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Journal articles on the topic 'Biogenetic intermediate'

Author: Grafiati

Published: 5 June 2025

Last updated: 15 July 2025

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1

Tietze, Lutz F., Stephan Henke, and Christoph Bärtels. "Biomimetic transformations of the biogenetic key intermediate secologanin." Tetrahedron 44, no. 23 (1988): 7145–53. http://dx.doi.org/10.1016/s0040-4020(01)86082-8.

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2

Gassner, Cemena, Ronny Hesse, Arndt W. Schmidt, and Hans-Joachim Knölker. "Total synthesis of the cyclic monoterpenoid pyrano[3,2-a]carbazole alkaloids derived from 2-hydroxy-6-methylcarbazole." Org. Biomol. Chem. 12, no. 33 (2014): 6490–99. http://dx.doi.org/10.1039/c4ob01151a.

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3

Fukuzawa, Akio, Yasunori Takasugi, and Akio Murai. "Prelaureatin, a new biogenetic key intermediate isolated from Laurencia nipponica." Tetrahedron Letters 32, no. 40 (1991): 5597–98. http://dx.doi.org/10.1016/0040-4039(91)80093-l.

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4

Guardia, Juan J., Antonio Fernández, José Justicia, et al. "Unprecedented Elimination Reactions of Cyclic Aldols: A New Biosynthetic Pathway toward the Taiwaniaquinoid Skeleton." Molecules 28, no. 4 (2023): 1524. http://dx.doi.org/10.3390/molecules28041524.

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The acid treatment of 6,7-seco-abietane dialdehydes gives, in high yield, the corresponding derivatives with the 4a-methyltetrahydrofluorene skeleton of taiwaniaquinoids. A mechanism involving the elimination of formic acid from the cyclic aldol intermediate is proposed here. This process can be postulated as a new biogenetic pathway from abietane diterpenes to taiwaniaquinoids. Using this novel reaction, the first enantiospecific synthesis of bioactive natural cupresol and taxodal has been obtained.

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5

Liu, Zhang-Bin, Yosuke Matsuo, Yoshinori Saito, Yong-Lin Huang, Dian-Peng Li, and Takashi Tanaka. "Identification of Unstable Ellagitannin Metabolites in the Leaves of Quercus dentata by Chemical Derivatization." Molecules 28, no. 3 (2023): 1246. http://dx.doi.org/10.3390/molecules28031246.

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The identification of unstable metabolites of ellagitannins having ortho-quinone structures or reactive carbonyl groups is important to clarify the biosynthesis and degradation of ellagitannins. Our previous studies on the degradation of vescalagin, a major ellagitannin of oak young leaves, suggested that the initial step of the degradation is regioselective oxidation to generate a putative quinone intermediate. However, this intermediate has not been identified yet. In this study, young leaves of Quercus dentata were extracted with 80% acetonitrile containing 1,2-phenylenediamine to trap unstable ortho-quinone metabolites, and subsequent chromatographic separation afforded a phenazine derivative of the elusive quinone intermediate of vescalagin. In addition, phenylenediamine adducts of liquidambin and dehydroascorbic acid were obtained, which is significant because liquidambin is a possible biogenetic precursor of C-glycosidic ellagitannins and ascorbic acid participates in the production of another C-glycosidic ellagitannin in matured oak leaves.

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6

Takayama, Hiromitsu, Tomotake Ichikawa, Mariko Kitajima, Norio Aimi, Dazy Lopez, and Maribel G. Nonato. "A new alkaloid, pandanamine; finding of an anticipated biogenetic intermediate in Pandanus amaryllifolius Roxb." Tetrahedron Letters 42, no. 16 (2001): 2995–96. http://dx.doi.org/10.1016/s0040-4039(01)00339-2.

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7

Takayama, Hiromitsu, Tomotake Ichikawa, Mariko Kitajima, Norio Aimi, Dazy Lopez, and Maribel G. Nonato. "ChemInform Abstract: A New Alkaloid, Pandanamine; Finding of an Anticipated Biogenetic Intermediate in Pandanus amaryllifolius Roxb." ChemInform 32, no. 29 (2010): no. http://dx.doi.org/10.1002/chin.200129184.

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8

Hu, Wei-Min, and Jun Wu. "Protoxylogranatin B, a Key Biosynthetic Intermediate from Xylocarpus granatum: Suggesting an Oxidative Cleavage Biogenetic Pathway to Limonoid." Open Natural Products Journal 3, no. 1 (2010): 1–5. http://dx.doi.org/10.2174/1874848101003010001.

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9

Morimoto, Yoshiki, and Chiho Yokoe. "Total synthesis of haliclamine A, a macrocyclic marine alkaloid related to the key biogenetic intermediate of manzamines." Tetrahedron Letters 38, no. 52 (1997): 8981–84. http://dx.doi.org/10.1016/s0040-4039(97)10368-9.

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10

Albrecht, Wolfgang, та Roland Tressl. "Studies on the Biosynthesis of γ–Decalactone in Sporobolomyces odorus". Zeitschrift für Naturforschung C 45, № 3-4 (1990): 207–16. http://dx.doi.org/10.1515/znc-1990-3-411.

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Abstract Incubation of racemic ethyl [2,2-2H2]-(E)-3,4-epoxydecanoate and the corresponding acid with intact cells of Sporobolomyces odorus led to the formation of deuterium labeled γ-decalaetone. The detection of labeled 2-decen-4-olide and 4-oxodecanoic acid made it possible to propose the biogenetic sequence leading to γ-decalactone. The determination of the en antiomeric ratio of the lactone revealed an unspecific metabolism of the precursor. In contrast to the (E)-isomer, after administration of ethyl [5,6-2H2]-(Z)-3,4-epoxydeeanoate no transformation could be detected. These results indicate that (E)-3,4-epoxydecanoic acid, formed from (E)-3-decenoyl-CoA , an intermediate of the β-oxidation of linoleic acid, is the genuine precursor in the biosynthesis of γ-decalactone.

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11

MORIMOTO, Y., and C. YOKOE. "ChemInform Abstract: Total Synthesis of Haliclamine A, a Macrocyclic Marine Alkaloid Related to the Key Biogenetic Intermediate of Manzamines." ChemInform 29, no. 15 (2010): no. http://dx.doi.org/10.1002/chin.199815224.

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12

Le Bivic, A., A. Quaroni, B. Nichols, and E. Rodriguez-Boulan. "Biogenetic pathways of plasma membrane proteins in Caco-2, a human intestinal epithelial cell line." Journal of Cell Biology 111, no. 4 (1990): 1351–61. http://dx.doi.org/10.1083/jcb.111.4.1351.

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We studied the sorting and surface delivery of three apical and three basolateral proteins in the polarized epithelial cell line Caco-2, using pulse-chase radiolabeling and surface domain-selective biotinylation (Le Bivic, A., F. X. Real, and E. Rodriguez-Boulan. 1989. Proc. Natl. Acad. Sci. USA. 86:9313-9317). While the basolateral proteins (antigen 525, HLA-I, and transferrin receptor) were targeted directly and efficiently to the basolateral membrane, the apical markers (sucrase-isomaltase [SI], aminopeptidase N [APN], and alkaline phosphatase [ALP]) reached the apical membrane by different routes. The large majority (80%) of newly synthesized ALP was directly targeted to the apical surface and the missorted basolateral pool was very inefficiently transcytosed. SI was more efficiently targeted to the apical membrane (greater than 90%) but, in contrast to ALP, the missorted basolateral pool was rapidly transcytosed. Surprisingly, a distinct peak of APN was detected on the basolateral domain before its accumulation in the apical membrane; this transient basolateral pool (at least 60-70% of the enzyme reaching the apical surface, as measured by continuous basal addition of antibodies) was efficiently transcytosed. In contrast with their transient basolateral expression, apical proteins were more stably localized on the apical surface, apparently because of their low endocytic capability in this membrane. Thus, compared with two other well-characterized epithelial models, MDCK cells and the hepatocyte, Caco-2 cells have an intermediate sorting phenotype, with apical proteins using both direct and indirect pathways, and basolateral proteins using only direct pathways, during biogenesis.

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13

Piovan, Anna, Raffaella Filippini, and Gabbriella Innocenti. "Coumarin Compounds in Coronilla scorpioides Callus Cultures." Natural Product Communications 9, no. 4 (2014): 1934578X1400900. http://dx.doi.org/10.1177/1934578x1400900415.

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Coronilla scorpioides (L.) W.D.J. Koch is known for producing several compounds with pharmaceutical interest, such as the hydroxycoumarins umbelliferone, scopoletin and daphnoretin, the dihydrofuranocoumarin marmesin, and the furocoumarin psoralen. In vitro callus cultures of C. scorpioides were established from hypocotyl, leaf, stem internode and root explants in order to evaluate the possibility of in vitro production of these active secondary metabolites. Calli were obtained with high frequency from all the explant types both in B5 and MS medium. However, after the third subculture, B5 medium, giving the best results, was selected for subsequent transfers. Homogeneous calli were kept either in darkness or in light. Chemical analyses showed that scopoletin and the intermediate products of the biogenetic pathway of psoralen, umbelliferone and marmesin, were always present in the calli and excreted into the media, while daphnoretin was never detected. Light seems to be a prerequisite for psoralen biosynthesis. Root-derived calli produced a significantly higher amount of psoralen (137.5 μg g−1 DW). Principal component analysis showed that umbelliferone, marmesin and psoralen contents are related to variables associated with different explant types.

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14

Yoshihara, Minoru, Cai Yang, Cui Zheng, et al. "Chemical conversion of (4S,5S)-(+)-germacrone 4,5-epoxide, a plausible biogenetic intermediate found in the essential oil of Zedoariae rhizoma from Yakushima, Japan." CHEMICAL & PHARMACEUTICAL BULLETIN 34, no. 1 (1986): 434–37. http://dx.doi.org/10.1248/cpb.34.434.

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15

Nuhant, Philippe, Marc David, Thomas Pouplin, Bernard Delpech та Christian Marazano. "α,α‘-Annulation of 2,6-Prenyl-Substituted Cyclohexanone Derivatives with Malonyl Chloride: Application to a Short Synthesis of (±)-Clusianone. Formation and Rearrangement of a Biogenetic-Like Intermediate". Organic Letters 9, № 2 (2007): 287–89. http://dx.doi.org/10.1021/ol062736s.

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16

Luis, Javier G., Lucía S. Andrés, and Winston Q. Fletcher. "Chemical evidence for the participation of a perepoxide intermediate in the reaction of singlet oxygen with mono-olefins in relationship with the biogenetic pathway to highly oxidized abietane diterpenes." Tetrahedron Letters 35, no. 1 (1994): 179–82. http://dx.doi.org/10.1016/0040-4039(94)88195-2.

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17

El Gamal, Abrahim, Vinayak Agarwal, Stefan Diethelm, et al. "Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase–thioesterase enzyme pair." Proceedings of the National Academy of Sciences 113, no. 14 (2016): 3797–802. http://dx.doi.org/10.1073/pnas.1519695113.

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Halogenated pyrroles (halopyrroles) are common chemical moieties found in bioactive bacterial natural products. The halopyrrole moieties of mono- and dihalopyrrole-containing compounds arise from a conserved mechanism in which a proline-derived pyrrolyl group bound to a carrier protein is first halogenated and then elaborated by peptidic or polyketide extensions. This paradigm is broken during the marine pseudoalteromonad bacterial biosynthesis of the coral larval settlement cue tetrabromopyrrole (1), which arises from the substitution of the proline-derived carboxylate by a bromine atom. To understand the molecular basis for decarboxylative bromination in the biosynthesis of 1, we sequenced two Pseudoalteromonas genomes and identified a conserved four-gene locus encoding the enzymes involved in its complete biosynthesis. Through total in vitro reconstitution of the biosynthesis of 1 using purified enzymes and biochemical interrogation of individual biochemical steps, we show that all four bromine atoms in 1 are installed by the action of a single flavin-dependent halogenase: Bmp2. Tetrabromination of the pyrrole induces a thioesterase-mediated offloading reaction from the carrier protein and activates the biosynthetic intermediate for decarboxylation. Insights into the tetrabrominating activity of Bmp2 were obtained from the high-resolution crystal structure of the halogenase contrasted against structurally homologous halogenase Mpy16 that forms only a dihalogenated pyrrole in marinopyrrole biosynthesis. Structure-guided mutagenesis of the proposed substrate-binding pocket of Bmp2 led to a reduction in the degree of halogenation catalyzed. Our study provides a biogenetic basis for the biosynthesis of 1 and sets a firm foundation for querying the biosynthetic potential for the production of 1 in marine (meta)genomes.

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18

Schaefer, Laura, William C. Uicker, Catherine Wicker-Planquart, Anne-Emmanuelle Foucher, Jean-Michel Jault, and Robert A. Britton. "Multiple GTPases Participate in the Assembly of the Large Ribosomal Subunit in Bacillus subtilis." Journal of Bacteriology 188, no. 23 (2006): 8252–58. http://dx.doi.org/10.1128/jb.01213-06.

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ABSTRACT GTPases have been demonstrated to be necessary for the proper assembly of the ribosome in bacteria and eukaryotes. Here, we show that the essential GTPases YphC and YsxC are required for large ribosomal subunit biogenesis in Bacillus subtilis. Sucrose density gradient centrifugation of large ribosomal subunits isolated from YphC-depleted cells and YsxC-depleted cells indicates that they are similar to the 45S intermediate previously identified in RbgA-depleted cells. The sedimentation of the large-subunit intermediate isolated from YphC-depleted cells was identical to the intermediate found in RbgA-depleted cells, while the intermediate isolated from YsxC-depleted cells sedimented slightly slower than 45S, suggesting that it is a novel intermediate. Analysis of the protein composition of the large-subunit intermediates isolated from either YphC-depleted cells or YsxC-depleted cells indicated that L16 and L36 are missing. Purified YphC and YsxC are able to interact with the ribosome in vitro, supporting a direct role for these two proteins in the assembly of the 50S subunit. Our results indicate that, as has been demonstrated for Saccharomyces cerevisiae ribosome biogenesis, bacterial 50S ribosome assembly requires the function of multiple essential GTPases.

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19

Ruiz, Natividad. "Lipid Flippases for Bacterial Peptidoglycan Biosynthesis." Lipid Insights 8s1 (January 2015): LPI.S31783. http://dx.doi.org/10.4137/lpi.s31783.

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The biosynthesis of cellular polysaccharides and glycoconjugates often involves lipid-linked intermediates that need to be translocated across membranes. Essential pathways such as N-glycosylation in eukaryotes and biogenesis of the peptidoglycan (PG) cell wall in bacteria share a common strategy where nucleotide-sugars are used to build a membrane-bound oligosaccharide precursor that is linked to a phosphorylated isoprenoid lipid. Once made, these lipid-linked intermediates must be translocated across a membrane so that they can serve as substrates in a different cellular compartment. How translocation occurs is poorly understood, although it clearly requires a transporter or flippase. Identification of these transporters is notoriously difficult, and, in particular, the identity of the flippase of lipid II, an intermediate required for PG biogenesis, has been the subject of much debate. Here, I will review the body of work that has recently fueled this controversy, centered on proposed flippase candidates FtsW, MurJ, and AmJ.

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20

Khalimonchuk, Oleh, Megan Bestwick, Brigitte Meunier, Talina C. Watts, and Dennis R. Winge. "Formation of the Redox Cofactor Centers during Cox1 Maturation in Yeast Cytochrome Oxidase." Molecular and Cellular Biology 30, no. 4 (2009): 1004–17. http://dx.doi.org/10.1128/mcb.00640-09.

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ABSTRACT The biogenesis of cytochrome c oxidase initiates with synthesis and maturation of the mitochondrion-encoded Cox1 subunit prior to the addition of other subunits. Cox1 contains redox cofactors, including the low-spin heme a center and the heterobimetallic heme a 3:CuB center. We sought to identify the step in the maturation of Cox1 in which the redox cofactor centers are assembled. Newly synthesized Cox1 is incorporated within one early assembly intermediate containing Mss51 in Saccharomyces cerevisiae. Subsequent Cox1 maturation involves the progression to downstream assembly intermediates involving Coa1 and Shy1. We show that the two heme a cofactor sites in Cox1 form downstream of Mss51- and Coa1-containing Cox1 intermediates. These Cox1 intermediates form normally in cells defective in heme a biosynthesis or in cox1 mutant strains with heme a axial His mutations. In contrast, the Shy1-containing Cox1 assembly intermediate is perturbed in the absence of heme a. Heme a 3 center formation in Cox1 appears to be chaperoned by Shy1. CuB site formation occurs near or at the Shy1-containing Cox1 assembly intermediate also. The CuB metallochaperone Cox11 transiently interacts with Shy1 by coimmunoprecipitation. The Shy1-containing Cox1 complex is markedly attenuated in cells lacking Cox11 but is partially restored with a nonfunctional Cox11 mutant. Thus, formation of the heterobimetallic CuB:heme a 3 site likely occurs in the Shy1-containing Cox1 complex.

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21

Schröder, H., J. Adam K. Taraz, and H. Budzikiewicz. "Dihydropyoverdinsulfonsäuren - Zwischenstufen bei der Biogenese? / Dihydropyoverdin Sulfonic Acids - Intermediates in the Biogenesis?" Zeitschrift für Naturforschung C 50, no. 9-10 (1995): 616–21. http://dx.doi.org/10.1515/znc-1995-9-1004.

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Abstract From the culture media of Pseudomonas aptata 4b and of Pseudomonas fluorescens ATCC 13525 5,6-dihydropyoverdin-7-sulfonic acids could be isolated. Their possible role in the biogenetic pathway leading to the pyoverdins will be discussed

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22

Ghisalba, Oreste. "Biosynthesis of Rifamycins (Ansamycins) and Microbial Production of Shikimate Pathway Precursors, Intermediates, and Metabolites." CHIMIA 39, no. 4 (1985): 79. https://doi.org/10.2533/chimia.1985.79.

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Is the elucidation of biosynthetic pathways of academic interest only, or are there enough valuable spin-offs to make biogenetic studies attractive for a research laboratory in a pharmaceutical company? In this short review it is demonstrated how an interdisciplinary approach to the biosynthesis of rifamycins resulted in the formulation of a general biosynthetic pathway for the whole group of ansamycins and related antibiotics. 3-Amino-5-hydroxybenzoic acid, a natural amino acid derived from the shikimate pathway has been identified as the starter unit for ansamycins and related antibiotics. The microbial mutants produced for this biogenetic study are very useful for the microbial production of shikimate pathway precursors or intermediates such as D(−)-ribulose or shikimic acid.

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23

Chen, Peng, Stephanie K. Sapperstein, Jonathan D. Choi, and Susan Michaelis. "Biogenesis of the Saccharomyces cerevisiae Mating Pheromone a-Factor." Journal of Cell Biology 136, no. 2 (1997): 251–69. http://dx.doi.org/10.1083/jcb.136.2.251.

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The Saccharomyces cerevisiae mating pheromone a-factor is a prenylated and carboxyl methylated extracellular peptide signaling molecule. Biogenesis of the a-factor precursor proceeds via a distinctive multistep pathway that involves COOH-terminal modification, NH2-terminal proteolysis, and a nonclassical export mechanism. In this study, we examine the formation and fate of a-factor biosynthetic intermediates to more precisely define the events that occur during a-factor biogenesis. We have identified four distinct a-factor biosynthetic intermediates (P0, P1, P2, and M) by metabolic labeling, immunoprecipitation, and SDSPAGE. We determined the biochemical composition of each by defining their NH2-terminal amino acid and COOH-terminal modification status. Unexpectedly, we discovered that not one, but two NH2-terminal cleavage steps occur during the biogenesis of a-factor. In addition, we have shown that COOH-terminal prenylation is required for the NH2-terminal processing of a-factor and that all the prenylated a-factor intermediates (P1, P2, and M) are membrane bound, suggesting that many steps of a-factor biogenesis occur in association with membranes. We also observed that although the biogenesis of a-factor is a rapid process, it is inherently inefficient, perhaps reflecting the potential for regulation. Previous studies have identified gene products that participate in the COOH-terminal modification (Ram1p, Ram2p, Ste14p), NH2-terminal processing (Ste24p, Axl1p), and export (Ste6p) of a-factor. The intermediates defined in the present study are discussed in the context of these biogenesis components to formulate an overall model for the pathway of a-factor biogenesis.

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24

Black, Joshua J., and Arlen W. Johnson. "Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast." RNA 28, no. 3 (2021): 371–89. http://dx.doi.org/10.1261/rna.079025.121.

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The two subunits of the eukaryotic ribosome are produced through quasi-independent pathways involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. One of the earliest intermediates of the small subunit (SSU or 40S) is the SSU processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors could induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S.

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25

Gu, Feng, and Jean Gruenberg. "Biogenesis of transport intermediates in the endocytic pathway." FEBS Letters 452, no. 1-2 (1999): 61–66. http://dx.doi.org/10.1016/s0014-5793(99)00561-x.

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26

Simpson, Jeremy C., Tommy Nilsson, and Rainer Pepperkok. "Biogenesis of Tubular ER-to-Golgi Transport Intermediates." Molecular Biology of the Cell 17, no. 2 (2006): 723–37. http://dx.doi.org/10.1091/mbc.e05-06-0580.

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Tubular transport intermediates (TTIs) have been described as one class of transport carriers in endoplasmic reticulum (ER)-to-Golgi transport. In contrast to vesicle budding and fusion, little is known about the molecular regulation of TTI synthesis, transport and fusion with target membranes. Here we have used in vivo imaging of various kinds of GFP-tagged proteins to start to address these questions. We demonstrate that under steady-state conditions TTIs represent ∼20% of all moving transport carriers. They increase in number and length when more transport cargo becomes available at the donor membrane, which we induced by either temperature-related transport blocks or increased expression of the respective GFP-tagged transport markers. The formation and motility of TTIs is strongly dependent on the presence of intact microtubules. Microinjection of GTPγS increases the frequency of TTI synthesis and the length of these carriers. When Rab proteins are removed from membranes by microinjection of recombinant Rab-GDI, the synthesis of TTIs is completely blocked. Microinjection of the cytoplasmic tails of the p23 and p24 membrane proteins also abolishes formation of p24-containing TTIs. Our data suggest that TTIs are ER-to-Golgi transport intermediates that form preferentially when transport-competent cargo exists in excess at the donor membrane. We propose a model where the interaction of the cytoplasmic tails of membrane proteins with microtubules are key determinants for TTI synthesis and may also serve as a so far unappreciated model for aspects of transport carrier formation.

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27

Saveanu, Cosmin, Abdelkader Namane, Pierre-Emmanuel Gleizes, et al. "Sequential Protein Association with Nascent 60S Ribosomal Particles." Molecular and Cellular Biology 23, no. 13 (2003): 4449–60. http://dx.doi.org/10.1128/mcb.23.13.4449-4460.2003.

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ABSTRACT Ribosome biogenesis in eukaryotes depends on the coordinated action of ribosomal and nonribosomal proteins that guide the assembly of preribosomal particles. These intermediate particles follow a maturation pathway in which important changes in their protein composition occur. The mechanisms involved in the coordinated assembly of the ribosomal particles are poorly understood. We show here that the association of preribosomal factors with pre-60S complexes depends on the presence of earlier factors, a phenomenon essential for ribosome biogenesis. The analysis of the composition of purified preribosomal complexes blocked in maturation at specific steps allowed us to propose a model of sequential protein association with, and dissociation from, early pre-60S complexes for several preribosomal factors such as Mak11, Ssf1, Rlp24, Nog1, and Nog2. The presence of either Ssf1 or Nog2 in complexes that contain the 27SB pre-rRNA defines novel, distinct pre-60S particles that contain the same pre-rRNA intermediates and that differ only by the presence or absence of specific proteins. Physical and functional interactions between Rlp24 and Nog1 revealed that the assembly steps are, at least in part, mediated by direct protein-protein interactions.

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28

Bacher, M. "Thapsakins: possible biogenetic intermediates towards insecticidal cyclopenta[b]benzofurans from Aglaia edulis." Phytochemistry 52, no. 2 (1999): 253–63. http://dx.doi.org/10.1016/s0031-9422(99)00185-5.

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29

Jomaa, Ahmad, Nikhil Jain, Joseph H. Davis, James R. Williamson, Robert A. Britton, and Joaquin Ortega. "Functional domains of the 50S subunit mature late in the assembly process." Nucleic Acids Research 42, no. 5 (2013): 3419–35. http://dx.doi.org/10.1093/nar/gkt1295.

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Abstract Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins L16, L27, L28, L33a, L35 and L36. Using a novel pulse labeling/quantitative mass spectrometry technique, we show that this particle is physiologically relevant and is capable of maturing into a complete 50S particle. Cryo-electron microscopy and chemical probing revealed that the central protuberance, the GTPase associating region and tRNA-binding sites in this intermediate are unstructured. These findings demonstrate that key functional sites of the 50S subunit remain unstructured until late stages of maturation, preventing the incomplete subunit from prematurely engaging in translation. Finally, structural and biochemical analysis of a ribosome particle depleted of L16 indicate that L16 binding is necessary for the stimulation of RbgA GTPase activity and, in turn, release of this co-factor, and for conversion of the intermediate to a complete 50S subunit.

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30

Blamowska, Marta, Walter Neupert, and Kai Hell. "Biogenesis of the mitochondrial Hsp70 chaperone." Journal of Cell Biology 199, no. 1 (2012): 125–35. http://dx.doi.org/10.1083/jcb.201205012.

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Chaperones mediate protein folding and prevent deleterious protein aggregation in the cell. However, little is known about the biogenesis of chaperones themselves. In this study, we report on the biogenesis of the yeast mitochondrial Hsp70 (mtHsp70) chaperone, which is essential for the functionality of mitochondria. We show in vivo and in organello that mtHsp70 rapidly folds after its import into mitochondria, with its ATPase domain and peptide-binding domain (PBD) adopting their structures independently of each other. Importantly, folding of the ATPase domain but not of the PBD was severely affected in the absence of the Hsp70 escort protein, Hep1. We reconstituted the folding of mtHsp70, demonstrating that Hep1 and ATP/ADP were required and sufficient for its de novo folding. Our data show that Hep1 bound to a folding intermediate of mtHsp70. Binding of an adenine nucleotide triggered release of Hep1 and folding of the intermediate into native mtHsp70. Thus, Hep1 acts as a specialized chaperone mediating the de novo folding of an Hsp70 chaperone.

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31

Li, Ming, and Danny J. Schnell. "Reconstitution of protein targeting to the inner envelope membrane of chloroplasts." Journal of Cell Biology 175, no. 2 (2006): 249–59. http://dx.doi.org/10.1083/jcb.200605162.

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The chloroplast envelope plays critical roles in the synthesis and regulated transport of key metabolites, including intermediates in photosynthesis and lipid metabolism. Despite this importance, the biogenesis of the envelope membranes has not been investigated in detail. To identify the determinants of protein targeting to the inner envelope membrane (IM), we investigated the targeting of the nucleus-encoded integral IM protein, atTic40. We found that pre-atTic40 is imported into chloroplasts and processed to an intermediate size (int-atTic40) before insertion into the IM. Int-atTic40 is soluble and inserts into the IM from the internal stromal compartment. We also show that atTic40 and a second IM protein, atTic110, can target and insert into isolated IM vesicles in vitro. Collectively, our experiments are consistent with a “postimport” mechanism in which the IM proteins are first imported from the cytoplasm and subsequently inserted into the IM from the stroma.

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Ni, Ling, Johann Schinnerl, Mei-fen Bao, Bing-jie Zhang, Jing Wu, and Xiang-hai Cai. "Two key biogenetic intermediates of Cephalotaxus alkaloids from Cephalotaxus oliveri and C. lanceolata." Tetrahedron Letters 57, no. 47 (2016): 5201–4. http://dx.doi.org/10.1016/j.tetlet.2016.10.026.

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Gruschke, Steffi, Katharina Römpler, Markus Hildenbeutel, et al. "The Cbp3–Cbp6 complex coordinates cytochrome b synthesis with bc1 complex assembly in yeast mitochondria." Journal of Cell Biology 199, no. 1 (2012): 137–50. http://dx.doi.org/10.1083/jcb.201206040.

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Respiratory chain complexes in mitochondria are assembled from subunits derived from two genetic systems. For example, the bc1 complex consists of nine nuclear encoded subunits and the mitochondrially encoded subunit cytochrome b. We recently showed that the Cbp3–Cbp6 complex has a dual function for biogenesis of cytochrome b: it is both required for efficient synthesis of cytochrome b and for protection of the newly synthesized protein from proteolysis. Here, we report that Cbp3–Cbp6 also coordinates cytochrome b synthesis with bc1 complex assembly. We show that newly synthesized cytochrome b assembled through a series of four assembly intermediates. Blocking assembly at early and intermediate steps resulted in sequestration of Cbp3–Cbp6 in a cytochrome b–containing complex, thereby making Cbp3–Cbp6 unavailable for cytochrome b synthesis and thus reducing overall cytochrome b levels. This feedback loop regulates protein synthesis at the inner mitochondrial membrane by directly monitoring the efficiency of bc1 complex assembly.

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Tooze, S. A., T. Flatmark, J. Tooze, and W. B. Huttner. "Characterization of the immature secretory granule, an intermediate in granule biogenesis." Journal of Cell Biology 115, no. 6 (1991): 1491–503. http://dx.doi.org/10.1083/jcb.115.6.1491.

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The events in the biogenesis of secretory granules after the budding of a dense-cored vesicle from the trans-Golgi network (TGN) were investigated in the neuroendocrine cell line PC12, using sulfate-labeled secretogranin II as a marker. The TGN-derived dense-cored vesicles, which we refer to as immature secretory granules, were found to be obligatory organellar intermediates in the biogenesis of the mature secretory granules which accumulate in the cell. Immature secretory granules were converted to mature secretory granules with a half-time of approximately 45 min. This conversion entailed an increase in their size, implying that the maturation of secretory granules includes a fusion event involving immature secretory granules. Pulse-chase labelling of PC12 cells followed by stimulation with high K+, which causes the release of secretogranin II, showed that not only mature, but also immature secretory granules were capable of undergoing regulated exocytosis. The kinetics of secretion of secretogranin II, as well as those of a constitutively secreted heparan sulfate proteoglycan, were reduced by treatment of PC12 cells with nocodazole, suggesting that both secretory granules and constitutive secretory vesicles are transported to the plasma membrane along microtubules. Our results imply that certain membrane proteins, e.g., those involved in the fusion of post-TGN vesicles with the plasma membrane, are sorted upon exit from the TGN, whereas other membrane proteins, e.g., those involved in the interaction of post-TGN vesicles with the cytoskeleton, may not be sorted.

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Lazarou, Michael, Matthew McKenzie, Akira Ohtake, David R. Thorburn, and Michael T. Ryan. "Analysis of the Assembly Profiles for Mitochondrial- and Nuclear-DNA-Encoded Subunits into Complex I." Molecular and Cellular Biology 27, no. 12 (2007): 4228–37. http://dx.doi.org/10.1128/mcb.00074-07.

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ABSTRACT Complex I of the respiratory chain is composed of at least 45 subunits that assemble together at the mitochondrial inner membrane. Defects in human complex I result in energy generation disorders and are also implicated in Parkinson's disease and altered apoptotic signaling. The assembly of this complex is poorly understood and is complicated by its large size and its regulation by two genomes, with seven subunits encoded by mitochondrial DNA (mtDNA) and the remainder encoded by nuclear genes. Here we analyzed the assembly of a number of mtDNA- and nuclear-gene-encoded subunits into complex I. We found that mtDNA-encoded subunits first assemble into intermediate complexes and require significant chase times for their integration into the holoenzyme. In contrast, a set of newly imported nuclear-gene-encoded subunits integrate with preexisting complex I subunits to form intermediates and/or the fully assembly holoenzyme. One of the intermediate complexes represents a subassembly associated with the chaperone B17.2L. By using isolated patient mitochondria, we show that this subassembly is a productive intermediate in complex I assembly since import of the missing subunit restores complex I assembly. Our studies point to a mechanism of complex I biogenesis involving two complementary processes, (i) synthesis of mtDNA-encoded subunits to seed de novo assembly and (ii) exchange of preexisting subunits with newly imported ones to maintain complex I homeostasis. Subunit exchange may also act as an efficient mechanism to prevent the accumulation of oxidatively damaged subunits that would otherwise be detrimental to mitochondrial oxidative phosphorylation and have the potential to cause disease.

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Jayalath, Kumudie, Sean Frisbie, Minhchau To, and Sanjaya Abeysirigunawardena. "Pseudouridine Synthase RsuA Captures an Assembly Intermediate That Is Stabilized by Ribosomal Protein S17." Biomolecules 10, no. 6 (2020): 841. http://dx.doi.org/10.3390/biom10060841.

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The ribosome is a large ribonucleoprotein complex that synthesizes protein in all living organisms. Ribosome biogenesis is a complex process that requires synchronization of various cellular events, including ribosomal RNA (rRNA) transcription, ribosome assembly, and processing and post-transcriptional modification of rRNA. Ribosome biogenesis is fine-tuned with various assembly factors, possibly including nucleotide modification enzymes. Ribosomal small subunit pseudouridine synthase A (RsuA) pseudouridylates U516 of 16S helix 18. Protein RsuA is a multi-domain protein that contains the N-terminal peripheral domain, which is structurally similar to the ribosomal protein S4. Our study shows RsuA preferably binds and pseudouridylates an assembly intermediate that is stabilized by ribosomal protein S17 over the native-like complex. In addition, the N-terminal domain truncated RsuA showed that the presence of the S4-like domain is important for RsuA substrate recognition.

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Basch, Marion, Mirjam Wagner, Stéphane Rolland, et al. "Msp1 cooperates with the proteasome for extraction of arrested mitochondrial import intermediates." Molecular Biology of the Cell 31, no. 8 (2020): 753–67. http://dx.doi.org/10.1091/mbc.e19-06-0329.

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During compromised protein import at the mitochondrial outer membrane, Msp1 and the proteasome are required for maintaining organellar biogenesis. Msp1 cooperates with the proteasome, which drives the extraction of arrested and mislocalized proteins at the import pore.

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Wang, Yi-Ping, Azeem Sharda, Shuang-Nian Xu, et al. "Malic enzyme 2 connects the Krebs cycle intermediate fumarate to mitochondrial biogenesis." Cell Metabolism 33, no. 5 (2021): 1027–41. http://dx.doi.org/10.1016/j.cmet.2021.03.003.

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Ambrosio, Andrea L., та Santiago M. Di Pietro. "Mechanism of platelet α-granule biogenesis: study of cargo transport and the VPS33B-VPS16B complex in a model system". Blood Advances 3, № 17 (2019): 2617–26. http://dx.doi.org/10.1182/bloodadvances.2018028969.

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Abstract Platelet α-granules play important roles in platelet function. They contain hundreds of proteins that are synthesized by the megakaryocyte or taken up by endocytosis. The trafficking pathways that mediate platelet α-granule biogenesis are incompletely understood, especially with regard to cargo synthesized by the megakaryocyte. Vacuolar-protein sorting 33B (VPS33B) and VPS16B are essential proteins for α-granule biogenesis, but they are largely uncharacterized. Here, we adapted a powerful method to directly map the pathway followed by newly synthesized cargo proteins to reach α-granules. Using this method, we revealed the recycling endosome as a key intermediate compartment in α-granule biogenesis. We then used CRISPR/Cas9 gene editing to knock out VPS33B in pluripotent stem cell–derived immortalized megakaryocyte cells (imMKCLs). Consistent with the observations in platelets from patients with VPS33B mutation, VPS33B-knockout (KO) imMKCLs have drastically reduced levels of α-granule proteins platelet factor 4, von Willebrand factor, and P-selectin. VPS33B and VPS16B form a distinct and small complex in imMKCLs with the same hydrodynamic radius as the recombinant VPS33B-VPS16B heterodimer purified from bacteria. Mechanistically, the VPS33B-VPS16B complex ensures the correct trafficking of α-granule proteins. VPS33B deficiency results in α-granule cargo degradation in lysosomes. VPS16B steady-state levels are significantly lower in VPS33B-KO imMKCLs, suggesting that VPS16B is destabilized in the absence of its partner. Exogenous expression of green fluorescent protein–VPS33B in VPS33B-KO imMKCLs reconstitutes the complex, which localizes to the recycling endosome, further defining this compartment as a key intermediate in α-granule biogenesis. These results advance our understanding of platelet α-granule biogenesis and open new avenues for the study of these organelles.

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Talmor-Neiman, Mali, Ran Stav, Wolfgang Frank, Bjoern Voss, and Tzahi Arazi. "Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss." Plant Journal 47, no. 1 (2006): 25–37. http://dx.doi.org/10.1111/j.1365-313x.2006.02768.x.

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Kaufman, Teodoro, María Méndez, and Andrea Bracca. "Isolation, Synthesis, and Biological Activity of Quindoline, a Valuable Indoloquinoline Natural Product and Useful Key Intermediate." Synthesis 50, no. 07 (2018): 1417–29. http://dx.doi.org/10.1055/s-0036-1591947.

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Quindoline is one of the simplest naturally occurring monomeric indoloquinoline alkaloids. Chemists exhibited interest in this compound before it was isolated from a natural source. The different approaches toward the total synthesis of the natural product and its performance in various biological tests are discussed. Aspects related to the isolation of quindoline from different ethnomedicinally relevant plants around the world are also reviewed.1 Introduction2 Isolation and Biogenetic Considerations3 Total Syntheses of Quindoline3.1 Early Synthetic Studies3.2 Syntheses from Benzenoids3.3 Syntheses from Indoles3.4 Syntheses from Quinolines4 Biological Activity Studies5 Conclusions

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Romano, Roberta, Paola Cordella, and Cecilia Bucci. "The Type III Intermediate Filament Protein Peripherin Regulates Lysosomal Degradation Activity and Autophagy." International Journal of Molecular Sciences 26, no. 2 (2025): 549. https://doi.org/10.3390/ijms26020549.

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Peripherin belongs to heterogeneous class III of intermediate filaments, and it is the only intermediate filament protein selectively expressed in the neurons of the peripheral nervous system. It has been previously discovered that peripherin interacts with proteins important for the endo-lysosomal system and for the transport to late endosomes and lysosomes, such as RAB7A and AP-3, although little is known about its role in the endocytic pathway. Here, we show that peripherin silencing affects lysosomal abundance but also positioning, causing the redistribution of lysosomes from the perinuclear area to the cell periphery. Moreover, peripherin silencing affects lysosomal activity, inhibiting EGFR degradation and the degradation of a fluorogenic substrate for proteases. Furthermore, we demonstrate that peripherin silencing affects lysosomal biogenesis by reducing the TFEB and TFE3 contents. Finally, in peripherin-depleted cells, the autophagic flux is strongly inhibited. Therefore, these data indicate that peripherin has an important role in regulating lysosomal biogenesis, and positioning and functions of lysosomes, affecting both the endocytic and autophagic pathways. Considering that peripherin is the most abundant intermediate filament protein of peripheral neurons, its dysregulation, affecting its functions, could be involved in the onset of several neurodegenerative diseases of the peripheral nervous system characterized by alterations in the endocytic and/or autophagic pathways.

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Jensen, Bryan C., Deirdre L. Brekken, Amber C. Randall, Charles T. Kifer, and Marilyn Parsons. "Species Specificity in Ribosome Biogenesis: a Nonconserved Phosphoprotein Is Required for Formation of the Large Ribosomal Subunit in Trypanosoma brucei." Eukaryotic Cell 4, no. 1 (2005): 30–35. http://dx.doi.org/10.1128/ec.4.1.30-35.2005.

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ABSTRACT In the protozoan parasite Trypanosoma brucei, the large rRNA, which is a single 3.4- to 5-kb species in most organisms, is further processed to form six distinct RNAs, two larger than 1 kb (LSU1 and LSU2) and four smaller than 220 bp. The small rRNA SR1 separates the two large RNAs, while the remaining small RNAs are clustered at the 3′ end of the precursor rRNA. One would predict that T. brucei possesses specific components to carry out these added processing events. We show here that the trypanosomatid-specific nucleolar phosphoprotein NOPP44/46 is involved in this further processing. Cells depleted of NOPP44/46 by RNA interference had a severe growth defect and demonstrated a defect in large-ribosomal-subunit biogenesis. Concurrent with this defect, a significant decrease in processing intermediates, particularly for SR1, was seen. In addition, we saw an accumulation of aberrant processing intermediates caused by cleavage within either LSU1 or LSU2. Though it is required for large-subunit biogenesis, we show that NOPP44/46 is not incorporated into the nascent particle. Thus, NOPP44/46 is an unusual protein in that it is both nonconserved and required for ribosome biogenesis.

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Ge, Liang, Livia Wilz, and Randy Schekman. "Biogenesis of autophagosomal precursors for LC3 lipidation from the ER-Golgi intermediate compartment." Autophagy 11, no. 12 (2015): 2372–74. http://dx.doi.org/10.1080/15548627.2015.1105422.

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Adam, Z., and N. E. Hoffman. "Biogenesis of a Photosystem I Light-Harvesting Complex (Evidence for a Membrane Intermediate)." Plant Physiology 102, no. 1 (1993): 35–43. http://dx.doi.org/10.1104/pp.102.1.35.

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de Vivar, A. "Structure and stereochemistry of mexicanin G, an intermediate in the biogenesis of helenanolides." Phytochemistry 23, no. 12 (1985): 2977–79. http://dx.doi.org/10.1016/s0031-9422(00)80617-2.

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de Vivar, Alfonso Romo, Guillermo Delgado, and Eduardo Huerta. "Structure and stereochemistry of mexicanin G, an intermediate in the biogenesis of helenanolides." Phytochemistry 24, no. 12 (1985): 2977–79. http://dx.doi.org/10.1016/0031-9422(85)80039-x.

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Zhu, Qin, and Xinyu Liu. "Molecular and genetic basis for early stage structural diversifications in hapalindole-type alkaloid biogenesis." Chemical Communications 53, no. 19 (2017): 2826–29. http://dx.doi.org/10.1039/c7cc00782e.

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Abetov, Danysh A., Vladimir S. Kiyan, Assylbek A. Zhylkibayev, et al. "Formation of mammalian preribosomes proceeds from intermediate to composed state during ribosome maturation." Journal of Biological Chemistry 294, no. 28 (2019): 10746–57. http://dx.doi.org/10.1074/jbc.ac119.008378.

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In eukaryotes, ribosome assembly is a rate-limiting step in ribosomal biogenesis that takes place in a distinctive subnuclear organelle, the nucleolus. How ribosomes get assembled at the nucleolar site by forming initial preribosomal complexes remains poorly characterized. In this study, using several human and murine cell lines, we developed a method for isolation of native mammalian preribosomal complexes by lysing cell nuclei through mild sonication. A sucrose gradient fractionation of the nuclear lysate resolved several ribonucleoprotein (RNP) complexes containing rRNAs and ribosomal proteins. Characterization of the RNP complexes with MS-based protein identification and Northern blotting–based rRNA detection approaches identified two types of preribosomes we named here as intermediate preribosomes (IPRibs) and composed preribosome (CPRib). IPRib complexes comprised large preribosomes (105S to 125S in size) containing the rRNA modification factors and premature rRNAs. We further observed that a distinctive CPRib complex consists of an 85S preribosome assembled with mature rRNAs and a ribosomal biogenesis factor, Ly1 antibody–reactive (LYAR), that does not associate with premature rRNAs and rRNA modification factors. rRNA-labeling experiments uncovered that IPRib assembly precedes CPRib complex formation. We also found that formation of the preribosomal complexes is nutrient-dependent because the abundances of IPRib and CPRib decreased substantially when cells were either deprived of amino acids or exposed to an mTOR kinase inhibitor. These findings indicate that preribosomes form via dynamic and nutrient-dependent processing events and progress from an intermediate to a composed state during ribosome maturation.

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Choi, Ilyeong, Young Jeon, Youngki Yoo, Hyun-Soo Cho, and Hyun-Sook Pai. "The in vivo functions of ARPF2 and ARRS1 in ribosomal RNA processing and ribosome biogenesis in Arabidopsis." Journal of Experimental Botany 71, no. 9 (2020): 2596–611. http://dx.doi.org/10.1093/jxb/eraa019.

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Abstract Yeast Rpf2 plays a critical role in the incorporation of 5S rRNA into pre-ribosomes by forming a binary complex with Rrs1. The protein characteristics and overexpression phenotypes of Arabidopsis Ribosome Production Factor 2 (ARPF2) and Arabidopsis Regulator of Ribosome Synthesis 1 (ARRS1) have been previously studied. Here, we analyze loss-of-function phenotypes of ARPF2 and ARRS1 using virus-induced gene silencing to determine their functions in pre-rRNA processing and ribosome biogenesis. ARPF2 silencing in Arabidopsis led to pleiotropic developmental defects. RNA gel blot analysis and circular reverse transcription–PCR revealed that ARPF2 depletion delayed pre-rRNA processing, resulting in the accumulation of multiple processing intermediates. ARPF2 fractionated primarily with the 60S ribosomal subunit. Metabolic rRNA labeling and ribosome profiling suggested that ARPF2 deficiency mainly affected 25S rRNA synthesis and 60S ribosome biogenesis. ARPF2 and ARRS1 formed the complex that interacted with the 60S ribosomal proteins RPL5 and RPL11. ARRS1 silencing resulted in growth defects, accumulation of processing intermediates, and ribosome profiling similar to those of ARPF2-silenced plants. Moreover, depletion of ARPF2 and ARRS1 caused nucleolar stress. ARPF2-deficient plants excessively accumulated anthocyanin and reactive oxygen species. Collectively, these results suggest that the ARPF2–ARRS1 complex plays a crucial role in plant growth and development by modulating ribosome biogenesis.

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