Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota

Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.

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Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase fromThermoplasma acidophilumin complex with the substratesn-glycerol 1-phosphate

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x19007453 ◽

2019 ◽

Vol 75 (7) ◽

pp. 470-479 ◽

Cited By ~ 1

Author(s):

Naoki Nemoto ◽

Ken-ichi Miyazono ◽

Masaru Tanokura ◽

Akihiko Yamagishi

Keyword(s):

Crystal Structure ◽

Simulation Analysis ◽

Membrane Lipid ◽

Dynamics Simulation ◽

Substrate Uptake ◽

Recognition Mechanism ◽

Lipid Molecule ◽

Group I ◽

Group Ii ◽

Phosphate Synthase

(S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation betweensn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS fromThermoplasma acidophilum(TaGGGPS) was determined at 2.35 Å resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (α3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (fromMethanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the β2–α2, α3* and α5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS.

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Lipid Remodeling Confers Osmotic Stress Tolerance to Embryogenic Cells during Cryopreservation

International Journal of Molecular Sciences ◽

10.3390/ijms22042174 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2174

Author(s):

Liang Lin ◽

Junchao Ma ◽

Qin Ai ◽

Hugh W. Pritchard ◽

Weiqi Li ◽

...

Keyword(s):

Lipid Metabolism ◽

Technology Development ◽

Membrane Lipids ◽

Species Conservation ◽

Membrane Lipid ◽

Cell Integrity ◽

Embryogenic Cells ◽

Osmotic Stress Tolerance ◽

Lipid Species ◽

Magnolia Officinalis

Plant species conservation through cryopreservation using plant vitrification solutions (PVS) is based in empiricism and the mechanisms that confer cell integrity are not well understood. Using ESI-MS/MS analysis and quantification, we generated 12 comparative lipidomics datasets for membranes of embryogenic cells (ECs) of Magnolia officinalis during cryogenic treatments. Each step of the complex PVS-based cryoprotocol had a profoundly different impact on membrane lipid composition. Loading treatment (osmoprotection) remodeled the cell membrane by lipid turnover, between increased phosphatidic acid (PA) and phosphatidylglycerol (PG) and decreased phosphatidylcholine (PC) and phosphatidylethanolamine (PE). The PA increase likely serves as an intermediate for adjustments in lipid metabolism to desiccation stress. Following PVS treatment, lipid levels increased, including PC and PE, and this effectively counteracted the potential for massive loss of lipid species when cryopreservation was implemented in the absence of cryoprotection. The present detailed cryobiotechnology findings suggest that the remodeling of membrane lipids and attenuation of lipid degradation are critical for the successful use of PVS. As lipid metabolism and composition varies with species, these new insights provide a framework for technology development for the preservation of other species at increasing risk of extinction.

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Impact of Membrane Lipids on UapA and AzgA Transporter Subcellular Localization and Activity in Aspergillus nidulans

Journal of Fungi ◽

10.3390/jof7070514 ◽

2021 ◽

Vol 7 (7) ◽

pp. 514

Author(s):

Mariangela Dionysopoulou ◽

George Diallinas

Keyword(s):

Plasma Membrane ◽

Subcellular Localization ◽

Aspergillus Nidulans ◽

Membrane Lipids ◽

Membrane Lipid ◽

Lipid Biosynthesis ◽

Transport Kinetics ◽

Negative Effect ◽

And Function

Recent biochemical and biophysical evidence have established that membrane lipids, namely phospholipids, sphingolipids and sterols, are critical for the function of eukaryotic plasma membrane transporters. Here, we study the effect of selected membrane lipid biosynthesis mutations and of the ergosterol-related antifungal itraconazole on the subcellular localization, stability and transport kinetics of two well-studied purine transporters, UapA and AzgA, in Aspergillus nidulans. We show that genetic reduction in biosynthesis of ergosterol, sphingolipids or phosphoinositides arrest A. nidulans growth after germling formation, but solely blocks in early steps of ergosterol (Erg11) or sphingolipid (BasA) synthesis have a negative effect on plasma membrane (PM) localization and stability of transporters before growth arrest. Surprisingly, the fraction of UapA or AzgA that reaches the PM in lipid biosynthesis mutants is shown to conserve normal apparent transport kinetics. We further show that turnover of UapA, which is the transporter mostly sensitive to membrane lipid content modification, occurs during its trafficking and by enhanced endocytosis, and is partly dependent on autophagy and Hect-type HulARsp5 ubiquitination. Our results point out that the role of specific membrane lipids on transporter biogenesis and function in vivo is complex, combinatorial and transporter-dependent.

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Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 fromXanthomonas campestrisreveals a novel quaternary structure assembled by five four-helix bundles

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21105 ◽

2006 ◽

Vol 65 (3) ◽

pp. 783-786 ◽

Cited By ~ 6

Author(s):

Li-Ying Lin ◽

Chung-Lun Ching ◽

Ko-Hsin Chin ◽

Shan-Ho Chou ◽

Nei-Li Chan

Keyword(s):

Crystal Structure ◽

Quaternary Structure ◽

Cytosolic Protein

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The first crystal structure of the peptidase domain of the U32 peptidase family

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715019549 ◽

2015 ◽

Vol 71 (12) ◽

pp. 2505-2512 ◽

Cited By ~ 4

Author(s):

Magdalena Schacherl ◽

Angelika A. M. Montada ◽

Elena Brunstein ◽

Ulrich Baumann

Keyword(s):

Crystal Structure ◽

Catalytic Mechanism ◽

Quaternary Structure ◽

Catalytic Domain ◽

Three Dimensional ◽

Zinc Ion ◽

Crystal Structure Analysis ◽

Dimensional Structure ◽

Sequence Motifs ◽

Conserved Sequence

The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins fromHelicobacterandSalmonella. The first crystal structure analysis of a U32 catalytic domain fromMethanopyrus kandleri(genemk0906) reveals a modified (βα)8TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to aStrep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.

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Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli

Structure ◽

10.1016/s0969-2126(99)80109-9 ◽

1999 ◽

Vol 7 (7) ◽

pp. 865-875 ◽

Cited By ~ 79

Author(s):

Igor A Shumilin ◽

Robert H Kretsinger ◽

Ronald H Bauerle

Keyword(s):

Crystal Structure ◽

Escherichia Coli ◽

Phosphate Synthase

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Membrane Lipids and Maximum Lifespan in Clownfish

10.21203/rs.3.rs-250784/v1 ◽

2021 ◽

Author(s):

PEDRO FRANCISCO ALMAIDA PAGÁN ◽

Alejandro Lucas-Sanchez ◽

Antonio Martinez-Nicolas ◽

Eva Terzibasi ◽

Maria Angeles Rol de Lama ◽

...

Keyword(s):

Lipid Composition ◽

Potential Model ◽

Membrane Lipids ◽

Membrane Lipid ◽

Maximum Lifespan ◽

Homeoviscous Adaptation ◽

Theory Of Aging ◽

Peroxidation Index ◽

Membrane Peroxidation ◽

Contradictory Data

Abstract The longevity-homeoviscous adaptation (LHA) theory of aging states that lipid composition of cell membranes is linked to metabolic rate and lifespan, which has been widely shown in mammals and birds but not sufficiently in fish. In this study, two species of the genus Amphiprion (A. percula and A. clarkii, with estimated maximum lifespan potentials [MLSP] of 30 and 9-16 years, respectively) and the damselfish Chromis viridis (estimated MLSP of 1-2 years) were chosen to test the LHA theory of aging in a potential model of exceptional longevity. Brain, livers and samples of skeletal muscle were collected for lipid analyses and integral part in the computation of membrane peroxidation indexes (PIn) from phospholipid (PL) fractions and PL fatty acid composition. When only the two anemonefish were compared, results pointed to the existence of a negative correlation between membrane PIn value and maximum life expectancy, well in line with the predictions from the LHA theory of aging. Nevertheless, contradictory data were obtained when the two clownfish were compared to the shorter-lived C. viridis. This results along with those obtained in previous studies on fish denote that the magnitude (and sometimes the direction) of the differences observed in membrane lipid composition and peroxidation index with MLSP cannot explain alone the diversity in longevity found among fishes.

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The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714023827 ◽

2014 ◽

Vol 70 (12) ◽

pp. 3212-3225 ◽

Cited By ~ 16

Author(s):

Tiila-Riikka Kiema ◽

Rajesh K. Harijan ◽

Malgorzata Strozyk ◽

Toshiyuki Fukao ◽

Stefan E. H. Alexson ◽

...

Keyword(s):

Crystal Structure ◽

Reaction Mechanism ◽

Active Site ◽

Quaternary Structure ◽

Fatty Acyl ◽

Physiological Importance ◽

Loop Domain ◽

Solution Studies ◽

Hydrolysis Of ◽

Insight Into

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

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Responses of Unsaturated Fatty Acid in Membrane Lipid and Antioxidant Enzymes to Chilling Stress in Sweet Sorghum (Sorghum bicolor (L.) Moench) Seedling

Journal of Agricultural Science ◽

10.5539/jas.v8n9p71 ◽

2016 ◽

Vol 8 (9) ◽

pp. 71 ◽

Cited By ~ 3

Author(s):

Yuanyuan Guo ◽

Shanshan Liu ◽

Zhen Yang ◽

Shanshan Tian ◽

Na Sui

Keyword(s):

Antioxidant Enzymes ◽

Fatty Acid ◽

Sorghum Bicolor ◽

Unsaturated Fatty Acid ◽

Sweet Sorghum ◽

Membrane Lipids ◽

Chilling Stress ◽

Fatty Acid Content ◽

Membrane Lipid ◽

Protective Enzyme

Low temperature is a major factor limiting the productivity and geographical distribution of many plant species. In this study, we investigated the effect of chilling stress (10 oC) on seedling growth in two sweet sorghum (Sorghum bicolor (L.) Moench) inbred lines (M-81E and Roma). Results showed that the chilling resistance of M-81E was higher than that of Roma. The Fv/Fm in leaves of M-81E decreased less than that of Roma during chilling stress. After 24 h of chilling stress, the Fv/Fm of M-81E and Roma decreased by 24.3 and 45.8%, respectively. Fo was also affected significantly during chilling stress. Malondialdehyde (MDA), an indicator of lipid peroxidation caused by ROS, increased during chilling stress. The contents of MDA increased less in leaves of M-81E than that in Roma under chilling stress. The antioxidant enzymes (SOD and APX) activity of M-81E was higher than those of Roma during chilling stress. The unsaturated fatty acid content and the double bond index (DBI) of major membrane lipids of MGDG, DGDG, SQDG, PC, PE and PG of M-81E significantly increased after 24 h of chilling treatment (10 oC). The DBI of MGDG, DGDG, SQDG, PC and PG of Roma significantly decreased. These results showed that the chilling tolerance of M-81E was higher than that of Roma by increasing of unsaturated fatty acid in membrane lipid and powerful protective enzyme system at seedling stage.

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