of several steps involved in the synthesis and the recycling of dolichol and its derivatives is still unknown, which hampers further research into this direction. In this review, we summarize the current knowledge on structural and functional aspects of dolichol metabolites. We will describe the metabolic disorders with a defect in known steps of dolichol biosynthesis and recycling in human and discuss their pathogenic mechanisms. Exploration of the developmental, cellular and biochemical defects associated with these disorders will provide a better understanding of the functions of this lipid class in human.

Nogo-B receptor is necessary for cellular dolichol biosynthesis and protein N-glycosylation

Dolichol monophosphate (Dol-P) functions as an obligate glycosyl carrier lipid in protein glycosylation reactions. Dol-P is synthesized by the successive condensation of isopentenyl diphosphate (IPP), with farnesyl diphosphate catalysed by a cis-isoprenyltransferase (cis-IPTase) activity. Despite the recognition of cis-IPTase activity 40 years ago and the molecular cloning of the human cDNA encoding the mammalian enzyme, the molecular machinery responsible for regulating this activity remains incompletely understood. Here, we identify Nogo-B receptor (NgBR) as an essential component of the Dol-P biosynthetic machinery. Loss of NgBR results in a robust deficit in cis-IPTase activity and Dol-P production, leading to diminished levels of dolichol-linked oligosaccharides and a broad reduction in protein N-glycosylation. NgBR interacts with the previously identified cis-IPTase hCIT, enhances hCIT protein stability, and promotes Dol-P production. Identification of NgBR as a component of the cis-IPTase machinery yields insights into the regulation of dolichol biosynthesis.

A missense mutation in DHDDS, encoding dehydrodolichyl diphosphate synthase, is associated with autosomal-recessive retinitis pigmentosa in Ashkenazi Jews

Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal degenerations caused by mutations in at least 50 genes. Using homozygosity mapping in Ashkenazi Jewish (AJ) patients with autosomal-recessive RP (arRP), we identified a shared 1.7 Mb homozygous region on chromosome 1p36.11. Sequence analysis revealed a founder homozygous missense mutation, c.124A>G (p.Lys42Glu), in the dehydrodolichyl diphosphate synthase gene (DHDDS) in 20 AJ patients with RP of 15 unrelated families. The mutation was not identified in an additional set of 109 AJ patients with RP, in 20 AJ patients with other inherited retinal diseases, or in 70 patients with retinal degeneration of other ethnic origins. The mutation was found heterozygously in 1 out of 322 ethnically matched normal control individuals. RT-PCR analysis in 21 human tissues revealed ubiquitous expression of DHDDS. Immunohistochemical analysis of the human retina with anti-DHDDS antibodies revealed intense labeling of the cone and rod photoreceptor inner segments. Clinical manifestations of patients who are homozygous for the c.124A>G mutation were within the spectrum associated with arRP. Most patients had symptoms of night and peripheral vision loss, nondetectable electroretinographic responses, constriction of visual fields, and funduscopic hallmarks of retinal degeneration. DHDDS is a key enzyme in the pathway of dolichol, which plays an important role in N-glycosylation of many glycoproteins, including rhodopsin. Our results support a pivotal role of DHDDS in retinal function and may allow for new therapeutic interventions for RP.

A novel cerebello-ocular syndrome with abnormal glycosylation due to abnormalities in dolichol metabolism

Cerebellar hypoplasia and slowly progressive ophthalmological symptoms are common features in patients with congenital disorders of glycosylation type I. In a group of patients with congenital disorders of glycosylation type I with unknown aetiology, we have previously described a distinct phenotype with severe, early visual impairment and variable eye malformations, including optic nerve hypoplasia, retinal coloboma, congenital cataract and glaucoma. Some of the symptoms overlapped with the phenotype in other congenital disorders of glycosylation type I subtypes, such as vermis hypoplasia, anaemia, ichtyosiform dermatitis, liver dysfunction and coagulation abnormalities. We recently identified pathogenic mutations in the SRD5A3 gene, encoding steroid 5α-reductase type 3, in a group of patients who presented with this particular phenotype and a common metabolic pattern. Here, we report on the clinical, genetic and metabolic features of 12 patients from nine families with cerebellar ataxia and congenital eye malformations diagnosed with SRD5A3-congenital disorders of glycosylation due to steroid 5α-reductase type 3 defect. This enzyme is necessary for the reduction of polyprenol to dolichol, the lipid anchor for N-glycosylation in the endoplasmic reticulum. Dolichol synthesis is an essential metabolic step in protein glycosylation. The current defect leads to a severely abnormal glycosylation state already in the early phase of the N-glycan biosynthesis pathway in the endoplasmic reticulum. We detected high expression of SRD5A3 in foetal brain tissue, especially in the cerebellum, consistent with the finding of the congenital cerebellar malformations. Based on the overlapping clinical, biochemical and genetic data in this large group of patients with congenital disorders of glycosylation, we define a novel syndrome of cerebellar ataxia associated with congenital eye malformations due to a defect in dolichol metabolism.

SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder

N-linked glycosylation is the most frequent modification of secreted and membrane-bound proteins in eukaryotic cells, disruption of which is the basis of the congenital disorders of glycosylation (CDGs). We describe a new type of CDG caused by mutations in the steroid 5alpha-reductase type 3 (SRD5A3) gene. Patients have mental retardation and ophthalmologic and cerebellar defects. We found that SRD5A3 is necessary for the reduction of the alpha-isoprene unit of polyprenols to form dolichols, required for synthesis of dolichol-linked monosaccharides, and the oligosaccharide precursor used for N-glycosylation. The presence of residual dolichol in cells depleted for this enzyme suggests the existence of an unexpected alternative pathway for dolichol de novo biosynthesis. Our results thus suggest that SRD5A3 is likely to be the long-sought polyprenol reductase and reveal the genetic basis of one of the earliest steps in protein N-linked glycosylation.

Structure and synthesis of polyisoprenoids used in N-glycosylation across the three domains of life

N-linked protein glycosylation was originally thought to be specific to eukaryotes, but evidence of this post-translational modification has now been discovered across all domains of life: Eucarya, Bacteria, and Archaea. In all cases, the glycans are first assembled in a step-wise manner on a polyisoprenoid carrier lipid. At some stage of lipid-linked oligosaccharide synthesis, the glycan is flipped across a membrane. Subsequently, the completed glycan is transferred to specific asparagine residues on the protein of interest. Interestingly, though the N-glycosylation pathway seems to be conserved, the biosynthetic pathways of the polyisoprenoid carriers, the specific structures of the carriers, and the glycan residues added to the carriers vary widely. In this review we will elucidate how organisms in each basic domain of life synthesize the polyisoprenoids that they utilize for N-linked glycosylation and briefly discuss the subsequent modifications of the lipid to generate a lipid-linked oligosaccharide.

Mass spectrometry analysis of polyisoprenoids alcohols and carotenoids via ESI(Li(+))-MS/MS

Direct analysis of polyisoprenoid alcohols by electrospray ionization mass spectrometry (ESI-MS) often produces poor results requiring off-line time- and sample-consuming derivatization techniques. In this chapter, we describe a simple ESI-MS approach for the direct analysis of polyisoprenoid alcohols from biological samples. Lithium iodide is used to promote cationization by intense formation of [M+Li](+) adducts. Detection of polyisoprenoids with mass determination can thus be performed with high sensitivity (LOD near 100 pM), whereas characteristic collision-induced dissociations observed for both dolichols and polyprenols permit investigation of their structure. We also describe a simple ESI-MS approach for the direct analysis of carotenoids in biological samples using lithium iodide to promote their ionization and the analysis of several carotenoids as proof-of-principle cases. Finally, we applied ESI(Li(+))-MS and ESI(Li(+))-MS/MS to investigate the presence of carotenoids in Plasmodium falciparum.

Application of supercritical fluid chromatography to the analysis of hydrophobic metabolites

This review describes the usefulness of supercritical fluid chromatography (SFC) in the analysis of hydrophobic metabolites. The use of SFC for the analysis of naturally occurring polyprenols markedly improves the chromatographic resolution of polyprenol homologues and their geometric isomers as compared to conventional HPLC. Under optimized SFC conditions, individual homologues with 10-100-mers were separated. Furthermore, we established an analytical system for the fingerprinting and profiling of diverse lipids through the usage of SFC-MS. When a cyanopropylated silica gel packed column was used for the separation, 14 lipids were successfully detected, and the time required for analysis was less than 15 min. The use of an octadecylsilylated column for the separation depended on the differences in the fatty acid side chains. SFC is a useful separation technology for hydrophobic metabolites, which are difficult to be separated by HPLC.

Distribution of dolichol in the serum and relationships between serum dolichol levels and various laboratory test values

We examined the correlations between serum dolichol levels and laboratory test parameters in patients affected by disease, as well as the distribution of dolichol in sera from patients with hyperbetalipoproteinemia and hyperalphalipoproteinemia. Serum dolichol was evaluated by a reverse-phase HPLC method. After centrifugation, the serum dolichol found in healthy controls was mainly associated with medium-sized particles of the high-density lipoprotein (HDL) fraction. For patients with hyperbetalipoproteinemia, serum dolichol was also associated with the medium HDL fractions. However, for hyperalphalipoproteinemia patients the levels of large HDL and serum dolichol were increased, and serum dolichol was mainly associated with the large HDL fraction. On laboratory tests of components, the dolichol level was not correlated with the values for markers of the liver and biliary system, with the values of renal function markers, with creatine kinase activity, amylase activity or uric acid concentration, but was correlated with total cholesterol, HDL-cholesterol and apoA-I concentrations, and with lactate dehydrogenase (LDH) activity. These results suggest that serum dolichol exclusively localized in HDL, and in subpopulation, that in normocholesterolemia or hyperbeta-cholesterolemia is associated with HDL(3), which is small sized and high density HDL, however, that in hyperalphacholesterolemia is associated with HDL(2), which is large sized and lower density HDL.

Effects of oxidative stress on the Dolichol content of isolated rat liver cells

Dolichol, a long-chain polyisoprenoid broadly distributed in all tissues and cellular membranes with unknown function(s), might have a role in free radical metabolism [it accumulates in older tissues and decreases after CCl4 (in liver) or phenylhydrazine (in spleen and liver) administration]. The effects of the NADPH-ADP-Fe system on Dolichol levels in isolated hepatocytes were explored and the time-course of changes was compared with the release of MDA in the incubation medium and the decrease in CoQ 9 and 10 and Vitamin E levels. Results showed that the system increased lipid peroxidation and decreased Dolichol and CoQ levels in-parallel fashions and lowered Vitamin E levels with shorter latency. Meanwhile, no increase in dead cells and no Dolichol release in the medium were detected. In conclusion, an increase in oxidative stress possibly caused a rapid degradation of dolichol by the same (unknown) mechanism responsible for the breakdown of Ubiquinone isoprenoid chains.

Targeting the formation of the cell wall core of M. tuberculosis

Mycobacteria have a unique cell wall, which is rich in drug targets. The cell wall core consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide connecting them. The detailed structure of the cell wall core is largely, although not completely, understood and will be presented. The biosynthetic pathways of all three components reveal significant drug targets that are the basis of present drugs and/or have potential for new drugs. These pathways will be reviewed and include enzymes involved in polyisoprene biosynthesis, soluble arabinogalactan precursor production, arabinogalactan polymerization, fatty acid synthesis, mycolate maturation, and soluble peptidoglycan precursor formation. Information relevant to targeting all these enzymes will be presented in tabular form. Selected enzymes will then be discussed in more detail. It is thus hoped this chapter will aid in the selection of targets for new drugs to combat tuberculosis.

A defect in dolichol phosphate biosynthesis causes a new inherited disorder with death in early infancy

The following study describes the discovery of a new inherited metabolic disorder, dolichol kinase (DK1) deficiency. DK1 is responsible for the final step of the de novo biosynthesis of dolichol phosphate. Dolichol phosphate is involved in several glycosylation reactions, such as N-glycosylation, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, and C- and O-mannosylation. We identified four patients who were homozygous for one of two mutations (c.295T-->A [99Cys-->Ser] or c.1322A-->C [441Tyr-->Ser]) in the corresponding hDK1 gene. The residual activity of mutant DK1 was 2%-4% when compared with control cells. The mutated alleles failed to complement the temperature-sensitive phenotype of DK1-deficient yeast cells, whereas the wild-type allele restored the normal growth phenotype. Affected patients present with a very severe clinical phenotype, with death in early infancy. Two of the patients died from dilative cardiomyopathy.

Electrospray ionization mass spectrometry analysis of polyisoprenoid alcohols via Li+ cationization

Direct analysis of polyisoprenoids by electrospray ionization mass spectrometry (ESI-MS) often produces poor results requiring off-line time and sample-consuming derivatization techniques. We describe a simple ESI-MS approach for the direct analysis of polyisoprenoids using several dolichols and polyprenols with different chain sizes as proof-of-principle cases. Lithium iodide is used to promote cationization by intense formation of [M+Li]+ adducts. Thus, detection of polyisoprenoids with mass determination can be performed with high sensitivity (limit of detection [LOD] approximately 100 rhoM), whereas characteristic collision-induced dissociations observed for both dolichols and polyprenols permit investigation of their structure. Using ESI(Li+)-MS and ESI(Li+)-MS/MS analysis, we screened for polyprenol products of an octaprenyl pyrophosphate synthase of Plasmodium falciparum and dolichols in a complex mixture of compounds produced by Leishmania amazonensis and P. falciparum.

Posttranslational protein modification in Archaea

One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

Accumulation of Dolichol in Older Tissues Satisfies the Proposed Criteria To Be Qualified a Biomarker of Aging

Criteria for defining biomarkers have been suggested. Accumulation of dolichol in tissues of older animals meets the following criteria: (a) levels of dolichol exhibit a quantitative correlation with age in all tissues and are not altered by several age-dependent diseases in the same direction as that of aging; (b) accumulation is not secondary to metabolic changes of aging and is altered appropriately by factors that modulate the aging rate like caloric restriction and physical exercise; (c) biomarker is applicable to different tissues across mammalian species, including humans, and to trisomy 21 and its hypothalamic digoxin-mediated model. Reliable changes in tissue dolichol levels are seen in relatively short intervals of time compared to over a life span, and levels can be tested on a small amount of tissue without causing death of the animal. In this article, we show applications to the study of host-graft interaction and detection of gender-related differences in biological age, and we discuss mechanism(s) of accumulation.

Chronic ethanol treatment: dolichol and retinol distribution in isolated rat liver cells

The aim of this study was to use chronic ethanol intoxication for 2 and 4 months as a means of studying the distribution of dolichol and retinol in isolated rat liver parenchymal cells, Kupffer cells, sinusoidal endothelial cells, and two subfractions of hepatic stellate cells: Ito 1 and Ito 2. Dolichol and retinol were studied in two batches of rats: on normal nutrition and after a load of vitamin A given 3 d before sacrifice. New observations reported are: (i) on normal nutrition, after 2 months of treatment, dolichol in HC seems to be the first target of chronic ethanol, while retinol is the first target in hepatic stellate cells; (ii) the various types of liver cells are differently affected by chronic ethanol, which highlights the importance of studying each type of sinusoidal cell; (iii) a load of vitamin A given when the damage has already occurred restores dolichol content in HC while retinol decreases; and, (iv) a link between dolichol and vitamin A metabolism might be supposed after the load of vitamin A: the percentage distribution of dolichol with 18 isoprene units (Dolichol -18) increases in all the control cells but decreases after chronic ethanol treatment. A different role of this dolichol and/or a different compartmentalization within the cell need to be further investigated.

Influence of chronic ethanol consumption on toxic effects of 1,2-dichloroethane: glycolipoprotein retention and impairment of dolichol concentration in rat liver microsomes and Golgi apparatus

Our previous investigations demonstrated that 1,2-dichloroethane (DCE) and chronic ethanol treatment separately are able to impair glycoprotein metabolism and secretion, and reduce dolichol concentration in liver membranes. The purpose of this study was to investigate whether chronic ethanol consumption can induce potentiation of rat liver damage due to DCE haloalkane used in several chemical processes and in agriculture. Rats were given 36% of their total energy as ethanol in the Lieber-DeCarli liquid diet for 8 weeks (CH group). The pair-fed control group received an isocaloric amount of dextrine-maltose (PF group). "In vitro" experiments: the DCE (6.5 mM) treatment of isolated hepatocytes from CH rats enhanced glycoprotein retention and further reduced glycoprotein secretion and 14C-glucosamine incorporation compared to the hepatocytes from CH or from PF and DCE treated rats. "In vivo" experiments: a marked decrease of dolichol concentration in microsomes (in which dolichyl phosphate is rate-limiting for the initial glycosylation of protein) and in Golgi membranes (in which total dolichol is very important for membrane permeability, fluidity and vesicle fusion) was observed in CH rats acutely treated with 628 mg/kg bw of DCE (CH+DCE) compared with CH or PF+DCE treated rats. These data suggest that chronic ethanol consumption increases DCE liver toxicity by affecting protein glycosylation processes and impairing glycolipoprotein secretion, with a concomitant retention at the level of the Golgi apparatus.

Dolichol levels in younger and older rat hearts heterotopically transplanted in younger recipients

Dolichol (D) levels increase dramatically in older tissue. An understanding of the exchangeability of D between tissues may be essential in order to understand the mechanism of the abnormal accumulation associated with aging. The question was investigated by the use of organ transplantation. D-poor hearts donated by 3-mon-old and D-rich by 22-mon-old male Lewis rats were transplanted heterotopically in 3-mon-old syngenic recipients, whose peripheral tissues and liver were poor in D. Native and transplanted hearts were taken 7 and 21 d after surgery. Native hearts of 3-mon- and 22-mon-old male Lewis rats served as control. D concentration and quantity were higher in older than in younger native hearts as expected. In the transplanted hearts, the quantity of D was unchanged, irrespective of the age of the donor and of the time of transplantation, whereas D concentration increased because of the remarkable disuse atrophy. No changes in D were observed in recipients' tissues. It is concluded that dolichol is not redistributed via circulation from the transplanted heart to the tissues and liver of the younger recipient.

Transmembrane movement of dolichol linked carbohydrates during N-glycoprotein biosynthesis in the endoplasmic reticulum

The process of N-linked glycosylation of secretory proteins is characterized by enzymatic reactions occurring on both sides of the endoplasmic reticulum (ER) membrane. On either side multiple glycosyltransferases participate in the stepwise addition of monosaccharides to core oligosaccharide unit that is attached to the lipid carrier dolichyl pyrophosphate. Cytoplasm-oriented glycosyltransferases use nucleotide-activated sugars as substrates, whereas lumen-oriented transferases that act later in the pathway make use of dolichyl phosphate-linked monosaccharides. The completely assembled core oligosaccharide is transferred to proteins on the lumenal side of the ER. The topological organization of this biosynthetic pathway requires the translocation of lipid-linked mono- and oligo-saccharides across the ER membrane. The transfer of the substrates and intermediates depend on specific translocators, i.e. so called flippases.

Lipid protein interactions: the assembly of CD1d1 with cellular phospholipids occurs in the endoplasmic reticulum

CD1d1 is a member of a family of lipid Ag-presenting molecules. The cellular ligands associated with CD1d1 were isolated and characterized by biochemical means as an approach to elucidate the mechanism by which CD1 molecules assemble in vivo. Natural ligands of mouse CD1d1 included cellular phosphatidylinositol and phosphatidylinositol-glycans that are synthesized in the endoplasmic reticulum. Further biochemical data revealed that the two CD1d1 mutants, one defective in recycling from-and-to the plasma membrane and the other in efficiently negotiating the secretory pathway, associated with phosphatidylinositol. Thus phosphatidylinositol associated with CD1d1 in the early secretory pathway. Phosphatidylinositol also associated with CD1d1 in Pig-A-deficient cells that are defective in the first glycosylation step of glycosylphosphatidylinositol biosynthesis. Moreover, cellular phosphatidylinositol-glycans are not Valpha14Jalpha15 natural T cell Ags. Therefore, we predict that cellular lipids occlude the hydrophobic Ag-binding groove of CD1 during assembly until they are exchanged for a glycolipid Ag(s) within the recycling compartment for display on the plasma membrane. In this manner, cellular lipids might play a chaperone-like role in the assembly of CD1d1 in vivo, akin to the function of invariant chain in MHC class II assembly.

Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis

The Escherichia coli undecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the betaA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four beta-strands (betaA-betaB-betaD-betaC) and two helices (alpha2 and alpha3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C(70) polymer rather than the C(55) polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C(30) intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C(55) product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C(55) product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25-200-fold decrease in k(cat) values. W75A showed an 8-fold increase of the FPP K(m) value, and 22-33-fold increases in the IPP K(m) values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release.

Effects of ageing and increased haemolysis on the levels of dolichol in rat spleen

Dolichol is a long-chain polyisoprenoid. No enzyme pathway for dolichol degradation was discovered. Dolichol accumulates in human and rodent tissues during ageing. Red blood cells contain a larger amount of dolichol and red blood cell life span is shorter in older rats. The effects of age and of the load of dolichol from red blood cell degradation on the ageing-associated accumulation of dolichol in spleen were studied in 2, 6, 12, 18 and 24 month-old male Sprague Dawley rats fed ad libitum (AL) or on an anti-ageing dietary regimen (EOD). Tissue dolichol was extracted and assayed by HPLC [J. Gerontol. 53A (1998) B87]. Levels of dolichol increased in spleen, liver, kidney and muscle in parallel fashion from the age of 2 to 12 months. Unexpectedly, spleen dolichol decreased in older rats whereas liver, kidney and muscle dolichol increased significantly. The effects of haemolysis on spleen dolichol were tested by the administration of phenylhydrazine. Results show that haemolysis does not increase, but rather decreases the levels of dolichol in erythroclastic organs. It is concluded that the levels of spleen dolichol may decrease in the absence of any known enzymatic degradative pathway if the spleen and its resident phagocytes are forced to cope with a higher number of red blood cells to be cleared. Free-radical mediated decomposition of dolichol by phagocytic cells during erythrophagocytosis might be involved in the process.