1
|
Martin-Solana E, Diaz-Lopez I, Mohamedi Y, Ventoso I, Fernandez JJ, Fernandez-Fernandez MR. Progressive alterations in polysomal architecture and activation of ribosome stalling relief factors in a mouse model of Huntington's disease. Neurobiol Dis 2024; 195:106488. [PMID: 38565397 DOI: 10.1016/j.nbd.2024.106488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Given their highly polarized morphology and functional singularity, neurons require precise spatial and temporal control of protein synthesis. Alterations in protein translation have been implicated in the development and progression of a wide range of neurological and neurodegenerative disorders, including Huntington's disease (HD). In this study we examined the architecture of polysomes in their native brain context in striatal tissue from the zQ175 knock-in mouse model of HD. We performed 3D electron tomography of high-pressure frozen and freeze-substituted striatal tissue from HD models and corresponding controls at different ages. Electron tomography results revealed progressive remodelling towards a more compacted polysomal architecture in the mouse model, an effect that coincided with the emergence and progression of HD related symptoms. The aberrant polysomal architecture is compatible with ribosome stalling phenomena. In fact, we also detected in the zQ175 model an increase in the striatal expression of the stalling relief factor EIF5A2 and an increase in the accumulation of eIF5A1, eIF5A2 and hypusinated eIF5A1, the active form of eIF5A1. Polysomal sedimentation gradients showed differences in the relative accumulation of 40S ribosomal subunits and in polysomal distribution in striatal samples of the zQ175 model. These findings indicate that changes in the architecture of the protein synthesis machinery may underlie translational alterations associated with HD, opening new avenues for understanding the progression of the disease.
Collapse
Affiliation(s)
- Eva Martin-Solana
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain
| | - Irene Diaz-Lopez
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Yamina Mohamedi
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain
| | - Ivan Ventoso
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Jose-Jesus Fernandez
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain; Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC). Av. Vega 4-6, 33940 El Entrego, Asturias, Spain.
| | - Maria Rosario Fernandez-Fernandez
- Centro Nacional de Biotecnología (CNB-CSIC). Campus UAM, Darwin 3, 28049 Madrid, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Av. Hospital Universitario s/n, 33011 Oviedo, Asturias, Spain; Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC). Av. Vega 4-6, 33940 El Entrego, Asturias, Spain.
| |
Collapse
|
2
|
Bhattacharya S, Dahmane T, Goger MJ, Rudolph MJ, Tumer NE. 1H, 13C, and 15N backbone and methyl group resonance assignments of ricin toxin A subunit. Biomol NMR Assign 2024:10.1007/s12104-024-10172-8. [PMID: 38642265 DOI: 10.1007/s12104-024-10172-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024]
Abstract
Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the N-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography. The current understanding of RTA's depurination mechanism relies exclusively on X-ray structures of the enzyme in the free state and complexed with transition state analogues. To date we have sparse evidence of conformational dynamics and allosteric regulation of RTA activity that can be exploited in the rational design of inhibitors. Thus, our primary goal here is to apply solution NMR techniques to probe the residue specific structural and dynamic coupling active in RTA as a prerequisite to understand the functional implications of an allosteric network. In this report we present de novo sequence specific amide and sidechain methyl chemical shift assignments of the 267 residue RTA in the free state and in complex with an 11-residue peptide (P11) representing the identical C-terminal sequence of the ribosomal P-stalk proteins. These assignments will facilitate future studies detailing the propagation of binding induced conformational changes in RTA complexed with inhibitors, antibodies, and biologically relevant targets.
Collapse
Affiliation(s)
- Shibani Bhattacharya
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA.
| | - Tassadite Dahmane
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA
| | - Michael J Goger
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA
| | - Michael J Rudolph
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA
| | - Nilgun E Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901-8520, USA
| |
Collapse
|
3
|
Zhang M, Zhang C. Preferential cleavage of upstream targets in concatenated miRNA/siRNA target sites support a 5'-3' scanning model for RISC target recognition. Biochem Biophys Res Commun 2024; 703:149662. [PMID: 38359613 DOI: 10.1016/j.bbrc.2024.149662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
RNA interference (RNAi) is becoming medicine for curing human diseases. Still, we lack a thorough understanding of some fundamental aspects of RNAi that affect its efficiency and accuracy. One such question is how RNA-induced silencing complex (RISC) can efficiently find its targets. To address this question, we developed a strategy that involves the expression of mRNAs containing concatenations of identical miRNA/siRNA target sites. These mRNAs were cleaved by co-expressed miRNAs in plant cells or by co-transfected siRNAs in mammalian cells. The mRNA cleavage events were then detected using the 5'RACE assay. Using this strategy, we found that RISCs preferentially cleave the upstream ones of concatenated target sites, consistent with a model that RISC scans mRNA in 5'→3' direction to approach its target sites. The stability of the cleaved mRNA fragments correlates with the complementarity between siRNA and its target sequence. When siRNA perfectly complements its target sequence, the cleaved mRNA fragment becomes stable and may be cleaved in a second round. Our findings have practical implications for designing siRNAs with increased efficiency and reduced off-target effects.
Collapse
Affiliation(s)
- Mancang Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China
| | - Changqing Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
4
|
Singh J, Singh S, Emam EAF, Varshney U. Role of Rmd9p in 3'-end processing of mitochondrial 15S rRNA in Saccharomyces cerevisiae. Mitochondrion 2024; 76:101876. [PMID: 38599301 DOI: 10.1016/j.mito.2024.101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Ribosome biogenesis, involving processing/assembly of rRNAs and r-proteins is a vital process. In Saccharomyces cerevisiae mitochondria, ribosomal small subunit comprises 15S rRNA (15S). While the 15S 5'-end processing uses Ccm1p and Pet127p, the mechanisms of the 3'-end processing remain unclear. We reveal involvement of Rmd9p in safeguarding/processing 15S 3'-end. Rmd9p deficiency results in a cleavage at a position 183 nucleotides upstream of 15S 3'-end, and in the loss of the 3'-minor domain. Rmd9p binds to the sequences in the 3'-end region of 15S, and a genetic interaction between rmd9 and dss1 indicates that Rmd9p regulates/limits mtEXO activity during the 3'-end spacer processing.
Collapse
Affiliation(s)
- Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Elhassan Ali Fathi Emam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
| |
Collapse
|
5
|
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
Collapse
Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
| |
Collapse
|
6
|
Lian K, Hammarström D, Hamarsland H, Mølmen KS, Moen SC, Ellefsen S. Glucose ingestion before and after resistance training sessions does not augment ribosome biogenesis in healthy moderately trained young adults. Eur J Appl Physiol 2024:10.1007/s00421-024-05446-x. [PMID: 38459192 DOI: 10.1007/s00421-024-05446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/09/2024] [Indexed: 03/10/2024]
Abstract
PURPOSE Resistance training-induced skeletal muscle hypertrophy seems to depend on ribosome biogenesis and content. High glucose treatment may augment ribosome biogenesis through potentiating resistance training-induced adaptations. This was investigated with total RNA and ribosomal RNA abundances as main outcomes, with relevant transcriptional/translational regulators (c-Myc/UBF/rpS6) as a secondary outcome. METHODS Sixteen healthy, moderately trained individuals [male/female, n = 9/7; age, 24.1 (3.3)] participated in a within-participant crossover trial with unilateral resistance training (leg press and knee extension, 3 sets of 10 repetitions maximum) and pre- and post-exercise ingestion of either glucose (3 × 30 g, 90 g total) or placebo supplements (Stevia rebaudiana, 3 × 0.3 g, 0.9 g total), together with protein (2 × 25 g, 50 g total), on alternating days for 12 days. Six morning resistance exercise sessions were conducted per condition, and the sessions were performed in an otherwise fasted state. Micro-biopsies were sampled from m. vastus lateralis before and after the intervention. RESULTS Glucose ingestion did not have beneficial effects on resistance training-induced increases of ribosomal content (mean difference 7.6% [- 7.2, 24.9], p = 0.34; ribosomal RNA, 47S/18S/28S/5.8S/5S, range 7.6-37.9%, p = 0.40-0.98) or levels of relevant transcriptional or translational regulators (c-MYK/UBF/rpS6, p = 0.094-0.292). Of note, both baseline and trained state data of total RNA showed a linear relationship with UBF; a ∼14% increase in total RNA corresponded to 1 SD unit increase in UBF (p = 0.003). CONCLUSION Glucose ingestion before and after resistance training sessions did not augment ribosomal RNA accumulation during twelve days of heavy-load resistance training in moderately trained young adults.
Collapse
Affiliation(s)
- Kristian Lian
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway.
| | - Daniel Hammarström
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Håvard Hamarsland
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Knut Sindre Mølmen
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Sara Christine Moen
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Stian Ellefsen
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| |
Collapse
|
7
|
Yang Y, Hou J, Luan J. Resistance mechanisms of Saccharomyces cerevisiae against silver nanoparticles with different sizes and coatings. Food Chem Toxicol 2024; 186:114581. [PMID: 38460669 DOI: 10.1016/j.fct.2024.114581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/15/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
To investigate the underlying resistance mechanisms of Saccharomyces cerevisiae against Ag-NPs with different particle sizes and coatings, transcriptome sequencing (RNA-seq) technology was used to characterize the transcriptomes from S. cerevisiae exposed to 20-PVP-Ag, 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag, respectively. The steroid biosynthesis was found as a general pathway for Ag-NPs stress responding, in which ERG6 and ERG3 were inhibited and ERG11, ERG25 and ERG5 were significantly up-regulated to resist the stress by supporting the later mutation and resistance and modulate drug efflux indirectly. The resistance mechanism of S. cerevisiae to 20-PVP-Ag seems different from that of 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag. Under the 20-PVP-Ag, transmembrane transporter activity, transition metal ion homeostasis and oxidative phosphorylation pathway were main resistance pathways to enhance cell transport processes. While 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag mainly impacted RNA binding, structural constituent of ribosome and ribosome pathway which can provide more energy to maintain the number and function of protein in cells. This study reveals the differences in resistance mechanisms of S. cerevisiae to Ag-NPs with different particle sizes and coatings, and explains several main regulatory mechanisms used to respond to silver stress. It will provide theoretical basis for the study of chemical risk assessment.
Collapse
Affiliation(s)
- Yue Yang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, PR China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, PR China.
| | - Jian Luan
- College of Life Sciences, Jilin Normal University, Jilin, 136000, PR China
| |
Collapse
|
8
|
Sekiguchi T, Ishii T, Funakoshi M, Kobayashi H, Furuno N. Interaction between Gtr2p and ribosomal Rps31p affects the incorporation of Rps31p into ribosomes of Saccharomyces cerevisiae. Biochem Biophys Res Commun 2024; 699:149499. [PMID: 38281328 DOI: 10.1016/j.bbrc.2024.149499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/07/2024] [Indexed: 01/30/2024]
Abstract
In yeast, ras-like small G proteins, Gtr1p and Gtr2p, form heterodimers that affect cell division, detect amino acids, and regulate the activity of TORC1, a protein complex that integrates various signals, including those related to nutrient availability, growth factors, and stress signals. To explore novel roles of Gtr2p, yeast two-hybrid screening was performed using gtr2S23Np, an active form of Gtr2p, which identified Rps31p and Rpl12p as Gtr2p-interacting proteins. In the present study, we found that Gtr2p, but not Gtr1p, interacts with Rps31p, a 40S ribosomal subunit, and a component of the ubiquitin fusion protein Ubi3p, which is essential for the initiation and elongation of translation. In yeast cells expressing gtr2Q66Lp, an inactive form of Gtr2p, the interaction between Rps31p and gtr2Q66Lp, as well as the level of exogenous expression of Rps31p, was reduced. However, the level of exogenous expression of Rpl12p was unaffected. Introducing a mutation in ubiquitin target lysine residues to arginine (rps31-K5R) restored the level of exogenously expressed Rps31p and rescued the rapamycin and caffeine sensitivity of gtr2Q66L cells. Sucrose density gradient centrifugation of yeast cell lysate expressing Rps31p and gtr2Q66Lp revealed that exogenously expressed Rps31p was poorly incorporated, whereas rps31-K5Rp was efficiently incorporated, into ribosomes. These results suggest that Gtr2p influences incorporation of Rps31p into ribosomes and contributes to drug resistance through its interaction with Rps31p.
Collapse
Affiliation(s)
- Takeshi Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Takashi Ishii
- Department of Nutrition and Dietetics, School of Family and Consumer Sciences, Kamakura Women's University, Kanagawa, 247-0056, Japan
| | - Minoru Funakoshi
- R&D Division, Marine Products Kimuraya Co., Ltd., 3307 Watari, Sakaiminato, Tottori, 684-0072, Japan
| | - Hideki Kobayashi
- Department of Human Nutrition, Faculty of Contemporary Sciences, Chugoku-Gakuen University, 83 Niwase, Okayama, 701-0197, Japan
| | - Nobuaki Furuno
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8526, Japan
| |
Collapse
|
9
|
Bian C, Zhang J, Zheng X, Qiao M, Li Y, Chen X, Si S. Synthesis and structure-activity relationships of novel 14-membered 2-fluoro ketolides with structural modification at the C11 position. Eur J Med Chem 2024; 267:116181. [PMID: 38354519 DOI: 10.1016/j.ejmech.2024.116181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
A series of novel C11 substituted 14-membered 2-fluoro ketolides were synthesized and evaluated for their antibacterial activity against erythromycin-resistant and erythromycin-susceptible clinical isolates and strains from ATCC. The overall antibacterial spectra of the semi-synthetic antibiotics are similar to that of telithromycin (TEL) and most of them exhibited excellent activity against Gram-positive bacteria (S. epidermidis, S. pneumoniae, S. aureus) and several Gram-negative bacteria (M. catarrhalis, H. influenza). Compounds 11c, 11g, 11h, 11q, 12a, 12b, 12d and 12e displayed 4-16 fold more potency than TEL against all the tested erythromycin-resistant S. epidermidis strains and S. pneumonia SPN19-8 and SPN19-8. Compounds 11b, 11c, 11e, 11g, 11h, 11q, 12a, 12b and 12c showed at least 8 fold potency than TEL against erythromycin-resistant M. catarrhalis BCA19-5 and BCA19-6. Molecular docking suggested compound 12d oriented the macrolide ring and side chain similarly to solithromycin (SOL). Noticeably an additional hydrogen bond was observed between the Lys90 residue of ribosome protein L22 and the carbamate group at the C11 position, which might provide a rational explanation for the enhanced antibacterial activity of target compounds. Therefore this research would offer a new perspective for further structural optimization of the C11 side chain. Based on the results of antibacterial activity, cytotoxicity and structural diversity, 5 compounds (11a, 11b, 11h, 12d and 12i) were selected for the stability testing of human liver microsomes and compound 11a exhibited preferable metabolic stability.
Collapse
Affiliation(s)
- Cong Bian
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Xiao Zheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Mengqian Qiao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Xiaofang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| |
Collapse
|
10
|
Dawane A, Deshpande S, Vijayaraghavreddy P, Vemanna RS. Polysome-bound mRNAs and translational mechanisms regulate drought tolerance in rice. Plant Physiol Biochem 2024; 208:108513. [PMID: 38513519 DOI: 10.1016/j.plaphy.2024.108513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. Drought stress at the anthesis stage in rice affects productivity due to the inefficiency of protein synthesis machinery. The effect of translational mechanisms on different pathways involved in cellular tolerance plays an important role. We report differential responses of translation-associated mechanisms in rice using polysome bound mRNA sequencing at anthesis stage drought stress in resistant Apo and sensitive IR64 genotypes. Apo maintained higher polysomes with 60 S-to-40 S and polysome-to-monosome ratios which directly correlate with protein levels under stress. IR64 has less protein levels under stress due to defective translation machinery and reduced water potential. Many polysome-bound long non-coding RNAs (lncRNA) were identified in both genotypes under drought, influencing translation. Apo had higher levels of N6-Methyladenosine (m6A) mRNA modifications that contributed for sustained translation. Translation machinery in Apo could maintain higher levels of photosynthetic machinery-associated proteins in drought stress, which maintain gas exchange, photosynthesis and yield under stress. The protein stability and ribosome biogenesis mechanisms favoured improved translation in Apo. The phytohormone signalling and transcriptional responses were severely affected in IR64. Our results demonstrate that, the higher translation ability of Apo favours maintenance of photosynthesis and physiological responses that are required for drought stress adaptation.
Collapse
Affiliation(s)
- Akashata Dawane
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Sanjay Deshpande
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | | | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India.
| |
Collapse
|
11
|
Mao Y, Qian SB. Making sense of mRNA translational "noise". Semin Cell Dev Biol 2024; 154:114-122. [PMID: 36925447 PMCID: PMC10500040 DOI: 10.1016/j.semcdb.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023]
Abstract
The importance of translation fidelity has been apparent since the discovery of genetic code. It is commonly believed that translation deviating from the main coding region is to be avoided at all times inside cells. However, ribosome profiling and mass spectrometry have revealed pervasive noncanonical translation. Both the scope and origin of translational "noise" are just beginning to be appreciated. Although largely overlooked, those translational "noises" are associated with a wide range of cellular functions, such as producing unannotated protein products. Furthermore, the dynamic nature of translational "noise" is responsive to stress conditions, highlighting the beneficial effect of translational "noise" in stress adaptation. Mechanistic investigation of translational "noise" will provide better insight into the mechanisms of translational regulation. Ultimately, they are not "noise" at all but represent a signature of cellular activities under pathophysiological conditions. Deciphering translational "noise" holds the therapeutic and diagnostic potential in a wide spectrum of human diseases.
Collapse
Affiliation(s)
- Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
12
|
Monem PC, Arribere JA. A ubiquitin language communicates ribosomal distress. Semin Cell Dev Biol 2024; 154:131-137. [PMID: 36963992 PMCID: PMC10878831 DOI: 10.1016/j.semcdb.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023]
Abstract
Cells entrust ribosomes with the critical task of identifying problematic mRNAs and facilitating their degradation. Ribosomes must communicate when they encounter and stall on an aberrant mRNA, lest they expose the cell to toxic and disease-causing proteins, or they jeopardize ribosome homeostasis and cellular translation. In recent years, ribosomal ubiquitination has emerged as a central signaling step in this process, and proteomic studies across labs and experimental systems show a myriad of ubiquitination sites throughout the ribosome. Work from many labs zeroed in on ubiquitination in one region of the small ribosomal subunit as being functionally significant, with the balance and exact ubiquitination sites determined by stall type, E3 ubiquitin ligases, and deubiquitinases. This review discusses the current literature surrounding ribosomal ubiquitination during translational stress and considers its role in committing translational complexes to decay.
Collapse
Affiliation(s)
- Parissa C Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Joshua A Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
13
|
Hochstoeger T, Chao JA. Towards a molecular understanding of the 5'TOP motif in regulating translation of ribosomal mRNAs. Semin Cell Dev Biol 2024; 154:99-104. [PMID: 37316417 DOI: 10.1016/j.semcdb.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Vertebrate cells have evolved a simple, yet elegant, mechanism for coordinated regulation of ribosome biogenesis mediated by the 5' terminal oligopyrimidine motif (5'TOP). This motif allows cells to rapidly adapt to changes in the environment by specifically modulating translation rate of mRNAs encoding the translation machinery. Here, we provide an overview of the origin of this motif, its characterization, and progress in identifying the key regulatory factors involved. We highlight challenges in the field of 5'TOP research, and discuss future approaches that we think will be able to resolve outstanding questions.
Collapse
Affiliation(s)
- Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| |
Collapse
|
14
|
Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie 2024; 217:20-30. [PMID: 37741547 DOI: 10.1016/j.biochi.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.
Collapse
Affiliation(s)
- Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France.
| |
Collapse
|
15
|
Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
Collapse
Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
| |
Collapse
|
16
|
Yang Q, Yu H, Li Q. Comparative Transcriptome Analysis Reveals the Role of Ribosome Reduction in Impeding Oogenesis in Female Triploid Crassostrea Gigas. Mar Biotechnol (NY) 2024; 26:125-135. [PMID: 38217752 DOI: 10.1007/s10126-024-10283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
The fecundity of triploid female Crassostrea gigas exhibited significant variation and was lower compared to diploid individuals. Previous studies categorized mature stage triploid female C. gigas into two groups: female α, characterized by a high number of oocytes, and female β, displaying few or no oocytes. To investigate the molecular mechanisms underlying irregular oogenesis and fecundity differences in triploid C. gigas, we performed a comparative analysis of gonad transcriptomes at different stages of gonadal development, including female α, female β, and diploids. During early oogenesis, functional enrichment analysis between female diploids and putative female β triploids revealed differently expressed genes (DEGs) in the ribosome and ribosome biogenesis pathways. Expression levels of DEGs in these pathways were significantly decreased in the putative female β triploid, suggesting a potential role of reduced ribosome levels in obstructing triploid oogenesis. Moreover, to identify regulatory pathways in gonad development, female oysters at the early and mature stages were compared. The DNA repair and recombination proteins pathways were enriched in female diploids and female α triploids but absent in female β triploids. Overall, we propose that decreased ribosome biogenesis in female triploids hinders the differentiation of germ stem cells, leading to the formation of a large number of abnormal germ cells and ultimately resulting in reduced fecundity. The variation in fertility among triploids appeared to be related to the degree of DNA damage repair during female gonad development. This study offers valuable insights into the oogenesis process in female triploid C. gigas.
Collapse
Affiliation(s)
- Qiong Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
17
|
Burghardt E, Rakijas J, Tyagi A, Majumder P, Olson BJSC, McDonald JA. Transcriptome analysis reveals temporally regulated genetic networks during Drosophila border cell collective migration. BMC Genomics 2023; 24:728. [PMID: 38041052 PMCID: PMC10693066 DOI: 10.1186/s12864-023-09839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Collective cell migration underlies many essential processes, including sculpting organs during embryogenesis, wound healing in the adult, and metastasis of cancer cells. At mid-oogenesis, Drosophila border cells undergo collective migration. Border cells round up into a small group at the pre-migration stage, detach from the epithelium and undergo a dynamic and highly regulated migration at the mid-migration stage, and stop at the oocyte, their final destination, at the post-migration stage. While specific genes that promote cell signaling, polarization of the cluster, formation of protrusions, and cell-cell adhesion are known to regulate border cell migration, there may be additional genes that promote these distinct active phases of border cell migration. Therefore, we sought to identify genes whose expression patterns changed during border cell migration. RESULTS We performed RNA-sequencing on border cells isolated at pre-, mid-, and post-migration stages. We report that 1,729 transcripts, in nine co-expression gene clusters, are temporally and differentially expressed across the three migration stages. Gene ontology analyses and constructed protein-protein interaction networks identified genes expected to function in collective migration, such as regulators of the cytoskeleton, adhesion, and tissue morphogenesis, but also uncovered a notable enrichment of genes involved in immune signaling, ribosome biogenesis, and stress responses. Finally, we validated the in vivo expression and function of a subset of identified genes in border cells. CONCLUSIONS Overall, our results identified differentially and temporally expressed genetic networks that may facilitate the efficient development and migration of border cells. The genes identified here represent a wealth of new candidates to investigate the molecular nature of dynamic collective cell migrations in developing tissues.
Collapse
Affiliation(s)
- Emily Burghardt
- Division of Biology, Kansas State University, 116 Ackert Hall, 1717 Claflin Rd, Manhattan, KS, 66506, USA
| | - Jessica Rakijas
- Division of Biology, Kansas State University, 116 Ackert Hall, 1717 Claflin Rd, Manhattan, KS, 66506, USA
| | - Antariksh Tyagi
- Division of Biology, Kansas State University, 116 Ackert Hall, 1717 Claflin Rd, Manhattan, KS, 66506, USA
| | - Pralay Majumder
- Department of Life Sciences, Presidency University, Kolkata, 700073, West Bengal, India
| | - Bradley J S C Olson
- Division of Biology, Kansas State University, 116 Ackert Hall, 1717 Claflin Rd, Manhattan, KS, 66506, USA.
| | - Jocelyn A McDonald
- Division of Biology, Kansas State University, 116 Ackert Hall, 1717 Claflin Rd, Manhattan, KS, 66506, USA.
| |
Collapse
|
18
|
Jia W, Yuan J, Li S, Cheng B. The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins. Biochim Biophys Acta Rev Cancer 2023; 1878:189018. [PMID: 37944831 DOI: 10.1016/j.bbcan.2023.189018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Dysregulated protein synthesis is a hallmark of tumors. mRNA translation reprogramming contributes to tumorigenesis, which is fueled by abnormalities in ribosome formation, tRNA abundance and modification, and translation factors. Not only malignant cells but also stromal cells within tumor microenvironment can undergo transformation toward tumorigenic phenotypes during translational reprogramming. Ribosome-inactivating proteins (RIPs) have garnered interests for their ability to selectively inhibit protein synthesis and suppress tumor growth. This review summarizes the role of dysregulated translation machinery in tumor development and explores the potential of RIPs in cancer treatment.
Collapse
Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China
| | - Jiaying Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Shu Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China.
| |
Collapse
|
19
|
Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
Collapse
Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
| |
Collapse
|
20
|
Shea J, Davis L, Quaye B, Gedeon T. Ribosome Abundance Control in Prokaryotes. Bull Math Biol 2023; 85:119. [PMID: 37861893 DOI: 10.1007/s11538-023-01212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Cell growth is an essential phenotype of any unicellular organism and it crucially depends on precise control of protein synthesis. We construct a model of the feedback mechanisms that regulate abundance of ribosomes in E. coli, a prototypical prokaryotic organism. Since ribosomes are needed to produce more ribosomes, the model includes a positive feedback loop central to the control of cell growth. Our analysis of the model shows that there can be only two coexisting equilibrium states across all 23 parameters. This precludes the existence of hysteresis, suggesting that the ribosome abundance changes continuously with parameters. These states are related by a transcritical bifurcation, and we provide an analytic formula for parameters that admit either state.
Collapse
Affiliation(s)
- Jacob Shea
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Bright Quaye
- Department of Economics, Washington University, St. Louis, MO, USA
| | - Tomas Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717, USA.
| |
Collapse
|
21
|
Höger B, Peifer C, Beitz E. Cell-free production of fluorescent proteins for the discovery of novel ribosome-targeting antibiotics. J Microbiol Methods 2023; 213:106814. [PMID: 37652138 DOI: 10.1016/j.mimet.2023.106814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023]
Abstract
Various issues including the overuse of antibiotics has led to the development of threatening multidrug-resistant bacterial strains urging development of novel anti-infectives. One quarter of current clinical phase III antibiotic drug candidates address ribosomal protein translation as a target. Here, we describe an effective cell-free in vitro screening system for inhibitors of bacterial ribosome activity with direct fluorescence read-out. Using ribosomal S30 extracts from Escherichia coli, Salmonella enterica, and Pseudomonas putida, the validity of this system is demonstrated by concentration-dependent inhibition of translation by a set of different classes of translation-targeting drugs. The single-compartment cell-free translation reaction is compatible with multi-well formats. Fluorophore formation of green fluorescent protein or monomeric NeonGreen occurs in an hour time frame without the need of adding reagents for secondary enzymatic detection saving handling time, and prohibiting false positives. As label-free readout, the dose response further allows for IC50 determination in the same setup. Together, we show that cell-free production of fluorescent proteins for the discovery of ribosome-targeting antibiotics is feasible and amenable to high-throughput applications.
Collapse
Affiliation(s)
- Bastian Höger
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, Kiel, Germany.
| |
Collapse
|
22
|
Mo J, Lv R, Qin X, Wu X, Chen H, Yan N, Shi J, Wu Y, Liu W, Kong RYC, Guo J. Mechanistic insights into hormesis induced by erythromycin in the marine alga Thalassiosira weissflogii. Ecotoxicol Environ Saf 2023; 263:115242. [PMID: 37441949 DOI: 10.1016/j.ecoenv.2023.115242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Erythromycin (ERY) is a typical macrolide antibiotic with large production and extensive use on a global scale. Detection of ERY in both freshwaters and coaster seawaters, as well as relatively high ecotoxicity of ERY have been documented. Notably, hormesis has been reported on several freshwater algae under ERY stress, where growth was promoted at relatively lower exposures but inhibited at higher treatment levels. On the contrary, there is limited information of ERY toxicity in marine algae, hampering the risk assessment on ERY in the coaster waters. The presence of hormesis may challenge the current concept of dose-response adopted in chemical risk assessment. Whether and how exposure to ERY can induce dose-dependent toxicity in marine algae remain virtually unknown, especially at environmentally relevant concentrations. The present study used a model marine diatom Thalassiosira weissflogii (T. weissflogii) to reveal its toxicological responses to ERY at different biological levels and decipher the underlying mechanisms. Assessment of multiple apical endpoints shows an evident growth promotion following ERY exposure at an environmentally relevant concentration (1 µg/L), associated with increased contents reactive oxygen species (ROS) and chlorophyll-a (Chl-a), activated signaling pathways related to ribosome biosynthesis and translation, and production of total soluble protein. By contrast, growth inhibition in the 750 and 2500 µg/L treatments was attributed to reduced viability, increased ROS formation, reduced content of total soluble protein, inhibited photosynthesis, and perturbed signaling pathways involved in xenobiotic metabolism, ribosome, metabolism of amino acid, and nitrogen metabolism. Measurements of multiple apical endpoints coupled with de novo transcriptomics analysis applied in the present study, a systems biology approach, can generate detailed mechanistic information of chemical toxicity including dose-response and species sensitivity difference used in environmental risk assessment.
Collapse
Affiliation(s)
- Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region.
| | - Runnan Lv
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xian Qin
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xintong Wu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Haibo Chen
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Neng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingchun Shi
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Yinglin Wu
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang, Guangdong 524048, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Richard Y C Kong
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| |
Collapse
|
23
|
Sinclair P, Hakeem J, Kumar SG, Loser D, Dixit K, Leist M, Kraushaar U, Kabbani N. Proteomic responses in the human dopaminergic LUHMES cell line to imidacloprid and its metabolites imidacloprid-olefin and desnitro-imidacloprid. Pestic Biochem Physiol 2023; 194:105473. [PMID: 37532312 DOI: 10.1016/j.pestbp.2023.105473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 08/04/2023]
Abstract
Neonicotinoids (neonics) are amongst the most commonly used class of pesticides globally. In the United States, imidacloprid (IMI) is extensively used for agriculture and in other common applications such as house-hold pest control. Regular exposure to IMI, and several of its known metabolites including IMI-olefin and desnitro-imidacloprid (DN-IMI), has been shown to be harmful to many organisms including mammals, birds, and fish. Studies show that neonics bind human nicotinicacetylcholine receptors (nAChRs) and cause cellular toxicity. In the dopaminergic Lund human mesencephalic (LUHMES) cell line, IMI and other neonics (10-100 μM) have been recently shown to activate intracellular calcium signaling through nAChRs. Thus, we examined proteomic responses of LUHMES cells to a 48-h treatment with 50 μM IMI, IMI-olefin, or DN-IMI. Our findings show differential effects of these neonics on cellular protein expression. Bioinformatic analysis of significantly altered proteins indicates an effect of IMI, IMI-olefin, and DN-IMI on protein synthesis and ribosomal function. These findings suggest a role for protein synthesis and transcriptional regulation in neonic-mediated dopaminergic neurotoxicity.
Collapse
Affiliation(s)
| | - Julia Hakeem
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Sreehari G Kumar
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Dominik Loser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Kushan Dixit
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457 Constance, Germany
| | - Udo Kraushaar
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Nadine Kabbani
- Interdisciplinary Program in Neuroscience, George Mason University; School of Systems Biology, George Mason University.
| |
Collapse
|
24
|
Matsuura-Suzuki E, Toh H, Iwasaki S. Human-rabbit Hybrid Translation System to Explore the Function of Modified Ribosomes. Bio Protoc 2023; 13:e4714. [PMID: 37456340 PMCID: PMC10339341 DOI: 10.21769/bioprotoc.4714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro translation systems are a useful biochemical tool to research translational regulation. Although the preparation of translation-competent cell extracts from mammals has often been a challenge, the commercially available rabbit reticulocyte lysate (RRL) is an exception. However, its valid use, investigating the mechanism of translation machinery such as ribosomes in RRL, presents an analytic hurdle. To overcome this issue, the hybrid translation system, which is based on the supplementation of purified human ribosomes into ribosome-depleted RRL, has been developed. Here, we describe the step-by-step protocol of this system to study translation driven by ribosomes lacking post-translational modifications of the ribosomal protein. Moreover, we combined this approach with a previously developed reporter mRNA to assess the processivity of translation elongation. This protocol could be used to study the potency of heterologous ribosomes.
Collapse
Affiliation(s)
- Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| |
Collapse
|
25
|
Altwegg KA, Pratap UP, Liu Z, Liu J, Sanchez JR, Yang X, Ebrahimi B, Panneerdoss DM, Li X, Sareddy GR, Viswanadhapalli S, Rao MK, Vadlamudi RK. Targeting PELP1 oncogenic signaling in TNBC with the small molecule inhibitor SMIP34. Breast Cancer Res Treat 2023; 200:151-162. [PMID: 37199805 PMCID: PMC10224866 DOI: 10.1007/s10549-023-06958-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023]
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Oncogenic PELP1 is frequently overexpressed in TNBC, and it has been demonstrated that PELP1 signaling is essential for TNBC progression. The therapeutic utility of targeting PELP1 in TNBC, however, remains unknown. In this study, we investigated the effectiveness of SMIP34, a recently developed PELP1 inhibitor for the treatment of TNBC. METHODS To ascertain the impact of SMIP34 treatment, we used seven different TNBC models for testing cell viability, colony formation, invasion, apoptosis, and cell cycle analysis. Western blotting and RT-qPCR were used to determine the mechanistic insights of SMIP34 action. Using xenograft and PDX tumors, the ability of SMIP34 in suppressing proliferation was examined both ex vivo and in vivo. RESULTS TNBC cells' viability, colony formation, and invasiveness were all decreased by SMIP34 in in vitro cell-based assays, while apoptosis was increased. SMIP34 treatment promoted the degradation of PELP1 through the proteasome pathway. RT-qPCR analyses confirmed that SMIP34 treatment downregulated PELP1 target genes. Further, SMIP34 treatment substantially downregulated PELP1 mediated extranuclear signaling including ERK, mTOR, S6 and 4EBP1. Mechanistic studies confirmed downregulation of PELP1 mediated ribosomal biogenesis functions including downregulation of cMyc and Rix complex proteins LAS1L, TEX-10, and SENP3. The proliferation of TNBC tumor tissues was decreased in explant experiments by SMIP34. Additionally, SMIP34 treatment markedly decreased tumor progression in both TNBC xenograft and PDX models. CONCLUSIONS Together, these findings from in vitro, ex vivo, and in vivo models show that SMIP34 may be a useful therapeutic agent for inhibiting PELP1 signaling in TNBC.
Collapse
Affiliation(s)
- Kristin A Altwegg
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Uday P Pratap
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Zexuan Liu
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Junhao Liu
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - John R Sanchez
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Xue Yang
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Department of Obstetrics and Gynecology, Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Behnam Ebrahimi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Durga Meenakshi Panneerdoss
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Xiaonan Li
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Gangadhara R Sareddy
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Suryavathi Viswanadhapalli
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Manjeet K Rao
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
- Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
- Audie L. Murphy Division, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
| |
Collapse
|
26
|
Aspnes GE, Coffey SB, Darout E, Dechert-Schmitt AM, Dullea RG, Kamlet AS, Limberakis C, Londregan AT, McClure KF, Menhaji-Klotz E, Piotrowski DW, Polivkova J, Raymer B, Ruggeri RB, Salatto CT, Tu M, Wei L, Xiao J. Small molecule inhibitors of PCSK9. SAR investigations of head and amine groups. Bioorg Med Chem Lett 2023:129394. [PMID: 37379958 DOI: 10.1016/j.bmcl.2023.129394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/02/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023]
Abstract
Our previous work on the optimization of a new class of small molecule PCSK9 mRNA translation inhibitors focused on empirical optimization of the amide tail region of the lead PF-06446846 (1). This work resulted in compound 3 that showed an improved safety profile. We hypothesized that this improvement was related to diminished binding of 3 to non-translating ribosomes and an apparent improvement in transcript selectivity. Herein, we describe our efforts to further optimize this series of inhibitors through modulation of the heterocyclic head group and the amine fragment. Some of the effort was guided by an emerging cryo electron microscopy structure of the binding mode of 1 in the ribosome. These efforts led to the identification of 15 that was deemed suitable for evaluation in a humanized PCSK9 mouse model and a rat toxicology study. Compound 15 demonstrated a dose dependent reduction of plasma PCSK9 levels. The rat toxicological profile was not improved over that of 1, which precluded 15 from further consideration as a clinical candidate.
Collapse
Affiliation(s)
- Gary E Aspnes
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Steven B Coffey
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Etzer Darout
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | | | - Robert G Dullea
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Adam S Kamlet
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Chris Limberakis
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Allyn T Londregan
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Kim F McClure
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Elnaz Menhaji-Klotz
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - David W Piotrowski
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.
| | - Jana Polivkova
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Brian Raymer
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Roger B Ruggeri
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | | | - Meihua Tu
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Liuqing Wei
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Jun Xiao
- Pfizer Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| |
Collapse
|
27
|
Liu Y, Sun K, Gan Y, Liu H, Yu J, Xu W, Zhang L, Chen D. RNA-Sequencing Reveals Gene Expression and Pathway Signatures in Umbilical Cord Blood Affected by Birth Delivery Mode. Phenomics 2023; 3:228-242. [PMID: 37325709 PMCID: PMC10260732 DOI: 10.1007/s43657-022-00086-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Cesarean section (CS) confers increased risk of type I diabetes, asthma, inflammatory bowel disease, celiac disease, overweight and obesity, etc., in the offspring. However, the underlying mechanism remains unknown. To investigate the influence of CS on gene expression in cord blood, we have performed RNA-sequencing followed by single-gene analysis, gene set enrichment analysis, gene co-expression network analysis, and interacting genes/proteins analysis in eight full-term infants born by elective CS and eight matched vaginally delivered (VD) infants. Crucial genes identified above were further validated in another 20 CS and 20 VD infants. We found for the first time that mRNA expression of genes involved in immune response (IL12A, INFG, IL1B, TNF, MIF, IL4, CA1, IFI27, HLA-DOB and EPHB1) and metabolism (DLK1, CYP2A6 and GATM) were significantly influenced by CS. Notably, serum TNF-α and IFN-γ were remarkably up-regulated in the CS infants (p = 5.0 × 10-4 and 3.0 × 10-3, respectively) compared to the VD infants. It is biologically plausible that CS may exert adverse impacts on offspring health through influencing expression of genes in the above processes. These findings will help understand the potential underlying mechanisms of the adverse health impacts of CS and identify biomarkers for future health of offspring born with different delivery modes. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00086-7.
Collapse
Affiliation(s)
- Yongjie Liu
- Ministry of Education and Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Kun Sun
- Shenzhen Bay Laboratory, Shenzhen, 518107 China
| | - Yuexin Gan
- Ministry of Education and Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Han Liu
- Department of Obstetrics and Gynaecology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025 China
| | - Juehua Yu
- Ministry of Education and Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
- Centre for Experimental Studies and Research, The First Affiliated Hospital of Kunming Medical University, Kunming, 650032 China
| | - Wei Xu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Lin Zhang
- Ministry of Education and Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
- Department of Obstetrics and Gynaecology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025 China
| | - Dan Chen
- Department of Gynecology, Third Xiangya Hospital of Central South University, Changsha, 410013 China
- Shanghai Fosun Pharmaceutical Industrial Development, Co., Ltd, Shanghai, 200233 China
| |
Collapse
|
28
|
Abstract
Darwin's assertion that "it is mere rubbish thinking, at present, of origin of life" (quoted from Peretó et al. 2009) is no longer valid. By synthesizing origin of life (OoL) research from its inception to recent findings, with a focus on (i) proof-of-principle prebiotically plausible syntheses and (ii) molecular relics of the ancient RNA World, we present a comprehensive up-to-date description of science's understanding of the OoL and the RNA World hypothesis. Based on these observations, we solidify the consensus that RNA evolved before coded proteins and DNA genomes, such that the biosphere began with an RNA core where much of the translation apparatus and related RNA architecture arose before RNA transcription and DNA replication. This supports the conclusion that the OoL was a gradual process of chemical evolution involving a series of transitional forms between prebiotic chemistry and the last universal common ancestor (LUCA) during which RNA played a central role, and that many of the events and their relative order of occurrence along this pathway are known. The integrative nature of this synthesis also extends previous descriptions and concepts and should help inform future questions and experiments about the ancient RNA World and the OoL.
Collapse
|
29
|
Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
Collapse
Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
30
|
Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
Collapse
Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| |
Collapse
|
31
|
Günnigmann M, Koubek J, Kramer G, Bukau B. Selective ribosome profiling as a tool to study interactions of translating ribosomes in mammalian cells. Methods Enzymol 2023; 684:1-38. [PMID: 37230585 DOI: 10.1016/bs.mie.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The processing, membrane targeting and folding of newly synthesized polypeptides is closely linked to their synthesis at the ribosome. A network of enzymes, chaperones and targeting factors engages ribosome-nascent chain complexes (RNCs) to support these maturation processes. Exploring the modes of action of this machinery is critical for our understanding of functional protein biogenesis. Selective ribosome profiling (SeRP) is a powerful method for interrogating co-translational interactions of maturation factors with RNCs. It provides proteome-wide information on the factor's nascent chain interactome, the timing of factor binding and release during the progress of translation of individual nascent chain species, and the mechanisms and features controlling factor engagement. SeRP is based on the combination of two ribosome profiling (RP) experiments performed on the same cell population. In one experiment the ribosome-protected mRNA footprints of all translating ribosomes of the cell are sequenced (total translatome), while the other experiment detects only the ribosome footprints of the subpopulation of ribosomes engaged by the factor of interest (selected translatome). The codon-specific ratio of ribosome footprint densities from selected over total translatome reports on the factor enrichment at specific nascent chains. In this chapter, we provide a detailed SeRP protocol for mammalian cells. The protocol includes instructions on cell growth and cell harvest, stabilization of factor-RNC interactions, nuclease digest and purification of (factor-engaged) monosomes, as well as preparation of cDNA libraries from ribosome footprint fragments and deep sequencing data analysis. Purification protocols of factor-engaged monosomes and experimental results are exemplified for the human ribosomal tunnel exit-binding factor Ebp1 and chaperone Hsp90, but the protocols are readily adaptable to other co-translationally acting mammalian factors.
Collapse
Affiliation(s)
- Manuel Günnigmann
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jiří Koubek
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| |
Collapse
|
32
|
Alferova VA, Maviza TP, Biryukov MV, Zakalyukina YV, Polshakov VI, Sergiev PV, Korshun VA, Osterman IA. Characterization of a novel natural tetracenomycin reveals crucial role of 4-hydroxy group in ribosome binding. Biochimie 2023; 206:150-153. [PMID: 36346253 DOI: 10.1016/j.biochi.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 12/01/2022]
Abstract
The aromatic polyketides tetracenomycins were recently found to be potent inhibitors of protein synthesis. Their binding site is located in a unique locus within the tunnel of the large ribosomal subunit. Here we report the isolation and structure elucidation of a novel natural tetracenomycin congener - O4-Me-tetracenomycin C (O4-Me-TcmC). This compound is isomeric to tetracenomycin X (TcmX), however, in contrast to TcmX, O4-Me-TcmC exhibited no antimicrobial activity and was unable to inhibit protein synthesis in vitro. Structural alignment of tetracenomycins to the binding locus from cryo-EM TcmX-70S ribosome data revealed the crucial role of the 4-hydroxyl group. These findings are important for further development of semi-synthetic tetracenomycins as potential antibacterials.
Collapse
Affiliation(s)
- Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia
| | - Tinashe P Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia
| | - Mikhail V Biryukov
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia; Department of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia; Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Yuliya V Zakalyukina
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia; Department of Soil Science, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, Moscow, 119021, Russia
| | - Ilya A Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028, Russia; Genetics and Life Sciences Research Center, Sirius University of Science and Technology, Sochi, 354340, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia.
| |
Collapse
|
33
|
Abstract
Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.
Collapse
Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| |
Collapse
|
34
|
Filipek K, Deryło K, Michalec-Wawiórka B, Zaciura M, González-Ibarra A, Krokowski D, Latoch P, Starosta AL, Czapiński J, Rivero-Müller A, Wawiórka L, Tchórzewski M. Identification of a novel alternatively spliced isoform of the ribosomal uL10 protein. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194890. [PMID: 36328276 DOI: 10.1016/j.bbagrm.2022.194890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is one of the key mechanisms extending the complexity of genetic information and at the same time adaptability of higher eukaryotes. As a result, the broad spectrum of isoforms produced by alternative splicing allows organisms to fine-tune their proteome; however, the functions of the majority of alternatively spliced protein isoforms are largely unknown. Ribosomal protein isoforms are one of the groups for which data are limited. Here we report characterization of an alternatively spliced isoform of the ribosomal uL10 protein, named uL10β. The uL10 protein constitutes the core element of the ribosomal stalk structure within the GTPase associated center, which represents the landing platform for translational GTPases - trGTPases. The stalk plays an important role in the ribosome-dependent stimulation of GTP by trGTPases, which confer unidirectional trajectory for the ribosome, allosterically contributing to the speed and accuracy of translation. We have shown that the newly identified uL10β protein is stably expressed in mammalian cells and is primarily located within the nuclear compartment with a minor signal within the cytoplasm. Importantly, uL10β is able to bind to the ribosomal particle, but is mainly associated with 60S and 80S particles; additionally, the uL10β undergoes re-localization into the mitochondria upon endoplasmic reticulum stress induction. Our results suggest a specific stress-related dual role of uL10β, supporting the idea of existence of specialized ribosomes with an altered GTPase associated center.
Collapse
Affiliation(s)
- Kamil Filipek
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Barbara Michalec-Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Monika Zaciura
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Alan González-Ibarra
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dawid Krokowski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Przemysław Latoch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Polish-Japanese Academy of Information Technology, Warsaw 02-008, Poland
| | - Agata L Starosta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 21-093 Lublin, Poland
| | - Leszek Wawiórka
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| |
Collapse
|
35
|
Chabronova A, van den Akker GGH, Housmans BAC, Caron MMJ, Cremers A, Surtel DAM, Wichapong K, Peffers MMJ, van Rhijn LW, Marchand V, Motorin Y, Welting TJM. Ribosomal RNA-based epitranscriptomic regulation of chondrocyte translation and proteome in osteoarthritis. Osteoarthritis Cartilage 2023; 31:374-385. [PMID: 36621590 DOI: 10.1016/j.joca.2022.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/08/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Osteoarthritis-related cartilage extracellular matrix remodeling is dependent on changes in chondrocyte protein expression. Yet, the role of ribosomes in chondrocyte translation regulation is unknown. In this exploratory study, we investigated ribosomal RNA (rRNA) epitranscriptomic-based ribosome heterogeneity in human articular chondrocytes and its relevance for osteoarthritis. METHODS Sequencing-based rRNA 2'-O-methylation profiling analysis (RiboMethSeq) was performed on non-OA primary human articular chondrocytes (n = 5) exposed for 14 days to osteoarthritic synovial fluid (14 donors, pooled, 20% v/v). The SW1353 SNORD71 KO cell pool was generated using LentiCRISPRv2/Cas9. The mode of translation initiation and fidelity were determined by dual-luciferase reporters. The cellular proteome was analyzed by LC-MS/MS and collagen type I protein expression was evaluated by immunoblotting. Loading of COL1A1 mRNA into polysomes was determined by sucrose gradient ultracentrifugation and fractionation. RESULTS We discovered that osteoarthritic synovial fluid instigates site-specific changes in the rRNA 2'-O-me profile of primary human articular chondrocytes. We identified five sites with differential 2'-O-me levels. The 2'-O-me status of 5.8S-U14 (one of identified differential 2'-O-me sites; decreased by 7.7%, 95% CI [0.9-14.5%]) was targeted by depleting the level of its guide snoRNA SNORD71 (50% decrease, 95% CI [33-64%]). This resulted in an altered ribosome translation modus (e.g., CrPV IRES, FC 3, 95% CI [2.2-4.1]) and promoted translation of COL1A1 mRNA which led to increased levels of COL1A1 protein (FC 1.7, 95% CI [1.3-2.0]). CONCLUSIONS Our data identify a novel concept suggesting that articular chondrocytes employ rRNA epitranscriptomic mechanisms in osteoarthritis development.
Collapse
Affiliation(s)
- A Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - G G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - B A C Housmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - M M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - A Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - D A M Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - K Wichapong
- Cardiovascular Research Institute Maastricht (CARIM), Department of Biochemistry, Maastricht University, Maastricht, the Netherlands
| | - M M J Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - L W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands
| | - V Marchand
- Université de Lorraine, UAR2008 IBSLor CNRS-INSERM, BioPole, Nancy, France
| | - Y Motorin
- Université de Lorraine, UAR2008 IBSLor CNRS-INSERM, BioPole, Nancy, France; Université de Lorraine, UMR7365 IMoPA, CNRS, BioPole, Nancy, France
| | - T J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, Maastricht, the Netherlands.
| |
Collapse
|
36
|
Huang G, Ma Y, Xie D, Zhao C, Zhu L, Xie G, Wu P, Wang W, Zhao Z, Cai Z. Evaluation of nanoplastics toxicity in the soil nematode Caenorhabditis elegans by iTRAQ-based quantitative proteomics. Sci Total Environ 2023; 862:160646. [PMID: 36493839 DOI: 10.1016/j.scitotenv.2022.160646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Plastic pollution is recognized as a major threat to ecosystems in the 21st century. Large plastic objects undergo biotic and abiotic degradation to generate micro- and nano-sized plastic pieces. Despite tremendous efforts to evaluate the adverse effects of microplastics, a comprehensive understanding of the toxicity of nanoplastics remains elusive, especially at the protein level. To this end, we used isobaric-tag-for-relative-and-absolute-quantitation-based quantitative proteomics to investigate the proteome dynamics of the soil nematode Caenorhabditis elegans in response to exposure to 100 nm polystyrene nanoplastics (PS-NPs). After 48 h of exposure to 0.1, 1, or 10 mg/L PS-NPs, 136 out of 1684 proteins were differentially expressed and 108 of these proteins were upregulated. These proteins were related to ribosome biogenesis, translation, proteolysis, kinases, protein processing in the endoplasmic reticulum, and energy metabolism. Remarkably, changes in proteome dynamics in response to exposure to PS-NPs were consistent with the phenotypic defects of C. elegans. Collectively, our findings demonstrate that disruption of proteome homeostasis is a biological consequence of PS-NPs accumulation in C. elegans, which provides insights into the molecular mechanisms underlying the toxicology of nanoplastics.
Collapse
Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Cunmin Zhao
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Guangshan Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Pengfei Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Wei Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, 999077, Hong Kong
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077, Hong Kong.
| |
Collapse
|
37
|
Abstract
The continued integrity of biological systems depends on a balance between interdependent elements at the molecular, cellular, and organismal levels. This is particularly true for the generation of ribosomes, which influence almost every aspect of cell and organismal biology. Ribosome biogenesis (RiBi) is an energetically demanding process that involves all three RNA polymerases, numerous RNA processing factors, chaperones, and the coordinated expression of 79-80 ribosomal proteins (r-proteins). Work over the last several decades has revealed that the dynamic regulation of ribosome production represents a major mechanism by which cells maintain homeostasis in response to changing environmental conditions and acute stress. More recent studies suggest that cells and tissues within multicellular organisms exhibit dramatically different levels of ribosome production and protein synthesis, marked by the differential expression of RiBi factors. Thus, distinct bottlenecks in the RiBi process, downstream of rRNA transcription, may exist within different cell populations of multicellular organisms during development and in adulthood. This review will focus on our current understanding of the mechanisms that link the complex molecular process of ribosome biogenesis with cellular and organismal physiology. We will discuss diverse topics including how different steps in the RiBi process are coordinated with one another, how MYC and mTOR impact RiBi, and how RiBi levels change between stem cells and their differentiated progeny. In turn, we will also review how regulated changes in ribosome production itself can feedback to influence cell fate and function.
Collapse
Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
| |
Collapse
|
38
|
Miyake T, McDermott JC. Re-organization of nucleolar architecture in myogenic differentiation. J Cell Sci 2023; 136:286887. [PMID: 36727534 DOI: 10.1242/jcs.260496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Myogenesis, the process of muscle differentiation, requires an extensive remodeling of the cellular transcriptome and proteome. Whereas the transcriptional program underpinning myogenesis is well characterized, the required adaptation in protein synthesis is incompletely understood. Enhanced protein synthesis necessitates ribosome biogenesis at the nucleolus. Nucleolar size and activity are inextricably linked with altered gene expression. Here, we report changes in nucleolar morphology and function during myogenic differentiation. Immunofluorescence analysis revealed alterations in nucleolar morphology that were dependent on the cellular state - proliferative or quiescent myogenic progenitors (myoblasts or reserve cells) contained multiple small nucleoli with a characteristic spherical shape, whereas multinucleated myotubes typically contained one large, often irregularly shaped nucleolus. These morphological alterations are consistent with changes to nucleolar phase separation properties. Re-organization of the nucleolar structure was correlated with enhanced rRNA production and protein translation. Inhibition of mTOR signaling with rapamycin perturbed nucleolar re-organization. Conversely, hyperactivated mTOR enhanced alterations in nucleolar morphology. These findings support the idea that there is an mTOR dependent re-organization of nucleolar structure during myogenesis, enhancing our understanding of myogenesis and possibly facilitating new approaches to therapeutic interventions in muscle pathologies.
Collapse
Affiliation(s)
- Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON M3J 1P3, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON M3J 1P3, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON M3J 1P3, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON M3J 1P3, Canada
| |
Collapse
|
39
|
Peerapen P, Chanthick C, Thongboonkerd V. Quantitative proteomics reveals common and unique molecular mechanisms underlying beneficial effects of caffeine and trigonelline on human hepatocytes. Biomed Pharmacother 2023; 158:114124. [PMID: 36521247 DOI: 10.1016/j.biopha.2022.114124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Caffeine and trigonelline are the major bioactive compounds in coffee. Caffeine alone or combined with other coffee compounds shows hepatoprotective effects. However, molecular mechanisms underlying such hepatoprotective effects remain unclear. We therefore addressed molecular effects of caffeine and trigonelline on human hepatocytes using quantitative proteomics followed by bioinformatic analyses to obtain topological and functional significance. HepG2 cells were treated with 100 μM caffeine or trigonelline for 24-h and evaluated by quantitative proteomics using nanoLC-ESI-LTQ-Orbitrap MS/MS. A total of 26 and 25 significantly altered proteins were identified in caffeine-treated and trigonelline-treated cells, respectively, compared with control cells. Topological analyses revealed that ribosomal and translation regulatory proteins predominantly served as the hub proteins associated with protein clusters. Functional analyses also revealed that these two bioactive compounds shared some molecular mechanisms via induction of translational processes. There were also other unique molecular functions and biological processes triggered or suppressed by either caffeine or trigonelline. These data highlight common and unique molecular mechanisms underlying the hepatoprotective effects of caffeine and trigonelline that may be useful for future clinical applications.
Collapse
Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanettee Chanthick
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
40
|
Raneri M, Alvarez-Ruiz E, Mossakovska D, Briani F. Cell-Based Fluorescent Screen Amenable to HTS to Identify Inhibitors of Bacterial Translation Initiation. Methods Mol Biol 2023; 2601:303-312. [PMID: 36445591 DOI: 10.1007/978-1-0716-2855-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A strategy that can be applied to the research of new molecules with antibacterial activity is to look for inhibitors of essential bacterial processes within large collections of chemically heterogeneous compounds. The implementation of this approach requires the development of assays aimed at the identification of molecules interfering with specific cell pathways that can also be used in high-throughput analysis of large chemical libraries. Here, we describe a fluorescence-based whole-cell assay in Escherichia coli devised to find inhibitors of the translation initiation pathway. Translation is a complex and essential mechanism. It involves numerous sub-steps performed by factors that are in many cases sufficiently dissimilar in bacterial and eukaryotic cells to be targetable with domain-specific drugs. As a matter of fact, translation has been proven as one of the few bacterial mechanisms pharmacologically tractable with specific antibiotics. The assay described in this updated chapter is tailored to the identification of molecules affecting the first stage of translation initiation, which is the most dissimilar step in bacteria versus mammals. The effect of the compounds under analysis is measured in living cells, thus allowing evaluation of their in vivo performance as inhibitors of translation initiation. Compared with other assays for antibacterials, the major advantages of this screen are its simplicity, high mechanism specificity, and amenability to scaling up to high-throughput analyses.
Collapse
Affiliation(s)
- Matteo Raneri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
- Sacco S.r.l., Cadorago, Italy
| | - Emilio Alvarez-Ruiz
- GlaxoSmithKline Platform Technologies and Science, Parque Tecnologico de Madrid, Madrid, Spain
| | - Danuta Mossakovska
- GlaxoSmithKline, Stevenage, Hertfordshire, UK
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| |
Collapse
|
41
|
Thärichen L, Englmeier R, Förster F. Sample Preparation of Isolated Mitochondria for Cryoelectron Tomography and In Situ Studies of Translation. Methods Mol Biol 2023; 2661:75-88. [PMID: 37166632 DOI: 10.1007/978-1-0716-3171-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cryoelectron tomography is a method to image biological samples three-dimensionally at molecular resolution. This modality provides insights into intracellular processes in their physiological settings. Obtaining a high-quality sample for cryoelectron tomography on mitochondria, however, can be challenging. In this chapter, we describe the crucial steps from sample preparation to data acquisition enabling studies of mitochondrial translation in situ by cryoelectron tomography. We provide detailed protocols for yeast and human mitochondria preparations yielding a high concentration of intact mitochondrial vesicles on cryo-EM grids. In addition, we describe a workflow for particle identification and spatial mapping in context of the organelle.
Collapse
Affiliation(s)
- Lena Thärichen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Robert Englmeier
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
42
|
Singh S, Lahry K, Mandava CS, Singh J, Shah RA, Sanyal S, Varshney U. Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli. RNA Biol 2023; 20:681-692. [PMID: 37676049 PMCID: PMC10486304 DOI: 10.1080/15476286.2023.2253395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast kinetics assay, the in vivo experiments show that Ltg causes accumulation of the 17S precursor of 16S rRNA and leads to a decrease in polysome levels in E. coli. IF2 overexpression in E. coli increases Ltg toxicity. However, the overexpression of initiator tRNA (i-tRNA) protects it from the Ltg toxicity. The depletion of i-tRNA or overexpression of its 3GC mutant (lacking the characteristic 3GC base pairs in anticodon stem) enhances Ltg toxicity, and this enhancement in toxicity is synthetic with IF2 overexpression. The Ltg treatment itself causes a detectable increase in IF2 levels in E. coli and allows initiation with an elongator tRNA, suggesting compromise in the fidelity/specificity of IF2 function. Also, Ltg causes increased accumulation of ribosome-binding factor A (RbfA) on 30S ribosomal subunit. Based on our genetic and biochemical investigations, we show that Ltg compromises the function of i-tRNA/IF2 complex in ribosome maturation.
Collapse
Affiliation(s)
- Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Jitendra Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
43
|
Bhattarai N, Cao B, Zeng SX, Lu H. Ribosomal Profiling by Gradient Fractionation of Cell Lysates. Methods Mol Biol 2023; 2666:149-155. [PMID: 37166663 DOI: 10.1007/978-1-0716-3191-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ribosomal profiling is a widely used technique for deep sequencing of ribosome-protected mRNA and for measuring ribosome status in cells. It is a powerful method that is typically employed for monitoring and measuring protein translation status and ribosome activity. Also, it has been used for monitoring the ribosomal stress-responsive events in the ribosome activity. Furthermore, this approach enables understanding of translational regulation, which is invisible in most proteomic approaches. Moreover, this method is known as an important approach for biological discovery such as identification of translation products. Hence, this methodology will be useful for studying cellular events engaging in ribosome assembly, ribosome biogenesis, ribosome activity, translation during the cell cycle, cell proliferation, and growth as well as the ribosomal stress response in mammalian cells.
Collapse
Affiliation(s)
- Nimisha Bhattarai
- Department of Biochemistry & Molecular Biology and Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Bo Cao
- Xavier University of Louisiana College of Pharmacy, New Orleans, LA, USA
| | - Shelya X Zeng
- Department of Biochemistry & Molecular Biology and Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Hua Lu
- Department of Biochemistry & Molecular Biology and Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.
| |
Collapse
|
44
|
Goltermann L, Andersen KL, Johansen HK, Molin S, La Rosa R. Macrolide therapy in Pseudomonas aeruginosa infections causes uL4 ribosomal protein mutations leading to high-level resistance. Clin Microbiol Infect 2022; 28:1594-1601. [PMID: 35988850 DOI: 10.1016/j.cmi.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/05/2022] [Accepted: 08/06/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Pseudomonas aeruginosa colonizes the cystic fibrosis (CF) airways causing chronic bacterial lung infections. CF patients are routinely treated with macrolides, however, P. aeruginosa is considered insusceptible as consequence of inadequate susceptibility testing leaving resistance mechanism completely overlooked. Here, we investigated a new mechanism of macrolide resistance caused by ribosomal protein mutations. METHODS Investigating a longitudinal collection of 529 isolates from CF patients and analysing 5758 protein sequences from different sources, mutations in P. aeruginosa's ribosomal proteins connected to macrolide resistance were identified. Using a modified susceptibility testing protocol, isolates harbouring a mutated uL4 ribosomal protein were tested for resistance against macrolide antibiotics and macrolide-induced quorum sensing modulation. Proteome and ribosome profiling were applied to assess the impact of the mutations on the bacterial physiology. RESULTS Five uL4 mutations were identified in isolates from different CF patients. Most mapped to the conserved loop region of uL4 and resulted in increased macrolide tolerance (>10-fold relative to wt strains). Greater concentrations (>10-fold) of macrolide antibiotic were needed to inhibit the growth, reduce swimming motility, and induce redox sensitivity of the uL4 mutants. 16 proteins involved in ribosome adaptation displayed altered expression possibly to compensate for the uL4 mutations, which changed the ribosome stoichiometry without negatively affecting bacterial physiology. CONCLUSIONS Macrolide antibiotics should, therefore, be considered as active antimicrobial agents against P. aeruginosa and resistance development should be contemplated when patients are treated with prolonged courses of macrolides. Importantly, improved macrolide susceptibility testing is necessary for the detection of resistant bacteria.
Collapse
Affiliation(s)
- Lise Goltermann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | | | - Helle Krogh Johansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Clinical Microbiology 9301, Rigshospitalet, 2100, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ruggero La Rosa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
45
|
Martínez-Férriz A, Ferrando A, Fathinajafabadi A, Farràs R. Ubiquitin-mediated mechanisms of translational control. Semin Cell Dev Biol 2022; 132:146-154. [PMID: 34952788 DOI: 10.1016/j.semcdb.2021.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/15/2022]
Abstract
mRNAs translation to proteins constitutes an important step of cellular gene expression that is highly regulated in response to different extracellular stimuli and stress situations. The fine control of protein synthesis is carried out both qualitatively and quantitatively, depending on the cellular demand at each moment. Post-translational modifications, in turn regulated by intracellular signaling pathways, play a key role in translation regulation. Among them, ubiquitination, whose role is becoming increasingly important in the control of translation, determines a correct balance between protein synthesis and degradation. In this review we focus on the role of ubiquitination (both degradative K48-linkage type and non-degradative K63-linkage type and monoubiquitination) in eukaryotic translation, both at the pre-translational level during the biogenesis/degradation of the components of translational machinery as well as at the co-translational level under stressful conditions. We also discuss other ubiquitin-dependent regulatory mechanisms of mRNA protection and resumption of translation after stress removal, where the ubiquitination of ribosomal proteins and associated regulatory proteins play an important role in the global rhythm of translation.
Collapse
Affiliation(s)
- Arantxa Martínez-Férriz
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alihamze Fathinajafabadi
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
| | - Rosa Farràs
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
| |
Collapse
|
46
|
Suzuki M, Tezuka K, Handa T, Sato R, Takeuchi H, Takao M, Tano M, Uchida Y. Upregulation of ribosome complexes at the blood-brain barrier in Alzheimer's disease patients. J Cereb Blood Flow Metab 2022; 42:2134-2150. [PMID: 35766008 PMCID: PMC9580172 DOI: 10.1177/0271678x221111602] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The cerebrovascular-specific molecular mechanism in Alzheimer's disease (AD) was investigated by employing comprehensive and accurate quantitative proteomics. Highly purified brain capillaries were isolated from cerebral gray and white matter of four AD and three control donors, and examined by SWATH (sequential window acquisition of all theoretical fragment ion spectra) proteomics. Of the 29 ribosomal proteins that were quantified, 28 (RPLP0, RPL4, RPL6, RPL7A, RPL8, RPL10A, RPL11, RPL12, RPL14, RPL15, RPL18, RPL23, RPL27, RPL27A, RPL31, RPL35A, RPS2, RPS3, RPS3A, RPS4X, RPS7, RPS8, RPS14, RPS16, RPS20, RPS24, RPS25, and RPSA) were significantly upregulated in AD patients. This upregulation of ribosomal protein expression occurred only in brain capillaries and not in brain parenchyma. The protein expression of protein processing and N-glycosylation-related proteins in the endoplasmic reticulum (DDOST, STT3A, MOGS, GANAB, RPN1, RPN2, SEC61B, UGGT1, LMAN2, and SSR4) were also upregulated in AD brain capillaries and was correlated with the expression of ribosomal proteins. The findings reported herein indicate that the ribosome complex, the subsequent protein processing and N-glycosylation-related processes are significantly and specifically upregulated in the brain capillaries of AD patients.
Collapse
Affiliation(s)
- Masayoshi Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kenta Tezuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takumi Handa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Risa Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hina Takeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Masaki Takao
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan.,Department of Clinical Laboratory, National Center of Neurology and Psychiatry, National Center Hospital, Kodaira, Japan
| | - Mitsutoshi Tano
- Department of Neurology and Brain Bank, Mihara Memorial Hospital, Isesaki, Japan
| | - Yasuo Uchida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| |
Collapse
|
47
|
Garaeva NS, Bikmullin AG, Fatkhullin BF, Validov SZ, Keiffer B, Yusupov MM, Usachev KS. Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus. Biomol NMR Assign 2022; 16:373-377. [PMID: 36070063 DOI: 10.1007/s12104-022-10106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The ribosomal maturation factor (RimP) is a 17.7 kDa protein and is the assembly factor of the 30S subunit. RimP is essential for efficient processing of 16S rRNA and maturation (assembly) of the 30S ribosome. It was suggested that RimP takes part in stabilization of the central pseudoknot at the early stages of the 30S subunit maturation, and this process may occur before the head domain assembly and later stages of the 30S assembly, but the mechanism of this interaction is still not fully understood. Here we report the assignment of the 1H, 13C and 15N chemical shift in the backbone and side chains of RimP from Staphylococcus aureus. Analysis of chemical shifts of the main chain using TALOS + suggests that the RimP contains eight β-strands and three α-helices with the topology α1-β1-β2-α2- β3- α3- β4- β5- β6- β7- β8. Structural studies of RimP and its complex with the ribosome by integrated structural biology approaches (NMR spectroscopy, X-ray diffraction analysis and cryoelectron microscopy) will allow further screening of highly selective inhibitors of the translation of S. aureus.
Collapse
Affiliation(s)
- Natalia S Garaeva
- Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
| | - Aydar G Bikmullin
- Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
| | - Bulat F Fatkhullin
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
- Institute of Protein Research, Russian Academy of Science, Institutskaya 4, Pushchino, Moscow Region, Russian Federation, 142290
| | - Shamil Z Validov
- Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
| | - Bruno Keiffer
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Marat M Yusupov
- Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Konstantin S Usachev
- Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008.
- Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008.
| |
Collapse
|
48
|
Lei J, Xiao W, Zhang J, Liu F, Xin C, Zhou B, Chen W, Song Z. Antifungal activity of vitamin D 3 against Candida albicans in vitro and in vivo. Microbiol Res 2022; 265:127200. [PMID: 36162148 DOI: 10.1016/j.micres.2022.127200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/04/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022]
Abstract
The incidence of intra-abdominal candidiasis (IAC), characterized by high morbidity and mortality, has become a serious concern. The limitations of current antifungal drugs on the market underscores the importance of the development of novel antifungal agents. In the present study, the antifungal activity of vitamin D3 (VD3) against various Candida species was investigated. In vitro, the broth microdilution method and solid plate assay confirmed that VD3 inhibited the growth of Candida spp. in a broad-spectrum, dose-dependent manner. VD3 also had a significant antifungal effect on the initiation, development, and maturation phases of biofilm formation in Candida albicans. The mechanism of VD3 action was explored by transcriptomics and reverse transcription quantitative PCR (RT-qPCR) analysis, and showed that VD3 affects ribosome biogenesis, coenzyme metabolism, and carbon metabolism. These results suggested that VD3 may have multitarget effects against C. albicans. In the murine IAC model, VD3 reduced the fungal burden in the liver, kidneys, and small intestine. Further histopathological analysis and quantification of plasma cytokine levels confirmed that VD3 treatment significantly decreased the infiltration of inflammatory cells and the levels of plasma interferon (IFN)-γ and tumor necrosis factor (TNF)-α. Taken together, these findings suggest a new antifungal mechanism for VD3 and indicate that VD3 could be an effective therapeutic agent for use in IAC treatment.
Collapse
|
49
|
Dupouy G, McDermott E, Cashell R, Scian A, McHale M, Ryder P, de Groot J, Lucca N, Brychkova G, McKeown PC, Spillane C. Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana. Plant Reprod 2022; 35:189-204. [PMID: 35247095 PMCID: PMC9352626 DOI: 10.1007/s00497-022-00440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for early embryo development in A. thaliana, as homozygous loss-of-function mutations in the PRPL5 gene impairs chloroplast development and leads to embryo failure to develop past the globular stage. We confirmed the prpl5 embryo-lethal phenotype by generating a mutant CRISPR/Cas9 line and by genetic complementation. As PRPL5 underwent transfer to the nuclear genome early in the evolution of Embryophyta, PRPL5 can be expected to have acquired a chloroplast transit peptide. We identify and validate the presence of an N-terminal chloroplast transit peptide, but unexpectedly also confirm the presence of a conserved and functional Nuclear Localization Signal on the protein C-terminal end. This study highlights the fundamental role of the plastid translation machinery during the early stages of embryo development in plants and raises the possibility of additional roles of plastid ribosomal proteins in the nucleus.
Collapse
Affiliation(s)
- Gilles Dupouy
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Emma McDermott
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Ronan Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Anna Scian
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Marcus McHale
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Joelle de Groot
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Noel Lucca
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, Aras de Brun, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
| |
Collapse
|
50
|
Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
Collapse
Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
| |
Collapse
|