Genomes and Genes
Summary: The natural growth and development within living CELLS.
- Leppik M, Liiv A, Remme J. Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly. Nucleic Acids Res. 2017;45:6098-6108 pubmed publisher..A plausible reason for pseudouridine-dependent inhibition of ribosome assembly is stabilization of rRNA structure, which leads to the folding traps of rRNA and to the retardation of the ribosome assembly. ..
- Wang J, Saha T, Zhang Y, Zhang C, Raikhel A. Juvenile hormone and its receptor methoprene-tolerant promote ribosomal biogenesis and vitellogenesis in the Aedes aegypti mosquito. J Biol Chem. 2017;292:10306-10315 pubmed publisher..In summary, our results indicate that JH is critical for inducing the expression of ribosomal protein genes and demonstrate that RRS1 mediates the JH signal to enhance both ribosomal biogenesis and vitellogenesis. ..
- Serfass J, Takahashi Y, Zhou Z, Kawasawa Y, Liu Y, Tsotakos N, et al. Endophilin B2 facilitates endosome maturation in response to growth factor stimulation, autophagy induction, and influenza A virus infection. J Biol Chem. 2017;292:10097-10111 pubmed publisher..Taken together, our findings suggest that endophilin B2 positively regulates the endocytic pathway in response to growth factor signaling, autophagy induction, and viral entry. ..
- Tan X, Wei J, Li B, Wang M, Bao Y. AtVps11 is essential for vacuole biogenesis in embryo and participates in pollen tube growth in Arabidopsis. Biochem Biophys Res Commun. 2017;491:794-799 pubmed publisher..Our study indicated that in Arabidopsis, Vps11 is required for vacuole biogenesis in embryo, which is essential for embryogenesis. It also plays a role in pollen tube growth but looks not required for vacuole biogenesis in pollen tube. ..
- Freeman Rosenzweig E, Xu B, Kuhn Cuellar L, Martinez Sanchez A, Schaffer M, Strauss M, et al. The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization. Cell. 2017;171:148-162.e19 pubmed publisher..More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles. ..
- Laubenthal L, Ruda L, Sultana N, Winkler J, Rehage J, Meyer U, et al. Effect of increasing body condition on oxidative stress and mitochondrial biogenesis in subcutaneous adipose tissue depot of nonlactating dairy cows. J Dairy Sci. 2017;100:4976-4986 pubmed publisher..Key transcription factors of mitochondrial biogenesis were largely unaffected. Thus, increased oxidative stress does not impair mitochondrial DNA. ..
- Su Z, Klein J, Du J, Franch H, Zhang L, Hassounah F, et al. Chronic kidney disease induces autophagy leading to dysfunction of mitochondria in skeletal muscle. Am J Physiol Renal Physiol. 2017;312:F1128-F1140 pubmed publisher..However, myofibrillar protein is not directly broken down through autophagy. Instead, CKD-induced upregulation of autophagy leads to dysfunction of mitochondria and decrease of ATP production. ..
- Peña C, Hurt E, Panse V. Eukaryotic ribosome assembly, transport and quality control. Nat Struct Mol Biol. 2017;24:689-699 pubmed publisher..We also highlight recent cryo-EM studies that provided unprecedented snapshots of ribosomes during assembly and quality control. ..
- Prakasam G, Singh R, Iqbal M, Saini S, Tiku A, Bamezai R. Pyruvate kinase M knockdown-induced signaling via AMP-activated protein kinase promotes mitochondrial biogenesis, autophagy, and cancer cell survival. J Biol Chem. 2017;292:15561-15576 pubmed publisher..On the basis of our observations, we propose an alternative therapeutic strategy of silencing either of the PKM isoforms along with AMPK in tumors. ..
- Liss V, Swart A, Kehl A, Hermanns N, Zhang Y, Chikkaballi D, et al. Salmonella enterica Remodels the Host Cell Endosomal System for Efficient Intravacuolar Nutrition. Cell Host Microbe. 2017;21:390-402 pubmed publisher..Our data demonstrate that formation of the SCV-SIF continuum allows Salmonella to bypass nutritional restriction in the intracellular environment by acquiring nutrients from the host cell endosomal system. ..
- Jean Beltran P, Cook K, Cristea I. Exploring and Exploiting Proteome Organization during Viral Infection. J Virol. 2017;91: pubmed publisher..Here, we highlight recent advances in microscopy and proteomic methods that have helped and will continue to help define mechanisms used by viruses to exploit host proteome organization. ..
- Li X, Yu W, Qian X, Xia Y, Zheng Y, Lee J, et al. Nucleus-Translocated ACSS2 Promotes Gene Transcription for Lysosomal Biogenesis and Autophagy. Mol Cell. 2017;66:684-697.e9 pubmed publisher..These results underscore the significance of nuclear ACSS2-mediated histone acetylation in maintaining cell homeostasis and tumor development. ..
- Waksman G. Structural and Molecular Biology of a Protein-Polymerizing Nanomachine for Pilus Biogenesis. J Mol Biol. 2017;429:2654-2666 pubmed publisher..Comparison with other nanomachines polymerizing other types of biological units, such as nucleotides during DNA replication, provides some unifying principles as to how multidomain proteins assemble biological polymers. ..
- Giampieri F, Alvarez Suarez J, Cordero M, Gasparrini M, Forbes Hernández T, Afrin S, et al. Strawberry consumption improves aging-associated impairments, mitochondrial biogenesis and functionality through the AMP-activated protein kinase signaling cascade. Food Chem. 2017;234:464-471 pubmed publisher..These in vivo results were then verified in vitro on HepG2 cells, confirming the involvement of AMPK in the beneficial effects exerted by strawberry against aging progression. ..
- Kamath D, Allgeyer B, Gregory S, Bielski M, Roelofsz D, Sabapathypillai S, et al. The C-terminus of ribosomal protein uS4 contributes to small ribosomal subunit biogenesis and the fidelity of translation. Biochimie. 2017;138:194-201 pubmed publisher..coli mutants and their likely structural effects on uS4-uS5 interactions. ..
- Qi W, Keenan H, Li Q, Ishikado A, Kannt A, Sadowski T, et al. Pyruvate kinase M2 activation may protect against the progression of diabetic glomerular pathology and mitochondrial dysfunction. Nat Med. 2017;23:753-762 pubmed publisher..Thus, PKM2 activation may protect against DN by increasing glucose metabolic flux, inhibiting the production of toxic glucose metabolites and inducing mitochondrial biogenesis to restore mitochondrial function. ..
- Fujii N, Narita T, Okita N, Kobayashi M, Furuta Y, Chujo Y, et al. Sterol regulatory element-binding protein-1c orchestrates metabolic remodeling of white adipose tissue by caloric restriction. Aging Cell. 2017;16:508-517 pubmed publisher..This indicated that Srebp-1c is a key regulator of metabolic remodeling leading to the beneficial effects of CR. ..
- Ferreira A, Cunha Oliveira T, Simões R, Carvalho F, Burgeiro A, Nordgren K, et al. Altered mitochondrial epigenetics associated with subchronic doxorubicin cardiotoxicity. Toxicology. 2017;390:63-73 pubmed publisher..These results suggest an interplay between mitochondrial dysfunction and epigenetic alterations, which may be a primary determinant of DOX-induced cardiotoxicity. ..
- Brun S, Abella N, Berciano M, Tapia O, Jaumot M, Freire R, et al. SUMO regulates p21Cip1 intracellular distribution and with p21Cip1 facilitates multiprotein complex formation in the nucleolus upon DNA damage. PLoS ONE. 2017;12:e0178925 pubmed publisher..Thus, SUMO and p21Cip1 regulate the transit of proteins through the nucleolus, and that disruption of nucleolar export by DNA damage induces SUMO and p21Cip1 to act as hub proteins to form a multiprotein complex in the nucleolus. ..
- Gómez Herreros F, Margaritis T, Rodríguez Galán O, Pelechano V, Begley V, Millán Zambrano G, et al. The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation. Nucleic Acids Res. 2017;45:9302-9318 pubmed publisher..On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes. ..
- Li B, Yue Y, Yuan Z, Zhang F, Li P, Song N, et al. Salmonella STM1697 coordinates flagella biogenesis and virulence by restricting flagellar master protein FlhD4C2 from recruiting RNA polymerase. Nucleic Acids Res. 2017;45:9976-9989 pubmed publisher..Finally, we describe a novel mechanism mediated by STM1697 in which Salmonella can inhibit the production of flagella antigen and escape from the host immune system...
- Li P, Liu Y, Burns N, Zhao K, Song R. SIRT1 is required for mitochondrial biogenesis reprogramming in hypoxic human pulmonary arteriolar smooth muscle cells. Int J Mol Med. 2017;39:1127-1136 pubmed publisher..Polydatin improves mitochondrial biogenesis and function by enhancing SIRT1 expression in hypoxic human PASMCs. ..
- Joshi A, Zhang H, Prinz W. Organelle biogenesis in the endoplasmic reticulum. Nat Cell Biol. 2017;19:876-882 pubmed publisherUnderstanding organelle biogenesis is a central focus of cell biology. Whereas some are generated from existing organelles, others can be generated de novo. Most de novo organelle biogenesis occurs in the endoplasmic reticulum (ER)...
- Liu X, Zhang Y, Ni M, Cao H, Signer R, Li D, et al. Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation. Nat Cell Biol. 2017;19:626-638 pubmed publisher..Our studies support a mechanism for post-transcriptional control of erythroid mitochondria and may have direct relevance to haematologic defects associated with mitochondrial diseases and ageing. ..
- Wang Q, Tang Y, Xu Y, Xu S, Jiang Y, Dong Q, et al. The X-linked deubiquitinase USP9X is an integral component of centrosome. J Biol Chem. 2017;292:12874-12884 pubmed publisher..Collectively, our experiments identified USP9X as an integral component of the centrosome where it functions to stabilize PCM1 and CEP55 and promote centrosome biogenesis. ..
- Scholpa N, Schnellmann R. Mitochondrial-Based Therapeutics for the Treatment of Spinal Cord Injury: Mitochondrial Biogenesis as a Potential Pharmacological Target. J Pharmacol Exp Ther. 2017;363:303-313 pubmed publisher..Therefore, this review also examines the unexplored therapeutic efficacy of pharmacological enhancement of mitochondrial biogenesis, which has the potential to more comprehensively improve mitochondrial function after SCI. ..
- Nechipurenko I, Berciu C, Sengupta P, Nicastro D. Centriolar remodeling underlies basal body maturation during ciliogenesis in Caenorhabditis elegans. elife. 2017;6: pubmed publisher..Our work provides a framework for future investigations into the mechanisms underlying BB remodeling. ..
- Nascimbeni A, Giordano F, Dupont N, Grasso D, Vaccaro M, Codogno P, et al. ER-plasma membrane contact sites contribute to autophagosome biogenesis by regulation of local PI3P synthesis. EMBO J. 2017;36:2018-2033 pubmed publisher..These results highlight the contribution of ER-plasma membrane tethers to autophagosome biogenesis regulation and support the importance of membrane contact sites in autophagy. ..
- Yan Y, Yang X, Zhao T, Zou Y, Li R, Xu Y. Salicylates promote mitochondrial biogenesis by regulating the expression of PGC-1? in murine 3T3-L1 pre-adipocytes. Biochem Biophys Res Commun. 2017;491:436-441 pubmed publisher..These results suggest that salicylate has a potential therapeutic capacity against mitochondrial dysfunction in diabetes. ..
- HellstrÃ¶m K, Kallio K, Utt A, Quirin T, Jokitalo E, Merits A, et al. Partially Uncleaved Alphavirus Replicase Forms Spherule Structures in the Presence and Absence of RNA Template. J Virol. 2017;91: pubmed publisher..Thus, partially cleaved replicase proteins play key roles that connect replication complex assembly, membrane deformation, and the different stages of RNA synthesis. ..
- Bruni G, Battle B, Kelly B, Zhang Z, Wang P. Comparative proteomic analysis of Gib2 validating its adaptor function in Cryptococcus neoformans. PLoS ONE. 2017;12:e0180243 pubmed publisher..Our study also highlights a multifaceted regulatory role of Gib2 in the growth and pathogenicity of C. neoformans. ..
- Calviño F, Kornprobst M, Schermann G, Birkle F, Wild K, Fischer T, et al. Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis. PLoS ONE. 2017;12:e0178752 pubmed publisher..We provide a first model of the 5'-ETS RNA from the internally hidden 5'-end up to the region that hybridizes to the 3'-hinge sequence of U3 snoRNA and validate a specific Utp4/5'-ETS interaction by CRAC analysis. ..
- Donato V, Bonora M, Simoneschi D, Sartini D, Kudo Y, Saraf A, et al. The TDH-GCN5L1-Fbxo15-KBP axis limits mitochondrial biogenesis in mouse embryonic stem cells. Nat Cell Biol. 2017;19:341-351 pubmed publisher..Thus, KBP proteolysis limits the accumulation of mitochondria in mESCs to preserve their optimal fitness, whereas KBP accumulation promotes mitochondrial biogenesis in differentiating cells. ..
- Lee A, Jang Y, Hong S, Chang S, Park S, Kim S, et al. Ephedrine-induced mitophagy via oxidative stress in human hepatic stellate cells. J Toxicol Sci. 2017;42:461-473 pubmed publisher..Excessive mitophagy lead to cell death through imbalance of autophagic flux. Moreover, antioxidants and reducing Parkin level could serve as therapeutic targets for ephedrine-induced hepatotoxicity. ..
- Nishimura T, Tamura N, Kono N, Shimanaka Y, Arai H, Yamamoto H, et al. Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains. EMBO J. 2017;36:1719-1735 pubmed publisher..These findings suggest that the autophagy-initiation complex, the PIS-enriched ER subdomain, and ATG9A vesicles together initiate autophagosome formation. ..
- Bosio M, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, et al. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res. 2017;45:4493-4506 pubmed publisher..Our observations point to GRFs as new multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions. ..