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Wang L, Tao X, Lin Z, Song N, Wu H, Mingrong Q. Enantioselective toxicity assessment of prothioconazole on earthworms (Eisenia foetida) in artificial soil environments. Comp Biochem Physiol C Toxicol Pharmacol 2024; 283:109941. [PMID: 38810898 DOI: 10.1016/j.cbpc.2024.109941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
The chiral fungicide prothioconazole (PTZ) is extensively employed in agricultural practices, prompting serious concern due to its environmental impact. PTZ is prone to undergo metabolism, leading to the formation of chiral prothioconazole-desthio (dPTZ) in the environment. However, limited knowledge exists regarding its enantioselective behavior and toxicity towards invertebrate organisms in soil ecosystems. In this study, R-(-)- and S-(+)- PTZ enantiomers were individually synthesized, and their stereoselective toxicity effects on earthworms (E. foetida) were studied in artificial soil under environmentally relevant concentration exposures. The results showed a significant accumulation of dPTZ in earthworms, surpassing the levels of PTZ. Moreover, the concentration of S-(-)- dPTZ in earthworms was notably higher than that of R-(+)- dPTZ after exposure, reaching peak levels on day 14. Concurrently, oxidative stress induced by S-(+)- PTZ enantiomers in earthworms exhibited a substantial increase compared to R-(-)- enantiomers on day 14, indicating a higher ecological risk associated with the former in non-target organisms. Transcriptome analysis unveiled distinct impacts on earthworm physiology. S-(+)-PTZ exposure significantly affected energy metabolism, immune responses and digestive systems. In contrast, R-(-)-PTZ exposure influenced the synthesis of carbohydrates, proteins, and lipids. These insights contribute to understanding the complex interactions between PTZ enantiomers and soil-dwelling organisms, providing a scientific foundation for advancing the application of high efficiency, low toxicity PTZ monomer pesticides.
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Affiliation(s)
- Likun Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Xuexin Tao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China; College of Chemical Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Ziyi Lin
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China; College of Chemical Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Ningying Song
- College of Chemical Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Huizhen Wu
- College of Chemical Engineering, Zhejiang Shuren University, Hangzhou, 310015, China.
| | - Qian Mingrong
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China.
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2
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Zhou D, Li Y, Xie X, Ding W, Chen L, Li T, Tang J, Tan X, Liu W, Heng Y, Xie Y, Chen L, Liu Q, Zhou S, Zhao J, Zhang G, Tan J, Liu Y, Shen R. Copy number variation of NAL23 causes narrow-leaf development in rice. J Genet Genomics 2024; 51:880-883. [PMID: 38641318 DOI: 10.1016/j.jgg.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/07/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Affiliation(s)
- Degui Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yajing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Wenyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Libin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Tie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jianian Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiyu Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Weizhi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yueqin Heng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Qi Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Shaochuan Zhou
- Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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3
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Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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4
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Tong L, Ye K, Chen Q, Wang X, Hu C, Xu Q, Zhou L, Zhan R, Tong Y. Proteomics shows that brain metastases of lung adenocarcinoma overexpress ribosomal proteins in response to gamma knife radiosurgery. Sci Rep 2024; 14:15646. [PMID: 38977703 PMCID: PMC11231244 DOI: 10.1038/s41598-024-58967-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/05/2024] [Indexed: 07/10/2024] Open
Abstract
Gamma knife radiosurgery (GKRS) is recommended as the first-line treatment for brain metastases of lung adenocarcinoma (LUAD) in many guidelines, but its specific mechanism is unclear. We aimed to study the changes in the proteome of brain metastases of LUAD in response to the hyperacute phase of GKRS and further explore the mechanism of differentially expressed proteins (DEPs). Cancer tissues were collected from a clinical trial for neoadjuvant stereotactic radiosurgery before surgical resection of large brain metastases (ChiCTR2000038995). Five brain metastasis tissues of LUAD were collected within 24 h after GKRS. Five brain metastasis tissues without radiotherapy were collected as control samples. Proteomics analysis showed that 163 proteins were upregulated and 25 proteins were downregulated. GO and KEGG enrichment analyses showed that the DEPs were closely related to ribosomes. Fifty-three of 70 ribosomal proteins were significantly overexpressed, while none of them were underexpressed. The risk score constructed from 7 upregulated ribosomal proteins (RPL4, RPS19, RPS16, RPLP0, RPS2, RPS26 and RPS25) was an independent risk factor for the survival time of LUAD patients. Overexpression of ribosomal proteins may represent a desperate response to lethal radiotherapy. We propose that targeted inhibition of these ribosomal proteins may enhance the efficacy of GKRS.
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Affiliation(s)
- Luqing Tong
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Ke Ye
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Qun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Xiaoxi Wang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Chi Hu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Qingsheng Xu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Lihui Zhou
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Renya Zhan
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
| | - Ying Tong
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
- Gamma Knife Centre, The First Affiliated Hospital, Zhejiang University School of Medicine, No.79 Qingchun Street, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
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5
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D’Andrea G, Deroma G, Miluzio A, Biffo S. The Paradox of Ribosomal Insufficiency Coupled with Increased Cancer: Shifting the Perspective from the Cancer Cell to the Microenvironment. Cancers (Basel) 2024; 16:2392. [PMID: 39001453 PMCID: PMC11240629 DOI: 10.3390/cancers16132392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Ribosomopathies are defined as inherited diseases in which ribosomal factors are mutated. In general, they present multiorgan symptoms. In spite of the fact that in cellular models, ribosomal insufficiency leads to a reduced rate of oncogenic transformation, patients affected by ribosomopathies present a paradoxical increase in cancer incidence. Several hypotheses that explain this paradox have been formulated, mostly on the assumption that altered ribosomes in a stem cell induce compensatory changes that lead to a cancer cell. For instance, the lack of a specific ribosomal protein can lead to the generation of an abnormal ribosome, an oncoribosome, that itself leads to altered translation and increased tumorigenesis. Alternatively, the presence of ribosomal stress may induce compensatory proliferation that in turns selects the loss of tumor suppressors such as p53. However, modern views on cancer have shifted the focus from the cancer cell to the tumor microenvironment. In particular, it is evident that human lymphocytes are able to eliminate mutant cells and contribute to the maintenance of cancer-free tissues. Indeed, many tumors develop in conditions of reduced immune surveillance. In this review, we summarize the current evidence and attempt to explain cancer and ribosomopathies from the perspective of the microenvironment.
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Affiliation(s)
- Giacomo D’Andrea
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Giorgia Deroma
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
| | - Stefano Biffo
- National Institute of Molecular Genetics, INGM Fondazione Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.D.); (G.D.); (A.M.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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6
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Roy SK, Srivastava S, McCance C, Shrivastava A, Morvant J, Shankar S, Srivastava RK. Clinical significance of PNO1 as a novel biomarker and therapeutic target of hepatocellular carcinoma. J Cell Mol Med 2024; 28:e18295. [PMID: 38722284 PMCID: PMC11081011 DOI: 10.1111/jcmm.18295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 03/25/2024] [Indexed: 05/12/2024] Open
Abstract
The RNA-binding protein PNO1 plays an essential role in ribosome biogenesis. Recent studies have shown that it is involved in tumorigenesis; however, its role in hepatocellular carcinoma (HCC) is not well understood. The purpose of this study was to examine whether PNO1 can be used as a biomarker of HCC and also examine the therapeutic potential of PNO1 knockout for the treatment of HCC. PNO1 expression was upregulated in HCC and associated with poor prognosis. PNO1 expression was positively associated with tumour stage, lymph node metastasis and poor survival. PNO1 expression was significantly higher in HCC compared to that in fibrolamellar carcinoma or normal tissues. Furthermore, HCC tissues with mutant Tp53 expressed higher PNO1 than those with wild-type Tp53. PNO1 knockout suppressed cell viability, colony formation and EMT of HCC cells. Since activation of Notch signalling pathway promotes HCC, we measured the effects of PNO1 knockout on the components of Notch pathway and its targets. PNO1 knockout suppressed Notch signalling by modulating the expression of Notch ligands and their receptors, and downstream targets. PNO1 knockout also inhibited genes involved in surface adhesion, cell cycle, inflammation and chemotaxis. PNO1 knockout also inhibited colony and spheroid formation, cell migration and invasion, and markers of stem cells, pluripotency and EMT in CSCs. Overall, our data suggest that PNO1 can be used as a diagnostic and prognostic biomarker of HCC, and knockout of PNO1 by CRISPR/Cas9 can be beneficial for the management of HCC by targeting CSCs.
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Affiliation(s)
- Sanjit K. Roy
- Stanley S. Scott Cancer Center, School of MedicineLouisiana State University HealthNew OrleansLouisianaUSA
| | | | - Caroline McCance
- Department of Cellular and Molecular BiologyTulane UniversityNew OrleansLouisianaUSA
| | | | - Jason Morvant
- Department of SurgeryOchsner Health SystemGretnaLouisianaUSA
| | - Sharmila Shankar
- Southeast Louisiana Veterans Health Care SystemNew OrleansLouisianaUSA
- John W. Deming Department of MedicineTulane University School of MedicineNew OrleansLouisianaUSA
| | - Rakesh K. Srivastava
- Stanley S. Scott Cancer Center, School of MedicineLouisiana State University HealthNew OrleansLouisianaUSA
- Southeast Louisiana Veterans Health Care SystemNew OrleansLouisianaUSA
- Department of GeneticsLouisiana State University Health Sciences Center – New OrleansNew OrleansLouisianaUSA
- GLAXDoverDelawareUSA
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Taha MS, Ahmadian MR. Fragile X Messenger Ribonucleoprotein Protein and Its Multifunctionality: From Cytosol to Nucleolus and Back. Biomolecules 2024; 14:399. [PMID: 38672417 PMCID: PMC11047961 DOI: 10.3390/biom14040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Silencing of the fragile X messenger ribonucleoprotein 1 (FMR1) gene and a consequent lack of FMR protein (FMRP) synthesis are associated with fragile X syndrome, one of the most common inherited intellectual disabilities. FMRP is a multifunctional protein that is involved in many cellular functions in almost all subcellular compartments under both normal and cellular stress conditions in neuronal and non-neuronal cell types. This is achieved through its trafficking signals, nuclear localization signal (NLS), nuclear export signal (NES), and nucleolar localization signal (NoLS), as well as its RNA and protein binding domains, and it is modulated by various post-translational modifications such as phosphorylation, ubiquitination, sumoylation, and methylation. This review summarizes the recent advances in understanding the interaction networks of FMRP with a special focus on FMRP stress-related functions, including stress granule formation, mitochondrion and endoplasmic reticulum plasticity, ribosome biogenesis, cell cycle control, and DNA damage response.
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Affiliation(s)
- Mohamed S. Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
- Research on Children with Special Needs Department, Institute of Medical Research and Clinical Studies, National Research Centre, Cairo 12622, Egypt
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
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Teli BB, Nagar P, Priyadarshini Y, Poonia P, Natarajan K. A CUG codon-adapted anchor-away toolkit for functional analysis of genes in Candida albicans. mSphere 2024; 9:e0070323. [PMID: 38251906 PMCID: PMC10900876 DOI: 10.1128/msphere.00703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Promoter shutoff of essential genes in the diploid Candida albicans has often been insufficient to create tight, conditional null alleles due to leaky expression and has been a stumbling block in pathogenesis research. Moreover, homozygous deletion of non-essential genes has often been problematic due to the frequent aneuploidy in the mutant strains. Rapid, conditional depletion of essential genes by the anchor-away strategy has been successfully employed in Saccharomyces cerevisiae and other model organisms. Here, rapamycin mediates the dimerization of human FK506-binding protein (FKBP12) and FKBP12-rapamycin-binding (FRB) domain-containing target protein, resulting in relocalization to altered sub-cellular locations. In this work, we used the ribosomal protein Rpl13 as the anchor and took two nuclear proteins as targets to construct a set of mutants in a proof-of-principle approach. We first constructed a rapamycin-resistant C. albicans strain by introducing a dominant mutation in the CaTOR1 gene and a homozygous deletion of RBP1, the ortholog of FKBP12, a primary target of rapamycin. The FKBP12 and the FRB coding sequences were then CUG codon-adapted for C. albicans by site-directed mutagenesis. Anchor-away strains expressing the essential TBP1 gene or the non-essential SPT8 gene as FRB fusions were constructed. We found that rapamycin caused rapid cessation of growth of the TBP-AA strain within 15 minutes and the SPT8-AA strain phenocopied the constitutive filamentous phenotype of the spt8Δ/spt8Δ mutant. Thus, the anchor-away toolbox for C. albicans developed here can be employed for genome-wide analysis to identify gene function in a rapid and reliable manner, further accelerating anti-fungal drug development in C. albicans. IMPORTANCE Molecular genetic studies thus far have identified ~27% open-reading frames as being essential for the vegetative growth of Candida albicans in rich medium out of a total 6,198 haploid set of open reading frames. However, a major limitation has been to construct rapid conditional alleles of essential C. albicans genes with near quantitative depletion of encoded proteins. Here, we have developed a toolbox for rapid and conditional depletion of genes that would aid studies of gene function of both essential and non-essential genes.
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Affiliation(s)
- Basharat Bashir Teli
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyanka Nagar
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Yumnam Priyadarshini
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Poonam Poonia
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Krishnamurthy Natarajan
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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9
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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] [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.
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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.
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10
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Zhang L, Tang F. Molecular mechanism of Serratia marcescens Bizio infection in Reticulitermes chinensis Snyder based on full-length SMRT transcriptome sequencing. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-13. [PMID: 38328866 DOI: 10.1017/s000748532300072x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Reticulitermes chinensis Snyder is an important pest in forestry and construction and is widely distributed in China. We found that Serratia marcescens Bizio strain SM1 has insecticidal activity to R. chinensis, but the pathogenic mechanism of SM1 to R. chinensis is not clear. Therefore, full-length transcriptome sequencing was performed on R. chinensis infected with SM1 and the control group. A total of 230 differentially expressed genes were identified by comparing SM1 infection group and the control group, among which 103 were downregulated and 127 were upregulated. We found downregulated genes in nine metabolic pathway categories, among which carbohydrate metabolism had the most downregulated genes, followed by energy metabolism and amino acid metabolism. We also found that some downregulated genes were related to pattern recognition receptors, cellular immunity, and humoral immunity, indicating that R. chinensis immunity was negatively affected by SM1 infection. In addition, some genes in signal transduction and genetic information processing pathways were downregulated. In this study, high-throughput full-length transcriptome analysis was used to analyse the pathogenic mechanism of SM1 to R. chinensis. The results of this study provide useful information for exploring the relationship between SM1 and R. chinensis, and provide theoretical support for the future application of SM1 and the prevention and treatment of R. chinensis.
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Affiliation(s)
- Ling Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Fang Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
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Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024; 12:137. [PMID: 38257964 PMCID: PMC10819399 DOI: 10.3390/microorganisms12010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Transcriptional variation has been studied but post-transcriptional modification due to RNA editing has not been investigated in Plasmodium. We investigated developmental stage-specific RNA editing in selected genes in Plasmodium falciparum 3D7. We detected extensive amination- and deamination-type RNA editing at 8, 16, 24, 32, 40, and 46 h in tightly synchronized Plasmodium. Most of the editing events were observed in 8 and 16 h ring-stage parasites. Extensive A-to-G deamination-type editing was detected more during the 16 h ring stage (25%) than the 8 h ring stage (20%). Extensive U-to-C amination-type editing was detected more during the 16 h ring stage (31%) than the 8 h ring stage (22%). In 28S, rRNA editing converted the loop structure to the stem structure. The hemoglobin binding activity of PF3D7_0216900 was also altered due to RNA editing. Among the expressed 28S rRNA genes, PF3D7_0532000 and PF3D7_0726000 expression was higher. Increased amounts of the transcripts of these two genes were found, particularly PF3D7_0726000 in the ring stage and PF3D7_0532000 in the trophozoite and schizont stages. Adenosine deaminase (ADA) expression did not correlate with the editing level. This first experimental report of RNA editing will help to identify the editing machinery that might be useful for antimalarial drug discovery and malaria control.
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Affiliation(s)
- Md Thoufic Anam Azad
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Nishi10-Kita 20, Sapporo 001-0020, Japan
| | - Umme Qulsum
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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12
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Ali N, Wolf C, Kanchan S, Veerabhadraiah SR, Bond L, Turner MW, Jorcyk CL, Hampikian G. 9S1R nullomer peptide induces mitochondrial pathology, metabolic suppression, and enhanced immune cell infiltration, in triple-negative breast cancer mouse model. Biomed Pharmacother 2024; 170:115997. [PMID: 38118350 PMCID: PMC10872342 DOI: 10.1016/j.biopha.2023.115997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
Nullomers are the shortest strings of absent amino acid (aa) sequences in a species or group of species. Primes are those nullomers that have not been detected in the genome of any species. 9S1R is a 5-aa peptide prime sequence attached to 5-arginine aa, used to treat triple negative breast cancer (TNBC) in an in vivo mouse model. This unique peptide, administered with a trehalose carrier (9S1R-NulloPT), offers enhanced solubility and exhibits distinct anti-cancer effects against TNBC. In our study, we investigated the effect of 9S1R-NulloPT on tumor growth, metabolism, metastatic burden, tumor immune-microenvironment (TME), and transcriptome of aggressive mouse TNBC tumors. Notably, treated mice had smaller tumors in the initial phase of the treatment, as compared to untreated control, and diminished in vivo and ex vivo bioluminescence at later-stages - indicative of metabolically quiescent, dying tumors. The treatment also caused changes in TME with increased infiltration of immune cells and altered tumor transcriptome, with 365 upregulated genes and 710 downregulated genes. Consistent with in vitro data, downregulated genes were enriched in cellular metabolic processes (179), specifically mitochondrial TCA cycle/oxidative phosphorylation (44), and translation machinery/ribosome biogenesis (45). The upregulated genes were associated with the developmental (13), ECM organization (12) and focal adhesion pathways (7). In conclusion, our study demonstrates that 9S1R-NulloPT effectively reduced tumor growth during its initial phase, altering the TME and tumor transcriptome. The treatment induced mitochondrial pathology which led to a metabolic deceleration in tumors, aligning with in vitro observations.
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Affiliation(s)
- Nilufar Ali
- Department of Biological Sciences, Boise State University, Boise, ID, USA.
| | - Cody Wolf
- Department of Biological Sciences, Boise State University, Boise, ID, USA; Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA
| | - Swarna Kanchan
- Department of Biological Sciences, Boise State University, Boise, ID, USA; Department of Biomedical Sciences, Jaon C. Edwards School of Medicine, Marshall University, Huntington, WV, USA
| | - Shivakumar R Veerabhadraiah
- Department of Orthopaedics, University of Utah, Salt Lake City, UT, USA; Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA
| | - Laura Bond
- Center of Biomedical Research Excellence in Matrix Biology, Boise State University, Boise, ID, USA
| | - Matthew W Turner
- Biomolecular Research Center, Boise State University, Boise, ID, USA; Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA
| | - Cheryl L Jorcyk
- Department of Biological Sciences, Boise State University, Boise, ID, USA; Biomolecular Research Center, Boise State University, Boise, ID, USA; Biomolecular Sciences Graduate Programs, Boise State University, Boise, ID, USA
| | - Greg Hampikian
- Department of Biological Sciences, Boise State University, Boise, ID, USA.
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13
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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] [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.
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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.
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Zgheib S, Taha N, Zeiger M, Glushonkov O, Lequeu T, Anton H, Didier P, Boutant E, Mély Y, Réal E. The human cellular protein NoL12 is a specific partner of the HIV-1 nucleocapsid protein NCp7. J Virol 2023; 97:e0004023. [PMID: 37695057 PMCID: PMC10537728 DOI: 10.1128/jvi.00040-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/12/2023] [Indexed: 09/12/2023] Open
Abstract
The human immunodeficiency virus-1 (HIV-1) nucleocapsid protein (NCp7) is a nucleic acid chaperone protein with two highly conserved zinc fingers. To exert its key roles in the viral cycle, NCp7 interacts with several host proteins. Among them, the human NoL12 protein (hNoL12) was previously identified in genome wide screens as a potential partner of NCp7. hNoL12 is a highly conserved 25 kDa nucleolar RNA-binding protein implicated in the 5'end processing of ribosomal RNA in the nucleolus and thus in the assembly and maturation of ribosomes. In this work, we confirmed the NCp7/hNoL12 interaction in cells by Förster resonance energy transfer visualized by Fluorescence Lifetime Imaging Microscopy and co-immunoprecipitation. The interaction between NCp7 and hNoL12 was found to strongly depend on their both binding to RNA, as shown by the loss of interaction when the cell lysates were pretreated with RNase. Deletion mutants of hNoL12 were tested for their co-immunoprecipitation with NCp7, leading to the identification of the exonuclease domain of hNoL12 as the binding domain for NCp7. Finally, the interaction with hNoL12 was found to be specific of the mature NCp7 and to require NCp7 basic residues. IMPORTANCE HIV-1 mature nucleocapsid (NCp7) results from the maturation of the Gag precursor in the viral particle and is thus mostly abundant in the first phase of the infection which ends with the genomic viral DNA integration in the cell genome. Most if not all the nucleocapsid partners identified so far are not specific of the mature form. We described here the specific interaction in the nucleolus between NCp7 and the human nucleolar protein 12, a protein implicated in ribosomal RNA maturation and DNA damage response. This interaction takes place in the cell nucleolus, a subcellular compartment where NCp7 accumulates. The absence of binding between hNoL12 and Gag makes hNoL12 one of the few known specific cellular partners of NCp7.
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Affiliation(s)
- Sarwat Zgheib
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Nedal Taha
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Manon Zeiger
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Oleksandr Glushonkov
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Thiebault Lequeu
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Halina Anton
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Pascal Didier
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Emmanuel Boutant
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Yves Mély
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Eléonore Réal
- CNRS, Laboratoire de Bioimagerie et Pathologies - LBP, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
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15
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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. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115242. [PMID: 37441949 DOI: 10.1016/j.ecoenv.2023.115242] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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.
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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
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16
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Yang Q, Yang B, Chen M. Partner of NOB1 homolog transcriptionally activated by E2F transcription factor 1 promotes the malignant progression and inhibits ferroptosis of pancreatic cancer. CHINESE J PHYSIOL 2023; 66:388-399. [PMID: 37929351 DOI: 10.4103/cjop.cjop-d-23-00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Pancreatic cancer (PC) is one of the deadliest malignancies. Partner of NOB1 homolog (PNO1) has been reported to be involved in tumorigenesis. However, the role of PNO1 in PC remains to be elucidated. The purpose of this study was to examine the effects of PNO1 on the progression of PC and the possible mechanism related to E2F transcription factor 1 (E2F1), a transcription factor predicted by the JASPAR database to bind to the PNO1 promoter region and promoted the proliferation of pancreatic ductal adenocarcinoma. First, PNO1 expression in PC tissues and its association with survival rate were analyzed by the Gene Expression Profiling Interactive Analysis database. Western blot and reverse transcription-quantitative polymerase chain reaction were used to evaluate PNO1 expression in several PC cell lines. After PNO1 silencing, cell proliferation, migration, and invasion were measured by colony formation assay, 5-ethynyl-2'-deoxyuridine staining, wound healing, and transwell assays. Then, the lipid reactive oxygen species in PANC-1 cells was estimated by using C11-BODIPY581/591 probe. The levels of glutathione, malondialdehyde, and iron were measured. The binding between PNO1 and E2F1 was confirmed by luciferase and chromatin immunoprecipitation (ChIP) assays. Subsequently, E2F1 was overexpressed in PANC-1 cells with PNO1 knockdown to perform the rescue experiments. Results revealed that PNO1 was highly expressed in PC tissues and PNO1 expression was positively correlated with overall survival rate and disease-free survival rate. Significantly elevated PNO1 expression was also observed in PC cell lines. PNO1 knockdown inhibited the proliferation, migration, and invasion of PANC-1 cells. Moreover, ferroptosis was promoted in PNO1-silenced PANC-1 cells. Results of luciferase and ChIP assays indicated that E2F1 could bind to PNO1 promoter region. Rescue experiments suggested that E2F1 overexpression reversed the impacts of PNO1 depletion on the malignant behaviors and ferroptosis in PANC-1 cells. Summing up, PNO1 transcriptionally activated by E2F1 promotes the malignant progression and inhibits the ferroptosis of PC.
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Affiliation(s)
- Qin Yang
- Department of Laboratory Medicine, General Hospital of Central Theatre Command, Wuhan, Hubei, China
| | - Bin Yang
- Department of Burn and Plastic Surgery, General Hospital of Central Theatre Command, Wuhan, Hubei, China
| | - Min Chen
- Department of Laboratory Medicine, General Hospital of Central Theatre Command, Wuhan, Hubei, China
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17
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Zhu P, Hou C, Liu M, Chen T, Li T, Wang L. Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol. BMC Genomics 2023; 24:493. [PMID: 37641002 PMCID: PMC10464338 DOI: 10.1186/s12864-023-09600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid-liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. RESULTS By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. CONCLUSION This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems.
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Affiliation(s)
- Peiyu Zhu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Manlin Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
| | - Likun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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Harold C. All these screens that we've done: how functional genetic screens have informed our understanding of ribosome biogenesis. Biosci Rep 2023; 43:BSR20230631. [PMID: 37335083 PMCID: PMC10329186 DOI: 10.1042/bsr20230631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023] Open
Abstract
Ribosome biogenesis is the complex and essential process that ultimately leads to the synthesis of cellular proteins. Understanding each step of this essential process is imperative to increase our understanding of basic biology, but also more critically, to provide novel therapeutic avenues for genetic and developmental diseases such as ribosomopathies and cancers which can arise when this process is impaired. In recent years, significant advances in technology have made identifying and characterizing novel human regulators of ribosome biogenesis via high-content, high-throughput screens. Additionally, screening platforms have been used to discover novel therapeutics for cancer. These screens have uncovered a wealth of knowledge regarding novel proteins involved in human ribosome biogenesis, from the regulation of the transcription of the ribosomal RNA to global protein synthesis. Specifically, comparing the discovered proteins in these screens showed interesting connections between large ribosomal subunit (LSU) maturation factors and earlier steps in ribosome biogenesis, as well as overall nucleolar integrity. In this review, a discussion of the current standing of screens for human ribosome biogenesis factors through the lens of comparing the datasets and discussing the biological implications of the areas of overlap will be combined with a look toward other technologies and how they can be adapted to discover more factors involved in ribosome synthesis, and answer other outstanding questions in the field.
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Affiliation(s)
- Cecelia M. Harold
- Department of Genetics, Yale School of Medicine, New Haven, CT, U.S.A
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19
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Ali N, Wolf C, Kanchan S, Veerabhadraiah SR, Bond L, Turner MW, Jorcyk CL, Hampikian G. Nullomer peptide increases immune cell infiltration and reduces tumor metabolism in triple negative breast cancer mouse model. RESEARCH SQUARE 2023:rs.3.rs-3097552. [PMID: 37461536 PMCID: PMC10350184 DOI: 10.21203/rs.3.rs-3097552/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Background Nullomers are the shortest strings of absent amino acid (aa) sequences in a species or group of species. Primes are those nullomers that have not been detected in the genome of any species. 9S1R is a 5-aa peptide derived from a prime sequence that is tagged with 5 arginine aa, used to treat triple negative breast cancer (TNBC) in an in vivo TNBC mouse model. 9S1R is administered in trehalose (9S1R-NulloPT), which enhances solubility and exhibits some independent effects against tumor growth and is thus an important component in the drug preparation. Method We examined the effect of 9S1R-NulloPT on tumor growth, metabolism, metastatic burden, necrosis, tumor immune microenvironment, and the transcriptome of aggressive mouse TNBC tumors. Results The peptide-treated mice had smaller tumors in the initial phase of the treatment, as compared to the untreated control, and reduced in vivo bioluminescence at later stages, which is indicative of metabolically inactive tumors. A decrease in ex vivo bioluminescence was also observed in the excised tumors of treated mice, but not in the secondary metastasis in the lungs. The treatment also caused changes in tumor immune microenvironment with increased infiltration of immune cells and margin inflammation. The treatment upregulated 365 genes and downregulated 710 genes in tumors compared to the untreated group. Consistent with in vitro findings in breast cancer cell lines, downregulated genes in the treated TNBC tumors include Cellular Metabolic Process Related genes (179), specifically mitochondrial genes associated with TCA cycle/oxidative phosphorylation (44), and translation machinery/ribosome biogenesis genes (45). Among upregulated genes, the Developmental Pathway (13), ECM Organization (12) and Focal Adhesion Related Pathways (7) were noteworthy. We also present data from a pilot study using a bilateral BC mouse model, which supports our findings. Conclusion In conclusion, although 9S1R-NulloPT was moderate at reducing the tumor volume, it altered the tumor immune microenvironment as well as the tumor transcriptome, rendering tumors metabolically less active by downregulating the mitochondrial function and ribosome biogenesis. This corroborates previously published in vitro findings.
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20
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Chaillou T, Montiel-Rojas D. Does the blunted stimulation of skeletal muscle protein synthesis by aging in response to mechanical load result from impaired ribosome biogenesis? FRONTIERS IN AGING 2023; 4:1171850. [PMID: 37256189 PMCID: PMC10225510 DOI: 10.3389/fragi.2023.1171850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023]
Abstract
Age-related loss of skeletal muscle mass leads to a reduction of strength. It is likely due to an inadequate stimulation of muscle protein synthesis (MPS) in response to anabolic stimuli, such as mechanical load. Ribosome biogenesis is a major determinant of translational capacity and is essential for the control of muscle mass. This mini-review aims to put forth the hypothesis that ribosome biogenesis is impaired by aging in response to mechanical load, which could contribute to the age-related anabolic resistance and progressive muscle atrophy. Recent animal studies indicate that aging impedes muscle hypertrophic response to mechanical overload. This is associated with an impaired transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I), a limited increase in total RNA concentration, a blunted activation of AKT/mTOR pathway, and an increased phosphorylation of AMPK. In contrast, an age-mediated impairment of ribosome biogenesis is unlikely in response to electrical stimulations. In human, the hypertrophic response to resistance exercise training is diminished with age. This is accompanied by a deficit in long-term MPS and an absence of increased total RNA concentration. The results addressing the acute response to resistance exercise suggest an impaired Pol I-mediated rDNA transcription and attenuated activation/expression of several upstream regulators of ribosome biogenesis in muscles from aged individuals. Altogether, emerging evidence indicates that impaired ribosome biogenesis could partly explain age-related anabolic resistance to mechanical load, which may ultimately contribute to progressive muscle atrophy. Future research should develop more advanced molecular tools to provide in-depth analysis of muscle ribosome biogenesis.
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21
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Zhang T, Shi Q, Gu H, Yu B, Yin S, Ge Q, Mo X, Liu X, Huang J. CCDC134 facilitates T cell activation through the regulation of early T cell receptor signaling. Front Immunol 2023; 14:1133111. [PMID: 37234153 PMCID: PMC10206301 DOI: 10.3389/fimmu.2023.1133111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
Modulation of surface T cell antigen receptor (TCR) expression is crucial for proper T cell development and maintenance of mature T cell function at steady state and upon stimulation. We previously determined that CCDC134 (coiled-coil domain containing 134), a cytokine-like molecule that served as a potential member of the γc cytokine family, contributes to antitumor responses by augmenting CD8+ T cell-mediated immunity. Here we show that T cell-specific deletion of Ccdc134 decreased peripheral mature CD4+ and CD8+ T cells, which resulted in impaired T cell homeostasis. Moreover, Ccdc134-deficient T cells exhibited an attenuated response to TCR stimulation in vitro, showing lower activation and proliferative capacity. This was further reflected in vivo, rendering mice refractory to T cell-mediated inflammatory and antitumor responses. More importantly, CCDC134 is associated with TCR signaling components, including CD3ϵ, and attenuated TCR signaling in Ccdc134-deficient T cells via altered CD3ϵ ubiquitination and degradation. Taken together, these findings suggest a role for CCDC134 as a positive regulator of TCR-proximal signaling and provide insight into the cell-intrinsic functional consequences of Ccdc134 deficiency in the attenuation of T cell-mediated inflammatory and antitumor responses.
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Affiliation(s)
- Tianzhuo Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Qianwen Shi
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Huining Gu
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Biaoyi Yu
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Sha Yin
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Shaanxi Institute for Pediatric Diseases, Xi’an Key Laboratory of Children’s Health and Diseases, Xi’an Children’s Hospital, The Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Qing Ge
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xiaoning Mo
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xiaofeng Liu
- Hepatopancreatobiliary Surgery Department I, Key laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jing Huang
- Department of Immunology, School of Basic Medical Sciences, Peking University, and National Health Commission (NHC) Key Laboratory of Medical Immunology, Peking University, Beijing, China
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22
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Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 2023; 14:2131. [PMID: 37080962 PMCID: PMC10119107 DOI: 10.1038/s41467-023-37838-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
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Affiliation(s)
- Chisa Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Taishi Yamamoto
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Eriko Matsuura-Suzuki
- 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
| | - Shouji Matsushima
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
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23
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Shan L, Xu G, Yao RW, Luan PF, Huang Y, Zhang PH, Pan YH, Zhang L, Gao X, Li Y, Cao SM, Gao SX, Yang ZH, Li S, Yang LZ, Wang Y, Wong CCL, Yu L, Li J, Yang L, Chen LL. Nucleolar URB1 ensures 3' ETS rRNA removal to prevent exosome surveillance. Nature 2023; 615:526-534. [PMID: 36890225 DOI: 10.1038/s41586-023-05767-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
The nucleolus is the most prominent membraneless condensate in the nucleus. It comprises hundreds of proteins with distinct roles in the rapid transcription of ribosomal RNA (rRNA) and efficient processing within units comprising a fibrillar centre and a dense fibrillar component and ribosome assembly in a granular component1. The precise localization of most nucleolar proteins and whether their specific localization contributes to the radial flux of pre-rRNA processing have remained unknown owing to insufficient resolution in imaging studies2-5. Therefore, how these nucleolar proteins are functionally coordinated with stepwise pre-rRNA processing requires further investigation. Here we screened 200 candidate nucleolar proteins using high-resolution live-cell microscopy and identified 12 proteins that are enriched towards the periphery of the dense fibrillar component (PDFC). Among these proteins, unhealthy ribosome biogenesis 1 (URB1) is a static, nucleolar protein that ensures 3' end pre-rRNA anchoring and folding for U8 small nucleolar RNA recognition and the subsequent removal of the 3' external transcribed spacer (ETS) at the dense fibrillar component-PDFC boundary. URB1 depletion leads to a disrupted PDFC, uncontrolled pre-rRNA movement, altered pre-rRNA conformation and retention of the 3' ETS. These aberrant 3' ETS-attached pre-rRNA intermediates activate exosome-dependent nucleolar surveillance, resulting in decreased 28S rRNA production, head malformations in zebrafish and delayed embryonic development in mice. This study provides insight into functional sub-nucleolar organization and identifies a physiologically essential step in rRNA maturation that requires the static protein URB1 in the phase-separated nucleolus.
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Affiliation(s)
- Lin Shan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pei-Hong Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Hang Pan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Gao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Li
- Cryo EM facility, Technology Center for Protein Sciences, School of Life Science, Tsinghua University, Beijing, China
| | - Shi-Meng Cao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuai-Xin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China
| | - Zheng-Hu Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Siqi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Catharine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
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24
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Sang W, Liu J, Xing Y, Feng C, Hu Q, Lang Y, Li X, Bao J, Jiang H. Transcriptome analysis of hepatopancreas of Chinese grass shrimp, Palaemonetes sinensis, infected by Enterocytospora artemiae. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108557. [PMID: 36669602 DOI: 10.1016/j.fsi.2023.108557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The emergence of the microsporidian, Enterocytospora artemiae, has caused serious economic losses to the aquaculture industry of Palaemonetes sinensis. The hepatopancreas is the main digestive and immune organ of P. sinensis, and the main site of E. artemiae infection. We used next-generation sequencing to determine the effects of E. artemiae parasitism on the hepatopancreas of P. sinensis at the transcriptome level. The hepatopancreas of P. sinensis was parasitized by E. artemiae, and 881 differentially expressed genes (DEGs) were obtained, of which 643 were upregulated and 238 were downregulated. These DEGs are mainly involved in DNA replication, transcription, translation, immunity, and metabolism. Among them, the cellular processes of DNA replication, transcription and translation are significantly strengthened, which may be related to the use of host ATP and nucleic acid by E. artemiae to achieve proliferation and damage to host cells to enhance DNA replication and repair. Moreover, to defend against E. artemiae, some immune genes related to antioxidation, such as glutathione metabolism, seleno compound metabolism, and cytochrome p450 2L1, were significantly upregulated, but simultaneously, tumor necrosis factor, NF-κB inhibitor α, and other immune-related genes were significantly down regulated, indicating that the parasitism of E. artemiae led to a significant decline in the immune defense ability of P. sinensis. From the perspective of metabolism, the metabolism-related DEGs of retinol, glycine, serine, and threonine metabolism, were significantly downregulated, resulting in insufficient nutrient absorption and decreased energy supply of the P. sinensis, which in turn affected their growth. The differential genes and pathways identified in this study can provide a reference basis to further elucidate the pathogenic mechanism of P. sinensis infected with E. artemiae and the prevention and control of microsporidia disease.
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Affiliation(s)
- Wenjia Sang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jun Liu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuenan Xing
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chengcheng Feng
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuxi Lang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jie Bao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
| | - Hongbo Jiang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
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25
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Murphy JC, Harrington EM, Schumann S, Vasconcelos EJR, Mottram TJ, Harper KL, Aspden JL, Whitehouse A. Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs. Nat Commun 2023; 14:300. [PMID: 36653366 PMCID: PMC9849454 DOI: 10.1038/s41467-023-35914-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Historically, ribosomes were viewed as unchanged homogeneous macromolecular machines with no regulatory capacity for mRNA translation. An emerging concept is that heterogeneity of ribosomal composition exists, exerting a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose high translational demands on the host during replication. We explore the possibility that KSHV manipulates ribosome biogenesis producing specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic replication. We demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and the KSHV ORF11 protein, with small ribosomal subunit precursor complexes during lytic replication. BUD23 depletion resulted in significantly reduced viral gene expression, culminating in dramatic reduction of infectious virion production. Ribosome profiling demonstrated BUD23 is essential for reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the downstream coding sequence. Results provide mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes facilitating efficient translation of viral mRNAs.
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Affiliation(s)
- James C Murphy
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Elena M Harrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sophie Schumann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Timothy J Mottram
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Katherine L Harper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK.
- Department of Biochemistry & Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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26
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Roy SK, Srivastava S, Hancock A, Shrivastava A, Morvant J, Shankar S, Srivastava RK. Inhibition of ribosome assembly factor PNO1 by CRISPR/Cas9 technique suppresses lung adenocarcinoma and Notch pathway: Clinical application. J Cell Mol Med 2023; 27:365-378. [PMID: 36625087 PMCID: PMC9889701 DOI: 10.1111/jcmm.17657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Growth is crucially controlled by the functional ribosomes available in cells. To meet the enhanced energy demand, cancer cells re-wire and increase their ribosome biogenesis. The RNA-binding protein PNO1, a ribosome assembly factor, plays an essential role in ribosome biogenesis. The purpose of this study was to examine whether PNO1 can be used as a biomarker for lung adenocarcinoma and also examine the molecular mechanisms by which PNO1 knockdown by CRISPR/Cas9 inhibited growth and epithelial-mesenchymal transition (EMT). The expression of PNO1 was significantly higher in lung adenocarcinoma compared to normal lung tissues. PNO1 expression in lung adenocarcinoma patients increased with stage, nodal metastasis, and smoking. Lung adenocarcinoma tissues from males expressed higher PNO1 than those from females. Furthermore, lung adenocarcinoma tissues with mutant Tp53 expressed higher PNO1 than those with wild-type Tp53, suggesting the influence of Tp53 status on PNO1 expression. PNO1 knockdown inhibited cell viability, colony formation, and EMT, and induced apoptosis. Since dysregulated signalling through the Notch receptors promotes lung adenocarcinoma, we measured the effects of PNO1 inhibition on the Notch pathway. PNO1 knockdown inhibited Notch signalling by suppressing the expression of Notch receptors, their ligands, and downstream targets. PNO1 knockdown also suppressed CCND1, p21, PTGS-2, IL-1α, IL-8, and CXCL-8 genes. Overall, our data suggest that PNO1 can be used as a diagnostic biomarker, and also can be an attractive therapeutic target for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Sanjit K. Roy
- Louisiana State University Health‐New Orleans, School of MedicineStanley S. Scott Cancer CenterNew OrleansLouisianaUSA,Southeast Louisiana Veterans Health Care SystemNew OrleansLouisianaUSA
| | | | - Andrew Hancock
- Department of Molecular and Cellular BiologyTulane UniversityNew OrleansLouisianaUSA
| | | | - Jason Morvant
- Department of SurgeryOchsner Health SystemGretnaLouisianaUSA
| | - Sharmila Shankar
- Louisiana State University Health‐New Orleans, School of MedicineStanley S. Scott Cancer CenterNew OrleansLouisianaUSA,Southeast Louisiana Veterans Health Care SystemNew OrleansLouisianaUSA,Department of GeneticsLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA,John W. Deming Department of MedicineTulane University School of MedicineNew OrleansLouisianaUSA,Kansas City VA Medical CenterKansas CityMissouriUSA
| | - Rakesh K. Srivastava
- Louisiana State University Health‐New Orleans, School of MedicineStanley S. Scott Cancer CenterNew OrleansLouisianaUSA,Southeast Louisiana Veterans Health Care SystemNew OrleansLouisianaUSA,Department of GeneticsLouisiana State University Health Sciences CenterNew OrleansLouisianaUSA,Kansas City VA Medical CenterKansas CityMissouriUSA
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27
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea,Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea,Corresponding author. Tel: +82-53-950-6352; Fax: +82-53-955-5522; E-mail:
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28
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Ryu HY. SUMO pathway is required for ribosome biogenesis. BMB Rep 2022; 55:535-540. [PMID: 36195568 PMCID: PMC9712707 DOI: 10.5483/bmbrep.2022.55.11.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2023] Open
Abstract
Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
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Affiliation(s)
- Hong-Yeoul Ryu
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Korea
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
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29
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Sharen G, Li X, Sun J, Zhang L, Xi W, Zhao X, Han F, Jia L, A R, Cheng H, Hou M. Silencing eL31 suppresses the progression of colorectal cancer via targeting DEPDC1. J Transl Med 2022; 20:493. [PMID: 36309731 PMCID: PMC9617412 DOI: 10.1186/s12967-022-03663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most commonly diagnosed human malignancies. Ribosomal protein L31 (RPL31, aka eL31) is a component of the 60S large ribosomal subunit, and its expression pattern and functional role in CRC have not been reported. Methods Herein, we identified that eL31 protein level was dramatically increased in CRC tissues through using IHC analysis. More notably, elevated eL31 was associated with larger tumor size and shorter overall survival. Besides, we evaluated the effects of eL31 depletion on CRC cell phenotypes in vitro. Results The data indicated that eL31 knockdown restricted CRC cell proliferation, migration and colony formation whilst enhancing cell apoptosis. Importantly, eL31 was also essential for CRC tumor growth in vivo, as demonstrated by impaired tumor growth markers and reduced Ki67 levels in xenografts from eL31-depleted cells. In addition, our evidence indicated that DEP domain containing 1 (DEPDC1) was a potential downstream target of eL31 in regulating CRC. Consistently, DEPDC1 depletion restrained CRC cell proliferation and migration, as well as facilitated cell apoptosis. More interestingly, DEPDC1 depletion could reverse the promotion effects of eL31 elevation on CRC cells. Conclusions Identification of eL31’s function in CRC may pave the way for future development of more specific and more effective targeted therapy strategies against CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03663-6.
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Gottmann P, Speckmann T, Stadion M, Zuljan E, Aga H, Sterr M, Büttner M, Santos PM, Jähnert M, Bornstein SR, Theis FJ, Lickert H, Schürmann A. Heterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice. Diabetes 2022; 71:1962-1978. [PMID: 35771990 PMCID: PMC9862397 DOI: 10.2337/db21-1030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/13/2022] [Indexed: 02/05/2023]
Abstract
Progressive dysfunction and failure of insulin-releasing β-cells are a hallmark of type 2 diabetes (T2D). To study mechanisms of β-cell loss in T2D, we performed islet single-cell RNA sequencing of two obese mouse strains differing in their diabetes susceptibility. With mice on a control diet, we identified six β-cell clusters with similar abundance in both strains. However, after feeding of a diabetogenic diet for 2 days, β-cell cluster composition markedly differed between strains. Islets of diabetes-resistant mice developed into a protective β-cell cluster (Beta4), whereas those of diabetes-prone mice progressed toward stress-related clusters with a strikingly different expression pattern. Interestingly, the protective cluster showed indications of reduced β-cell identity, such as downregulation of GLUT2, GLP1R, and MafA, and in vitro knockdown of GLUT2 in β-cells-mimicking its phenotype-decreased stress response and apoptosis. This might explain enhanced β-cell survival of diabetes-resistant islets. In contrast, β-cells of diabetes-prone mice responded with expression changes indicating metabolic pressure and endoplasmic reticulum stress, presumably leading to later β-cell loss. In conclusion, failure of diabetes-prone mice to adapt gene expression toward a more dedifferentiated state in response to rising blood glucose levels leads to β-cell failure and diabetes development.
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Affiliation(s)
- Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Thilo Speckmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mandy Stadion
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Erika Zuljan
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Heja Aga
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Michael Sterr
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Maren Büttner
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Patrícia Martínez Santos
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Stefan R. Bornstein
- Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Diabetes, School of Life Course Science and Medicine, King’s College London, London, U.K
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Heiko Lickert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Nutritional Sciences, University of Potsdam, Nuthetal, Germany
- Corresponding author: Annette Schürmann,
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31
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Nelson ME, Riva SG, Cvejic A. SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing. BMC Bioinformatics 2022; 23:328. [PMID: 35941549 PMCID: PMC9361618 DOI: 10.1186/s12859-022-04860-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-cell RNA-sequencing is revolutionising the study of cellular and tissue-wide heterogeneity in a large number of biological scenarios, from highly tissue-specific studies of disease to human-wide cell atlases. A central task in single-cell RNA-sequencing analysis design is the calculation of cell type-specific genes in order to study the differential impact of different replicates (e.g. tumour vs. non-tumour environment) on the regulation of those genes and their associated networks. The crucial task is the efficient and reliable calculation of such cell type-specific 'marker' genes. These optimise the ability of the experiment to isolate highly-specific cell phenotypes of interest to the analyser. However, while methods exist that can calculate marker genes from single-cell RNA-sequencing, no such method places emphasise on specific cell phenotypes for downstream study in e.g. differential gene expression or other experimental protocols (spatial transcriptomics protocols for example). Here we present SMaSH, a general computational framework for extracting key marker genes from single-cell RNA-sequencing data which reliably characterise highly-specific and niche populations of cells in numerous different biological data-sets. RESULTS SMaSH extracts robust and biologically well-motivated marker genes, which characterise a given single-cell RNA-sequencing data-set better than existing computational approaches for general marker gene calculation. We demonstrate the utility of SMaSH through its substantial performance improvement over several existing methods in the field. Furthermore, we evaluate the SMaSH markers on spatial transcriptomics data, demonstrating they identify highly localised compartments of the mouse cortex. CONCLUSION SMaSH is a new methodology for calculating robust markers genes from large single-cell RNA-sequencing data-sets, and has implications for e.g. effective gene identification for probe design in downstream analyses spatial transcriptomics experiments. SMaSH has been fully-integrated with the ScanPy framework and provides a valuable bioinformatics tool for cell type characterisation and validation in every-growing data-sets spanning over 50 different cell types across hundreds of thousands of cells.
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Affiliation(s)
- M E Nelson
- European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK. .,Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK. .,Wellcome - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK. .,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
| | - S G Riva
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK.,Wellcome - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK.,Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1RQ, UK
| | - A Cvejic
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK. .,Wellcome - Medical Research Council Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1RQ, UK.
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32
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Bulygin KN, Malygin AA, Graifer DM, Karpova GG. The functional role of the eukaryote-specific motif YxxPKxYxK of the human ribosomal protein eS26 in translation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194842. [PMID: 35817369 DOI: 10.1016/j.bbagrm.2022.194842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022]
Abstract
The protein eS26 is a structural component of the eukaryotic small ribosomal subunit involved in the formation of the mRNA binding channel in the region of the exit site. By applying site-directed cross-linking to mammalian 80S ribosomes, it has been shown that the same mRNA nucleotide residues are implicated in the interaction with both eS26 and translation initiation factor 3 (eIF3) and that contacts of the protein with mRNAs are mediated by its eukaryote-specific motif YxxPKxYxK. To examine the role of eS26 in translation, we transfected HEK293T cells with plasmid constructs encoding the wild-type FLAG-labeled protein (wt-eS26FLAG) or its forms with either a single substitution of any conserved amino acid residue in the above motif, or a simultaneous replacement of all the five ones (5A). The western blot analysis of fractions of polysome profiles from the transfected cells revealed no effects of the single mutations in eS26, but showed that the replacement of the five conserved residues led to the increased share of the light polysome fraction compared to that detected with control, wt-eS26FLAG-producing cells. In addition, the above fraction exhibited the enhanced content of the eIF3e subunit that is known to promote selective translation. These findings, together with real-time PCR data on the relative contents of specific mRNAs in light and heavy polysomes from cells producing the mutant 5A compared to those from control cells, suggest a possible involvement of the YxxPKxYxK motif of eS26 in the fine regulation of translation to maintain the required balance of synthesized proteins.
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Affiliation(s)
- Konstantin N Bulygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.
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McElreavey K, Pailhoux E, Bashamboo A. DHX37 and 46,XY DSD: A New Ribosomopathy? Sex Dev 2022; 16:194-206. [PMID: 35835064 DOI: 10.1159/000522004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022] Open
Abstract
Recently, a series of recurrent missense variants in the RNA-helicase DHX37 have been reported associated with either 46,XY gonadal dysgenesis, 46,XY testicular regression syndrome (TRS), or anorchia. All affected children have non-syndromic forms of disorders/differences of sex development (DSD). These variants, which involve highly conserved amino acids within known functional domains of the protein, are predicted by in silico tools to have a deleterious effect on helicase function. DHX37 is required for ribosome biogenesis in eukaryotes, and how these variants cause DSD is unclear. The relationship between DHX37 and human congenital disorders is complex as compound heterozygous as well as de novo heterozygous missense variants in DHX37 are also associated with a complex congenital developmental syndrome (NEDBAVC, neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies; OMIM 618731), consisting of microcephaly, global developmental delay, seizures, facial dysmorphia, and kidney and cardiac anomalies. Here, we will give a brief overview of ribosome biogenesis and the role of DHX37 in this process. We will discuss variants in DHX37, their contribution to human disease in the general context of human ribosomopathies, and the possible disease mechanisms that may be involved.
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Affiliation(s)
- Kenneth McElreavey
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris, France
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Anu Bashamboo
- Human Developmental Genetics, CNRS UMR3738, Institut Pasteur, Paris, France
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34
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Saghaleyni R, Malm M, Moruzzi N, Zrimec J, Razavi R, Wistbacka N, Thorell H, Pintar A, Hober A, Edfors F, Chotteau V, Berggren PO, Grassi L, Zelezniak A, Svensson T, Hatton D, Nielsen J, Robinson JL, Rockberg J. Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells. Cell Rep 2022; 39:110936. [PMID: 35705050 DOI: 10.1016/j.celrep.2022.110936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/05/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Recombinant protein production can cause severe stress on cellular metabolism, resulting in limited titer and product quality. To investigate cellular and metabolic characteristics associated with these limitations, we compare HEK293 clones producing either erythropoietin (EPO) (secretory) or GFP (non-secretory) protein at different rates. Transcriptomic and functional analyses indicate significantly higher metabolism and oxidative phosphorylation in EPO producers compared with parental and GFP cells. In addition, ribosomal genes exhibit specific expression patterns depending on the recombinant protein and the production rate. In a clone displaying a dramatically increased EPO secretion, we detect higher gene expression related to negative regulation of endoplasmic reticulum (ER) stress, including upregulation of ATF6B, which aids EPO production in a subset of clones by overexpression or small interfering RNA (siRNA) knockdown. Our results offer potential target pathways and genes for further development of the secretory power in mammalian cell factories.
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Affiliation(s)
- Rasool Saghaleyni
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Magdalena Malm
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Noah Moruzzi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, 17176 Stockholm, Sweden
| | - Jan Zrimec
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Ronia Razavi
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Num Wistbacka
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Hannes Thorell
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Anton Pintar
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Veronique Chotteau
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Industrial Biotechnology, 106 91 Stockholm, Sweden
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, 17176 Stockholm, Sweden
| | - Luigi Grassi
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Aleksej Zelezniak
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Thomas Svensson
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, 41258 Gothenburg, Sweden
| | - Diane Hatton
- Cell Culture & Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan L Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, 41258 Gothenburg, Sweden.
| | - Johan Rockberg
- KTH - Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Protein Science, 106 91 Stockholm, Sweden.
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Otto C, Kastner C, Schmidt S, Uttinger K, Baluapuri A, Denk S, Rosenfeldt MT, Rosenwald A, Roehrig F, Ade CP, Schuelein-Voelk C, Diefenbacher ME, Germer CT, Wolf E, Eilers M, Wiegering A. RNA polymerase I inhibition induces terminal differentiation, growth arrest, and vulnerability to senolytics in colorectal cancer cells. Mol Oncol 2022; 16:2788-2809. [PMID: 35673898 PMCID: PMC9348601 DOI: 10.1002/1878-0261.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
Ribosomal biogenesis and protein synthesis are deregulated in most cancers, suggesting that interfering with translation machinery may hold significant therapeutic potential. Here, we show that loss of the tumor suppressor adenomatous polyposis coli (APC), which constitutes the initiating event in the adenoma carcinoma sequence for colorectal cancer (CRC), induces the expression of RNA polymerase I (RNAPOL1) transcription machinery, and subsequently upregulates ribosomal DNA (rDNA) transcription. Targeting RNAPOL1 with a specific inhibitor, CX5461, disrupts nucleolar integrity, and induces a disbalance of ribosomal proteins. Surprisingly, CX5461-induced growth arrest is irreversible and exhibits features of senescence and terminal differentiation. Mechanistically, CX5461 promotes differentiation in an MYC-interacting zinc-finger protein 1 (MIZ1)- and retinoblastoma protein (Rb)-dependent manner. In addition, the inhibition of RNAPOL1 renders CRC cells vulnerable towards senolytic agents. We validated this therapeutic effect of CX5461 in murine- and patient-derived organoids, and in a xenograft mouse model. These results show that targeting ribosomal biogenesis together with targeting the consecutive, senescent phenotype using approved drugs is a new therapeutic approach, which can rapidly be transferred from bench to bedside.
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Affiliation(s)
- Christoph Otto
- Experimental Visceral Surgery, Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany
| | - Carolin Kastner
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany.,Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany
| | - Stefanie Schmidt
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany.,Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany
| | - Konstantin Uttinger
- Experimental Visceral Surgery, Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany
| | - Apoorva Baluapuri
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany
| | - Sarah Denk
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany.,Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany
| | | | | | - Florian Roehrig
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany
| | | | - Markus E Diefenbacher
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany
| | - Christoph-Thomas Germer
- Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Germany
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Germany
| | - Armin Wiegering
- Experimental Visceral Surgery, Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany.,Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Germany.,Department of General, Visceral, Transplantation, Vascular and Pediatric Surgery (Department of Surgery I), University Hospital Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Germany
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36
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Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23116174. [PMID: 35682850 PMCID: PMC9181716 DOI: 10.3390/ijms23116174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
A number of mutations in the RPS20 gene encoding the ribosomal protein uS10 have been found to be associated with a predisposition to hereditary non-polyposis colorectal carcinoma (CRC). We transfected HEK293T cells with constructs carrying the uS10 minigene with mutations identical to those mentioned above and examined the effects of the produced proteins on the cellular transcriptome. We showed that uS10 with mutations p.V50SfsX23 or p.L61EfsX11 cannot be incorporated into 40S ribosomal subunits, while the protein with the missense mutation p.V54L functionally replaces the respective endogenous protein in the 40S subunit assembly and the translation process. The comparison of RNA-seq data obtained from cells producing aberrant forms of uS10 with data for those producing the wild-type protein revealed overlapping sets of upregulated and downregulated differently expressed genes (DEGs) related to several pathways. Among the limited number of upregulated DEGs, there were genes directly associated with the progression of CRC, e.g., PPM1D and PIGN. Our findings indicate that the accumulation of the mutant forms of uS10 triggers a cascade of cellular events, similar to that which is triggered when the cell responds to a large number of erroneous proteins, suggesting that this may increase the risk of cancer.
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37
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Wang Q, Liu JH, Wen B, Gao JZ, Chen ZZ. Gut microbiota communities of reciprocal hybrids from koi (Cyprinus carpio) and goldfish (Carassius auratus) are more similar to koi than goldfish. J Appl Microbiol 2022; 133:960-971. [PMID: 35543337 DOI: 10.1111/jam.15616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
AIMS To investigate the gut microbiota communities of reciprocal hybrids and inbred lines of koi (Cyprinus carpio) and goldfish (Carassius auratus), as well as the genetic effect of intestinal microbiota between hybrids and parents. METHODS AND RESULTS The reciprocal hybrids and inbred lines derived from the parents, koi and goldfish, were established. Then the bacterial 16S rRNA gene of intestinal contents was sequenced using Illumina Miseq PE300. Alpha diversity in the two types of hybrids was lower than inbred lines of koi or goldfish and was highest in goldfish, followed by koi. For beta diversity, microbial samples presented clear clusters and the two types of hybrids were more similar to koi than goldfish, indicating the gut microbiota of the reciprocal hybrids was more affected by koi. The dominant phyla were Proteobacteria, Actinobacteria and Firmicutes in koi, and Proteobacteria, Fusobacteria and Actinobacteria in goldfish, and Proteobacteria, Fusobacteria and Firmicutes in the reciprocal hybrids. In the case of Proteobacteria, the dominant classes were Alphaproteobacteria and Gammaproteobacteria in four fish. The dominant genera were norank_f_Rhizobiales_Incertae_Sedis and Plesiomonas in koi, Cetobacterium in goldfish, and Cetobacterium and ZOR0006 in the reciprocal hybrids. PICRUSt1 predictive function analysis showed that the reciprocal hybrids had lower abundance in the most functional categories than koi and goldfish. CONCLUSIONS The gut microbiota of reciprocal hybrids was more affected by koi. Two types of hybrids possessed the same dominated phyla and were different from the inbred lines of koi and goldfish. SIGNIFICANCE AND IMPACT OF THE STUDY It enhanced our understanding of gut microbiota of hybrid lines of goldfish and koi and provided a new perspective for the selective breeding of gut microbiota traits.
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Affiliation(s)
- Qin Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jun-Heng Liu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Bin Wen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jian-Zhong Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Zai-Zhong Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.,Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
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Abstract
Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4–6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9. Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.
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Wang Z, Zhang C, Warden CD, Liu Z, Yuan YC, Guo C, Wang C, Wang J, Wu X, Ermel R, Vonderfecht SL, Wang X, Brown C, Forman S, Yang Y, James You M, Chen W. Loss of SIRT1 inhibits hematopoietic stem cell aging and age-dependent mixed phenotype acute leukemia. Commun Biol 2022; 5:396. [PMID: 35484199 PMCID: PMC9051098 DOI: 10.1038/s42003-022-03340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/05/2022] [Indexed: 01/07/2023] Open
Abstract
Aging of hematopoietic stem cells (HSCs) is linked to various blood disorders and malignancies. SIRT1 has been implicated in healthy aging, but its role in HSC aging is poorly understood. Surprisingly, we found that Sirt1 knockout improved the maintenance of quiescence of aging HSCs and their functionality as well as mouse survival in serial bone marrow transplantation (BMT) recipients. The majority of secondary and tertiary BMT recipients of aging wild type donor cells developed B/myeloid mixed phenotype acute leukemia (MPAL), which was markedly inhibited by Sirt1 knockout. SIRT1 inhibition also reduced the growth and survival of human B/myeloid MPAL cells. Sirt1 knockout suppressed global gene activation in old HSCs, prominently the genes regulating protein synthesis and oxidative metabolism, which may involve multiple downstream transcriptional factors. Our results demonstrate an unexpected role of SIRT1 in promoting HSC aging and age-dependent MPAL and suggest SIRT1 may be a new therapeutic target for modulating functions of aging HSCs and treatment of MPAL.
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Affiliation(s)
- Zhiqiang Wang
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA ,grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Chunxiao Zhang
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Charles David Warden
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Zheng Liu
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Yate-Ching Yuan
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Chao Guo
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Charles Wang
- grid.410425.60000 0004 0421 8357Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA ,grid.43582.380000 0000 9852 649XPresent Address: Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350 USA
| | - Jinhui Wang
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Xiwei Wu
- grid.410425.60000 0004 0421 8357Integrative Genomics Core, Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Richard Ermel
- grid.410425.60000 0004 0421 8357Center for Comparative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | | | - Xiuli Wang
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Christine Brown
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Stephen Forman
- grid.410425.60000 0004 0421 8357Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010 USA
| | - Yaling Yang
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - M. James You
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - WenYong Chen
- grid.410425.60000 0004 0421 8357Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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Saghi M, InanlooRahatloo K, Alavi A, Kahrizi K, Najmabadi H. Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery. BMC Med Genomics 2022; 15:89. [PMID: 35436926 PMCID: PMC9014605 DOI: 10.1186/s12920-022-01237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized. Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacial anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III. Methods We performed RNA sequencing on blood samples to obtain insights into the biological pathways influenced by POLR3B mutation. We applied the results of our RNA-Seq analysis to several gene ontology programs such as ToppGene, Enrichr, KEGG. Results A significant decrease in expression of several spliceosomal RNAs, ribosomal proteins, and transcription factors was detected in the affected, compared to unaffected, family members. Conclusions We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes, and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2 and GATA1 contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of the spliceosome and ribosomal proteins in intellectual disability. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01237-5.
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Affiliation(s)
- Mostafa Saghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Kashif M, Asalam M, Al Shehri SS, Kumar B, Singh N, Akhtar MS. Recombinant expression and biophysical characterization of Mrt4 protein that involved in mRNA turnover and ribosome assembly from Saccharomyces cerevisiae. Bioengineered 2022; 13:9103-9113. [PMID: 35387555 PMCID: PMC9161856 DOI: 10.1080/21655979.2022.2055951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The mRNA turnover and ribosome assembly are facilitated by Mrt4 protein from Saccharomyces cerevisiae. In present study, we are reporting the cloning, expression and homogeneous purification of recombinant Mrt4. Mrt4 is a 236-amino-acid-long nuclear protein that plays a very crucial role in mRNA turnover and ribosome assembly during the translation process. mrt4 gene was amplified by polymerase chain reaction and cloned in expression vector pET23a (+) under the bacteriophage T7-inducible promoter and lac operator. Furthermore, protein was purified to homogeneity using immobilized metal affinity chromatography (IMAC) and its homogeneous purification was further validated by immunoblotting with anti-His antibody. The far-UV CD spectra represent that Mrt4 has a typical α helix with characteristic negative minima at 222 and 208 nm. At physiological pH, the fluorescence spectra and CD spectra showed properly folded tertiary and secondary structures of Mrt4, respectively. Saccharomyces Mrt4 protein possesses putative bipartite NLS (nuclear localization signal) at the N-terminal part followed by two well-conserved domains, rRNA-binding domains and translation factor (TF) binding domain. PIPSA analysis evaluates electrostatic interaction properties of proteins and concluded that Mrt4 protein can be used as a fingerprint for classifying Mrt4-like mRNA turnover protein from various species. The availability of an ample amount of protein may help in its biochemical and biophysical characterization, crystallization and identification of new interacting partners of Mrt4.
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Affiliation(s)
- Mohd Kashif
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohd Asalam
- MSB Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saad S Al Shehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences,Taif University, Taif, Saudi Arabia
| | - Bhupendra Kumar
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Neha Singh
- MSB Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Md Sohail Akhtar
- MSB Division, CSIR-Central Drug Research Institute, Lucknow, India
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Transcriptome Analysis of the Marine Nematode Litoditis marina in a Chemically Defined Food Environment with Stearic Acid Supplementation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Stearic acid represents one of the most abundant fatty acids in the Western diet and profoundly regulates health and diseases of animals and human beings. We previously showed that stearic acid supplementation promoted development of the terrestrial model nematode Caenorhabditis elegans in chemically defined CeMM food environment. However, whether stearic acid regulates development of other nematodes remains unknown. Here, we found that dietary supplementation with stearic acid could promote the development of the marine nematode Litoditis marina, belonging to the same family as C. elegans, indicating the conserved roles of stearic acid in developmental regulation. We further employed transcriptome analysis to analyze genome-wide transcriptional signatures of L. marina with dietary stearic acid supplementation. We found that stearic acid might promote development of L. marina via upregulation of the expression of genes involved in aminoacyl-tRNA biosynthesis, translation initiation and elongation, ribosome biogenesis, and transmembrane transport. In addition, we observed that the expression of neuronal signaling-related genes was decreased. This study provided important insights into how a single fatty acid stearic acid regulates development of marine nematode, and further studies with CRISPR genome editing will facilitate demonstrating the molecular mechanisms underlying how a single metabolite regulates animal development and health.
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Jüttner M, Ferreira-Cerca S. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Mol Biol Evol 2022; 39:6547259. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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Dastidar SG, Nair D. A Ribosomal Perspective on Neuronal Local Protein Synthesis. Front Mol Neurosci 2022; 15:823135. [PMID: 35283723 PMCID: PMC8904363 DOI: 10.3389/fnmol.2022.823135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Continued mRNA translation and protein production are critical for various neuronal functions. In addition to the precise sorting of proteins from cell soma to distant locations, protein synthesis allows a dynamic remodeling of the local proteome in a spatially variable manner. This spatial heterogeneity of protein synthesis is shaped by several factors such as injury, guidance cues, developmental cues, neuromodulators, and synaptic activity. In matured neurons, thousands of synapses are non-uniformly distributed throughout the dendritic arbor. At any given moment, the activity of individual synapses varies over a wide range, giving rise to the variability in protein synthesis. While past studies have primarily focused on the translation factors or the identity of translated mRNAs to explain the source of this variation, the role of ribosomes in this regard continues to remain unclear. Here, we discuss how several stochastic mechanisms modulate ribosomal functions, contributing to the variability in neuronal protein expression. Also, we point out several underexplored factors such as local ion concentration, availability of tRNA or ATP during translation, and molecular composition and organization of a compartment that can influence protein synthesis and its variability in neurons.
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Kiparaki M, Khan C, Folgado-Marco V, Chuen J, Moulos P, Baker NE. The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function. eLife 2022; 11:e71705. [PMID: 35179490 PMCID: PMC8933008 DOI: 10.7554/elife.71705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 02/09/2022] [Indexed: 11/26/2022] Open
Abstract
Ribosomal Protein (Rp) gene haploinsufficiency affects translation rate, can lead to protein aggregation, and causes cell elimination by competition with wild type cells in mosaic tissues. We find that the modest changes in ribosomal subunit levels observed were insufficient for these effects, which all depended on the AT-hook, bZip domain protein Xrp1. Xrp1 reduced global translation through PERK-dependent phosphorylation of eIF2α. eIF2α phosphorylation was itself sufficient to enable cell competition of otherwise wild type cells, but through Xrp1 expression, not as the downstream effector of Xrp1. Unexpectedly, many other defects reducing ribosome biogenesis or function (depletion of TAF1B, eIF2, eIF4G, eIF6, eEF2, eEF1α1, or eIF5A), also increased eIF2α phosphorylation and enabled cell competition. This was also through the Xrp1 expression that was induced in these depletions. In the absence of Xrp1, translation differences between cells were not themselves sufficient to trigger cell competition. Xrp1 is shown here to be a sequence-specific transcription factor that regulates transposable elements as well as single-copy genes. Thus, Xrp1 is the master regulator that triggers multiple consequences of ribosomal stresses and is the key instigator of cell competition.
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Affiliation(s)
- Marianthi Kiparaki
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming”VariGreece
| | - Chaitali Khan
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
| | | | - Jacky Chuen
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming”VariGreece
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
- Department of Developmental and Molecular Biology, Albert Einstein College of MedicineThe BronxUnited States
- Department of Opthalmology and Visual Sciences, Albert Einstein College of MedicineThe BronxUnited States
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Li SF, Zhang SB, Lv YY, Zhai HC, Hu YS, Cai JP. Transcriptome analysis reveals the underlying mechanism of heptanal against Aspergillus flavus spore germination. Appl Microbiol Biotechnol 2022; 106:1241-1255. [DOI: 10.1007/s00253-022-11783-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
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Jüttner M, Ferreira-Cerca S. A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. Methods Mol Biol 2022; 2533:3-22. [PMID: 35796979 PMCID: PMC9761495 DOI: 10.1007/978-1-0716-2501-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Ribosomes are universally conserved ribonucleoprotein complexes involved in the decoding of the genetic information contained in messenger RNAs into proteins. Accordingly, ribosome biogenesis is a fundamental cellular process required for functional ribosome homeostasis and to preserve satisfactory gene expression capability.Although the ribosome is universally conserved, its biogenesis shows an intriguing degree of variability across the tree of life . These differences also raise yet unresolved questions. Among them are (a) what are, if existing, the remaining ancestral common principles of ribosome biogenesis ; (b) what are the molecular impacts of the evolution history and how did they contribute to (re)shape the ribosome biogenesis pathway across the tree of life ; (c) what is the extent of functional divergence and/or convergence (functional mimicry), and in the latter case (if existing) what is the molecular basis; (d) considering the universal ribosome conservation, what is the capability of functional plasticity and cellular adaptation of the ribosome biogenesis pathway?In this review, we provide a brief overview of ribosome biogenesis across the tree of life and try to illustrate some potential and/or emerging answers to these unresolved questions.
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Affiliation(s)
- Michael Jüttner
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Regensburg Center for Biochemistry-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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Rosselló JA, Maravilla AJ, Rosato M. The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:788911. [PMID: 35283933 PMCID: PMC8908318 DOI: 10.3389/fpls.2022.788911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.
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Hernández RB, de Souza-Pinto NC, Kleinjans J, van Herwijnen M, Piepers J, Moteshareie H, Burnside D, Golshani A. Manganese-Induced Neurotoxicity through Impairment of Cross-Talk Pathways in Human Neuroblastoma Cell Line SH-SY5Y Differentiated with Retinoic Acid. TOXICS 2021; 9:toxics9120348. [PMID: 34941782 PMCID: PMC8704659 DOI: 10.3390/toxics9120348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 01/29/2023]
Abstract
Manganese (Mn) is an important element; yet acute and/or chronic exposure to this metal has been linked to neurotoxicity and neurodegenerative illnesses such as Parkinson’s disease and others via an unknown mechanism. To better understand it, we exposed a human neuroblastoma cell model (SH-SY5Y) to two Mn chemical species, MnCl2 and Citrate of Mn(II) (0–2000 µM), followed by a cell viability assay, transcriptomics, and bioinformatics. Even though these cells have been chemically and genetically modified, which may limit the significance of our findings, we discovered that by using RA-differentiated cells instead of undifferentiated SH-SY5Y cell line, both chemical species induce a similar toxicity, potentially governed by disruption of protein metabolism, with some differences. The MnCl2 altered amino acid metabolism, which affects RNA metabolism and protein synthesis. Citrate of Mn(II), however, inhibited the E3 ubiquitin ligases–target protein degradation pathway, which can lead to the buildup of damaged/unfolded proteins, consistent with histone modification. Finally, we discovered that Mn(II)-induced cytotoxicity in RA-SH-SY5Y cells shared 84 percent of the pathways involved in neurodegenerative diseases.
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Affiliation(s)
- Raúl Bonne Hernández
- Laboratory of Bioinorganic and Environmental Toxicology—LABITA, Department of Chemistry, Federal University of São Paulo, Rua Prof. Artur Riedel, 275, Diadema 09972-270, SP, Brazil
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
- Correspondence: ; Tel.: +55-11-3385-4137 (ext. 3522)
| | - Nadja C. de Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes, 748, Butantã, São Paulo 05508-900, SP, Brazil;
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Marcel van Herwijnen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Jolanda Piepers
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Houman Moteshareie
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Daniel Burnside
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Ashkan Golshani
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
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