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Gutierrez RF, Ciol H, Carrillo Barra AL, Leonardo DA, Avaca-Crusca JS, Thiemann OH, Zanchin NIT, Araujo APU. Assigning roles in Chlamydomonas ribosome biogenesis: The conserved factor NIP7. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141045. [PMID: 39216654 DOI: 10.1016/j.bbapap.2024.141045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/31/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Ribosome biogenesis (RB) is a highly conserved process across eukaryotes that results in the assembly of functional ribosomal subunits. Studies in Saccharomyces cerevisiae and Homo sapiens have identified numerous RB factors (RBFs), including the NIP7 protein, which is involved in late-stage pre-60S ribosomal maturation. NIP7 expression has also been observed in Chlamydomonas reinhardtii, highlighting its evolutionary significance. This study aimed to characterize the function of the NIP7 protein from C. reinhardtii (CrNip7) through protein complementation assays and a paromomycin resistance test, assessing its ability to complement the role of NIP7 in yeast. Protein interaction studies were conducted via yeast two-hybrid assay to identify potential protein partners of CrNip7. Additionally, rRNA modeling analysis was performed using the predicted structure of CrNip7 to investigate its interaction with rRNA. The study revealed that CrNip7 can complement the role of NIP7 in yeast, implicating CrNip7 in the biogenesis of the 60S ribosomal subunit. Furthermore, two possible partner proteins of CrNip7, UNC-p and G-patch, were identified through yeast two-hybrid assay. The potential of these proteins to interact with CrNip7 was explored through in silico analyses. Furthermore, nucleic acid interaction was also evaluated, indicating the involvement of the N- and C-terminal domains of CrNIP7 in interacting with rRNA. Collectively, our findings provide valuable insights into the RBFs CrNip7, offering novel information for comparative studies on RB among eukaryotic model organisms, shedding light on its evolutionary conservation and functional role across species.
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Affiliation(s)
- Raissa Ferreira Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Heloisa Ciol
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Angélica L Carrillo Barra
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Diego Antonio Leonardo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Juliana S Avaca-Crusca
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | - Otavio H Thiemann
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil
| | | | - Ana P Ulian Araujo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo 13560-970, PO Box 369, Brazil.
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2
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Wang L, Chen B, Ma B, Wang Y, Wang H, Sun X, Tan BC. Maize Dek51 encodes a DEAD-box RNA helicase essential for pre-rRNA processing and seed development. Cell Rep 2024; 43:114673. [PMID: 39196780 DOI: 10.1016/j.celrep.2024.114673] [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: 05/13/2024] [Revised: 07/09/2024] [Accepted: 08/08/2024] [Indexed: 08/30/2024] Open
Abstract
Pre-rRNA processing is essential to ribosome biosynthesis. However, the processing mechanism is not fully understood in plants. Here, we report a DEAD-box RNA helicase DEK51 that mediates the 3' end processing of 18S and 5.8S pre-rRNA in maize (Zea mays L.). DEK51 is localized in the nucleolus, and loss of DEK51 arrests maize seed development and blocks the 3' end processing of 18S and 5.8S pre-rRNA. DEK51 interacts with putative key factors in nuclear RNA exosome-mediated pre-rRNA processing, including ZmMTR4, ZmSMO4, ZmRRP44A, and ZmRRP6L2. This suggests that DEK51 facilitates pre-rRNA processing by interacting with the exosome. Loss of ZmMTR4 function arrests seed development and blocks the 3' end processing of 18S and 5.8S pre-rRNA, similar to dek51. DEK51 also interacts with endonucleases ZmUTP24 and ZmRCL1, suggesting that it may also be involved in the cleavage at site A2. These results show the critical role of DEK51 in promoting 3' end processing of pre-rRNA.
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Affiliation(s)
- Le Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Baoyin Chen
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bing Ma
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hongqiu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaotong Sun
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
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3
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Tao Y, Wu L, Volodymyr V, Hu P, Hu H, Li C. Identification of the ribosomal protein L18 (RPL18) gene family reveals that TaRPL18-1 positively regulates powdery mildew resistance in wheat. Int J Biol Macromol 2024; 280:135730. [PMID: 39322125 DOI: 10.1016/j.ijbiomac.2024.135730] [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: 06/03/2024] [Revised: 09/12/2024] [Accepted: 09/14/2024] [Indexed: 09/27/2024]
Abstract
The Ribosomal protein L18 (RPL18) protein gene family plays an important role in plant growth, development and stress response. Although the RPL18 genes have been identified in several plant species, the RPL18 gene family in wheat (Triticum aestivum) is still unexplored. This study found 8 TaRPL18 genes, each of which has a significantly different gene sequence length and is evenly distributed on the chromosome; Additionally, these proteins have similar physicochemical characteristics as well as secondary and tertiary structures. 17 RPL18 genes in 4 species (wheat, Arabidopsis, rice, and maize) were classified into 5 groups, and the TaRPL18 genes within the same group showed similar structures and conserved motifs. Analysis of the cis-acting elements in the TaRPL18 genes promoter regions revealed the presence of developmental and stress-responsive elements in the majority of the genes. Through yeast two-hybrid (Y2H) experiments, it was confirmed that the powdery mildew resistance protein TaPm46 physically interacts with the Class IV TaRPL18-1. Functional analysis indicated that TaRPL18-1-silenced wheat plants show reduced resistance to powdery mildew compared to the wild type (WT), with decreased expression levels of PAL and PPO genes, and increased expression levels of the PR gene. The findings of this study provide a basis for clarifying the function of the TaRPL18 genes and will be useful for the selection of disease-resistant varieties of wheat.
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Affiliation(s)
- Ye Tao
- School of Agriculture/Henan Engineering Research Center of Crop Genome Editing/Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine
| | - Liuliu Wu
- School of Agriculture/Henan Engineering Research Center of Crop Genome Editing/Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China; Sumy National Agrarian University, Sumy 40021, Ukraine
| | | | - Ping Hu
- School of Agriculture/Henan Engineering Research Center of Crop Genome Editing/Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Haiyan Hu
- School of Agriculture/Henan Engineering Research Center of Crop Genome Editing/Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Chengwei Li
- School of Agriculture/Henan Engineering Research Center of Crop Genome Editing/Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation/Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Henan Institute of Science and Technology, Xinxiang 453003, China; Henan Agricultural University, Zhengzhou 450000, China.
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4
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Li HY, Wang M, Jiang X, Jing Y, Wu Z, He Y, Yan K, Sun S, Ma S, Ji Z, Wang S, Belmonte JCI, Qu J, Zhang W, Wei T, Liu GH. CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver. Nucleic Acids Res 2024:gkae740. [PMID: 39258545 DOI: 10.1093/nar/gkae740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence. Consequently, absence of RPL22 delays hMPCs from becoming senescent, while an excess of RPL22 accelerates the senescence process. Mechanistically, we found in senescent hMPCs, RPL22 accumulates within the nucleolus. This accumulation triggers a cascade of events, including heterochromatin decompaction with concomitant degradation of key heterochromatin proteins, specifically heterochromatin protein 1γ (HP1γ) and heterochromatin protein KRAB-associated protein 1 (KAP1). Subsequently, RPL22-dependent breakdown of heterochromatin stimulates the transcription of ribosomal RNAs (rRNAs), triggering cellular senescence. In summary, our findings unveil a novel role for nucleolar RPL22 as a destabilizer of heterochromatin and a driver of cellular senescence, shedding new light on the intricate mechanisms underlying the aging process.
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Affiliation(s)
- Hong-Yu Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaobin Jing
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifang He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- CAS key laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Taotao Wei
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
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5
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Hussain A. DEAD Box RNA Helicases: Biochemical Properties, Role in RNA Processing and Ribosome Biogenesis. Cell Biochem Biophys 2024; 82:427-434. [PMID: 38430409 DOI: 10.1007/s12013-024-01240-w] [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: 12/12/2022] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
DEAD box RNA helicases are a versatile group of ATP dependent enzymes that play an essential role in cellular processes like transcription, RNA processing, ribosome biogenesis and translation. These enzymes perform structural rearrangement of complex RNA molecules and enhance the productive folding of RNA and organization of macromolecular complexes. In this review article besides providing the outline about structural organization of helicases, an in-depth discussion will be done on the biochemical properties of RNA helicases like their substrate binding, binding and hydrolysis of ATP and related conformational changes that are important for functioning of the RNA helicase enzymes. I will extensively discuss the physiological role of RNA helicases in RNA processing and ribosome biogenesis.
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Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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6
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Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
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Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
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7
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da Silva Filho JLB, Pestana RKN, da Silva Júnior WJ, Coelho Filho MA, Ferreira CF, de Oliveira EJ, Kido EA. Exploiting DNA methylation in cassava under water deficit for crop improvement. PLoS One 2024; 19:e0296254. [PMID: 38386677 PMCID: PMC10883565 DOI: 10.1371/journal.pone.0296254] [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: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 02/24/2024] Open
Abstract
DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.
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Affiliation(s)
| | | | - Wilson José da Silva Júnior
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - Ederson Akio Kido
- Laboratório de Genética Molecular de Plantas, Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
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8
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Li M, Gao S, Yang P, Li H. Improvement of ribonucleic acid production in Cyberlindnera jadinii and optimization of fermentation medium. AMB Express 2024; 14:24. [PMID: 38358520 PMCID: PMC10869677 DOI: 10.1186/s13568-024-01679-3] [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: 06/19/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
To enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett-Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH2PO4) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH2PO4, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.
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Affiliation(s)
- Mengting Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuhong Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Pengcheng Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hejin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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9
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Li K, Zhang Q, Liu H, Wang F, Li A, Ding T, Mu Q, Zhao H, Wang P. Arabidopsis NOTCHLESS plays an important role in root and embryo development. PLANT SIGNALING & BEHAVIOR 2023; 18:2245616. [PMID: 37573563 PMCID: PMC10424599 DOI: 10.1080/15592324.2023.2245616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023]
Abstract
Ribosome biogenesis is a fundamental process in eukaryotic cells. NOTCHLESS (NLE) is involved in 60S ribosome biogenesis in yeast, but its role in Arabidopsis (A. thaliana) remains exclusive. Here, we found that Arabidopsis NLE (AtNLE) is highly conservative in phylogeny, which encoding a WD40-repeat protein. AtNLE is expressed in actively dividing tissues. AtNLE-GFP is localized in the nucleus. AtNLE physically interacts with the MIDAS domain of AtMDN1, a protein involved in the biogenesis of the 60S ribosomal subunit in Arabidopsis. The underexpressing mutant nle-2 shows short roots and reduced cell number in the root meristem. In addition, the null mutant nle-1 is embryo lethal, and defective embryos are arrested at the early globular stage. This work suggests that AtNLE interacts with AtMDN1, and AtNLE functions in root and embryo development.
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Affiliation(s)
- Ke Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Qingtian Zhang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Huiping Liu
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Fengxia Wang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Ao Li
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Tingting Ding
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
- Shandong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Qian Mu
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Hongjun Zhao
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
| | - Pengfei Wang
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan, PR China
- Shandong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Jinan, China
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10
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Zhou L, Ding X, Wang Z, Zhou S, Qin S, Sun X, Wang X, Li M. BmRRS1 Protein Inhibits the Proliferation of Baculovirus Autographa californica Nucleopolyhedrovirus in Silkworm, Bombyx mori. Int J Mol Sci 2023; 25:306. [PMID: 38203476 PMCID: PMC10779178 DOI: 10.3390/ijms25010306] [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: 11/17/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The study of functional genes involved in baculovirus infection is vital for its wide application in pest biocontrol. This study utilized the Autographa californica nucleopolyhedrovirus (AcMNPV) and silkworm as models to elucidate the role of BmRRS1, which has been found to exhibit notable differential expression between resistant and susceptible silkworm strains. The results showed that it was evolutionarily conserved in selected species. Among different tissues, it was expressed at the highest level in the gonads, followed by the hemolymph and silk glands; among the different developmental stages, it was the highest in the second instar, followed by the pupae and adults. Moreover, its vital role in suppressing AcMNPV infection was verified by the decreased expression of lef3 and vp39 protein after overexpression of BmRRS1 as well as by the increased expression of the viral gene lef3 and the viral protein vp39 after siRNA treatment against BmRRS1 expression in BmN cells. Additionally, the direct interaction between BmRRS1 and AcMNPV was detected by the GST pull-down assay. Finally, the homologue of BmRRS1 in Spodoptera frugiperda was found to be involved in larval resistance to AcMNPV. In a word, BmRRS1 plays a vital role in AcMNPV resistance in silkworms, and this might be related to the direct interaction with AcMNPV. The results of this study provide a potential target for protecting silkworm larvae from virus infection and controlling agricultural and forestry pests.
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Affiliation(s)
- Liqin Zhou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
| | - Xinyi Ding
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
| | - Zhisheng Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
| | - Si Zhou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xueyang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Muwang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; (L.Z.); (X.D.); (Z.W.); (S.Z.); (S.Q.); (X.S.); (X.W.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
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11
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Scull CE, Twa G, Zhang Y, Yang NJ, Hunter RN, Augelli-Szafran CE, Schneider DA. Small Molecule RBI2 Disrupts Ribosome Biogenesis through Pre-rRNA Depletion. Cancers (Basel) 2023; 15:3303. [PMID: 37444413 PMCID: PMC10340317 DOI: 10.3390/cancers15133303] [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: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Cancer cells are especially sensitive to perturbations in ribosome biogenesis as they rely on finely tuned protein homeostasis to facilitate their rapid growth and proliferation. While ribosome synthesis and cancer have a well-established relationship, ribosome biogenesis has only recently drawn interest as a cancer therapeutic target. In this study, we exploited the relationship between ribosome biogenesis and cancer cell proliferation by using a potent ribosome biogenesis inhibitor, RBI2 (Ribosome Biogenesis Inhibitor 2), to perturb cancer cell growth and viability. We demonstrate herein that RBI2 significantly decreases cell viability in malignant melanoma cells and breast cancer cell lines. Treatment with RBI2 dramatically and rapidly decreased ribosomal RNA (rRNA) synthesis, without affecting the occupancy of RNA polymerase I (Pol I) on the ribosomal DNA template. Next-generation RNA sequencing (RNA-seq) revealed that RBI2 and previously described ribosome biogenesis inhibitor CX-5461 induce distinct changes in the transcriptome. An investigation of the content of the pre-rRNAs through RT-qPCR revealed an increase in the polyadenylation of cellular rRNA after treatment with RBI2, constituting a known pathway by which rRNA degradation occurs. Northern blotting revealed that RBI2 does not appear to impair or alter rRNA processing. Collectively, these data suggest that RBI2 inhibits rRNA synthesis differently from other previously described ribosome biogenesis inhibitors, potentially acting through a novel pathway that upregulates the turnover of premature rRNAs.
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Affiliation(s)
- Catherine E. Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy Twa
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Naiheng J. Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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13
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Kim KR, Park SY, Kim H, Hong JM, Kim SY, Yu JN. Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus. Genes (Basel) 2023; 14:1149. [PMID: 37372329 DOI: 10.3390/genes14061149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.
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Affiliation(s)
- Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - So Young Park
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Heesoo Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong Min Hong
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Sun-Yu Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Jeong-Nam Yu
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
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14
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Newman M, Li G, Martínez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. J Fungi (Basel) 2023; 9:359. [PMID: 36983527 PMCID: PMC10056406 DOI: 10.3390/jof9030359] [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: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Affiliation(s)
- Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hunter Lynch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sawyer Andersen
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Madison Newman
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Gengtan Li
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Domingo Martínez-Soto
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Shira Milo-Cochavi
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dilay Hazal Ayhan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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15
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Li G, Mart Nez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527873. [PMID: 36798233 PMCID: PMC9934661 DOI: 10.1101/2023.02.09.527873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected global transcription factor profiles (TFomes) and their potential roles in coordinating CCs and ACs functions to accomplish host-specific pathogenicity. Remarkably, we found a clear positive correlation between the sizes of TFome and proteome of an organism, and FOSC TFomes are larger due to the acquisition of ACs. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls are highly conserved. Among 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 are most significantly expanded to 671 and 167 genes per family, including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3%, including a disordered protein Ren1. Expression profiles revealed a steady expression of conserved TF families and specific activation of AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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16
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Yang C, Tang L, Qin L, Zhong W, Tang X, Gong X, Xie W, Li Y, Xia S. mRNA Turnover Protein 4 Is Vital for Fungal Pathogenicity and Response to Oxidative Stress in Sclerotinia sclerotiorum. Pathogens 2023; 12:pathogens12020281. [PMID: 36839553 PMCID: PMC9960052 DOI: 10.3390/pathogens12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Ribosome assembly factors have been extensively studied in yeast, and their abnormalities may affect the assembly process of ribosomes and cause severe damage to cells. However, it is not clear whether mRNA turnover protein 4 (MRT4) functions in the fungal growth and pathogenicity in Sclerotinia sclerotiorum. Here, we identified the nucleus-located gene SsMRT4 using reverse genetics, and found that knockdown of SsMRT4 resulted in retard mycelia growth and complete loss of pathogenicity. Furthermore, mrt4 knockdown mutants showed almost no appressorium formation and oxalic acid production comparing to the wild-type and complementary strains. In addition, the abilities to ROS elimination and resistance to oxidative and osmotic stresses were also seriously compromised in mrt4 mutants. Overall, our study clarified the role of SsMRT4 in S. sclerotiorum, providing new insights into ribosome assembly in regulating pathogenicity and resistance to environmental stresses of fungi.
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Affiliation(s)
- Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lan Tang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Weiping Zhong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Wenqi Xie
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yifu Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- Correspondence:
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17
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Protein-Coding Region Derived Small RNA in Exosomes from Influenza A Virus-Infected Cells. Int J Mol Sci 2023; 24:ijms24010867. [PMID: 36614310 PMCID: PMC9820831 DOI: 10.3390/ijms24010867] [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: 11/22/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Exosomes may function as multifactorial mediators of cell-to-cell communication, playing crucial roles in both physiological and pathological processes. Exosomes released from virus-infected cells may contain RNA and proteins facilitating infection spread. The purpose of our study was to analyze how the small RNA content of exosomes is affected by infection with the influenza A virus (IAV). Exosomes were isolated by ultracentrifugation after hemadsorption of virions and their small RNA content was identified using high-throughput sequencing. As compared to mock-infected controls, 856 RNA transcripts were significantly differentially expressed in exosomes from IAV-infected cells, including fragments of 458 protein-coding (pcRNA), 336 small, 28 long intergenic non-coding RNA transcripts, and 33 pseudogene transcripts. Upregulated pcRNA species corresponded mainly to proteins associated with translation and antiviral response, and the most upregulated among them were RSAD2, CCDC141 and IFIT2. Downregulated pcRNA species corresponded to proteins associated with the cell cycle and DNA packaging. Analysis of differentially expressed pseudogenes showed that in most cases, an increase in the transcription level of pseudogenes was correlated with an increase in their parental genes. Although the role of exosome RNA in IAV infection remains undefined, the biological processes identified based on the corresponding proteins may indicate the roles of some of its parts in IAV replication.
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18
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Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
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Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
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19
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Ishwarya Lakshmi VG, Sreedhar M, JhansiLakshmi V, Gireesh C, Rathod S, Bohar R, Deshpande S, Laavanya R, Kiranmayee KNSU, Siddi S, Vanisri S. Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice. Front Genet 2022; 13:914131. [PMID: 35899197 PMCID: PMC9309266 DOI: 10.3389/fgene.2022.914131] [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: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Rice (Oryza sativa L.) is an important source of nutrition for the world's burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (Stål)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers.
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Affiliation(s)
- V. G. Ishwarya Lakshmi
- Department of Genetics and Plant Breeding, College of Agriculture, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - M. Sreedhar
- Administrative Office, PJTSAU, Hyderabad, India
| | | | - C. Gireesh
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Santosha Rathod
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Rajaguru Bohar
- CGIAR Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - R. Laavanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Sreedhar Siddi
- Agricultural Research Station, PJTSAU, Peddapalli, India
| | - S. Vanisri
- Institute of Biotechnology, PJTSAU, Hyderabad, India
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20
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Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
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Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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21
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He X, Wu F, Wang L, Li L, Zhang G. Integrated application of transcriptomics and metabolomics provides insights into condition index difference mechanisms in the Pacific oyster (Crassostrea gigas). Genomics 2022; 114:110413. [PMID: 35716821 DOI: 10.1016/j.ygeno.2022.110413] [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: 12/22/2021] [Revised: 05/04/2022] [Accepted: 06/12/2022] [Indexed: 11/25/2022]
Abstract
The condition index (CI) is an economically important tool for assessing the quality of oysters, such as the Pacific oyster Crassostrea gigas. However, little is known about the mechanisms that underlie differences in CI between different C. gigas populations. In this study, we integrated transcriptomic and metabolomic profiling to investigate the mechanisms that underlie the differences between high- and low-CI groups in one- and two-year-old populations of C. gigas. The results indicate that differences in CI were associated with the regulation of growth-related genes, the FoxO signaling pathway, and the complex regulation of carbohydrate, lipid, amino acid, and energy metabolism. Moreover, the mechanisms underlying these differences differed between the populations. This study is the first to elucidate the molecular and chemical mechanisms associated with CI, and the results will be helpful for breeding higher quality oysters.
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Affiliation(s)
- Xin He
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100039, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fucun Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Luping Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China
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22
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Mutation of an Essential 60S Ribosome Assembly Factor MIDASIN 1 Induces Early Flowering in Arabidopsis. Int J Mol Sci 2022; 23:ijms23126509. [PMID: 35742952 PMCID: PMC9223865 DOI: 10.3390/ijms23126509] [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: 04/29/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Ribosome biogenesis is tightly associated with plant growth and reproduction. Mutations in genes encoding ribosomal proteins (RPs) or ribosome biogenesis factors (RBFs) generally result in retarded growth and delayed flowering. However, the early-flowering phenotype resulting from the ribosome biogenesis defect is rarely reported. We previously identified that the AAA-ATPase MIDASIN 1 (MDN1) functions as a 60S RBF in Arabidopsis. Here, we found that its weak mutant mdn1-1 is early-flowering. Transcriptomic analysis showed that the expression of FLOWERING LOCUS C (FLC) is down-regulated, while that of some autonomous pathway genes and ABSCISIC ACID-INSENSITIVE 5 (ABI5) is up-regulated in mdn1-1. Phenotypic analysis revealed that the flowering time of mdn1-1 is severely delayed by increasing FLC expression, suggesting that the early flowering in mdn1-1 is likely associated with the downregulation of FLC. We also found that the photoperiod pathway downstream of CONSTANTS (CO) and FLOWERING LOCUS T (FT) might contribute to the early flowering in mdn1-1. Intriguingly, the abi5-4 allele completely blocks the early flowering in mdn1-1. Collectively, our results indicate that the ribosome biogenesis defect elicited by the mutation of MDN1 leads to early flowering by affecting multiple flowering regulation pathways.
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23
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Chen J, Huang Y, Zhang K. The DEAD-Box Protein Rok1 Coordinates Ribosomal RNA Processing in Association with Rrp5 in Drosophila. Int J Mol Sci 2022; 23:ijms23105685. [PMID: 35628496 PMCID: PMC9146779 DOI: 10.3390/ijms23105685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Ribosome biogenesis and processing involve the coordinated action of many components. The DEAD-box RNA helicase (Rok1) is essential for cell viability, and the depletion of Rok1 inhibits pre-rRNA processing. Previous research on Rok1 and its cofactor Rrp5 has been performed primarily in yeast. Few functional studies have been performed in complex multicellular eukaryotes. Here, we used a combination of genetics and developmental experiments to show that Rok1 and Rrp5, which localize to the nucleolus, play key roles in the pre-rRNA processing and ribosome assembly in D. melanogaster. The accumulation of pre-rRNAs caused by Rok1 depletion can result in developmental defects. The loss of Rok1 enlarged the nucleolus and led to stalled ribosome assembly and pre-rRNA processing in the nucleolus, thereby blocking rRNA maturation and exacerbating the inhibition of mitosis in the brain. We also discovered that rrp54-2/4-2 displayed significantly increased ITS1 signaling by fluorescence in situ hybridization, and a reduction in ITS2. Rrp5 signal was highly enriched in the core of the nucleolus in the rok1167/167 mutant, suggesting that Rok1 is required for the accurate cellular localization of Rrp5 in the nucleolus. We have thus uncovered functions of Rok1 that reveal important implications for ribosome processing in eukaryotes.
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Affiliation(s)
- Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- Correspondence: (J.C.); (Y.H.); Tel.: +86-20-87597440 (J.C.)
| | - Yuantai Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- Correspondence: (J.C.); (Y.H.); Tel.: +86-20-87597440 (J.C.)
| | - Kang Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
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24
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Li M, Zhang J, Bai Q, Fang L, Song H, Cao Y. Non-homologous End Joining-Mediated Insertional Mutagenesis Reveals a Novel Target for Enhancing Fatty Alcohols Production in Yarrowia lipolytica. Front Microbiol 2022; 13:898884. [PMID: 35547152 PMCID: PMC9082995 DOI: 10.3389/fmicb.2022.898884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Non-homologous end joining (NHEJ)-mediated integration is effective in generating random mutagenesis to identify beneficial gene targets in the whole genome, which can significantly promote the performance of the strains. Here, a novel target leading to higher protein synthesis was identified by NHEJ-mediated integration that seriously improved fatty alcohols biosynthesis in Yarrowia lipolytica. One batch of strains transformed with fatty acyl-CoA reductase gene (FAR) showed significant differences (up to 70.53-fold) in fatty alcohol production. Whole-genome sequencing of the high-yield strain demonstrated that a new target YALI0_A00913g ("A1 gene") was disrupted by NHEJ-mediated integration of partial carrier DNA, and reverse engineering of the A1 gene disruption (YlΔA1-FAR) recovered the fatty alcohol overproduction phenotype. Transcriptome analysis of YlΔA1-FAR strain revealed A1 disruption led to strengthened protein synthesis process that was confirmed by sfGFP gene expression, which may account for enhanced cell viability and improved biosynthesis of fatty alcohols. This study identified a novel target that facilitated synthesis capacity and provided new insights into unlocking biosynthetic potential for future genetic engineering in Y. lipolytica.
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Affiliation(s)
- Mengxu Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinlai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Qiuyan Bai
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Lixia Fang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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25
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Zhang L, Lin J, Weng M, Wen Y, Zhang Y, Deng W. RPLP1, an NS4B-interacting protein, enhances production of CSFV through promoting translation of viral genome. Virulence 2022; 13:370-386. [PMID: 35129423 PMCID: PMC8824197 DOI: 10.1080/21505594.2022.2033500] [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: 11/05/2022] Open
Abstract
Classical swine fever virus (CSFV), the etiological agent of classical swine fever (CSF), causes serious financial losses to the pig industry. Using yeast two-hybrid screening, we have previously identified ribosomal protein RPLP1 as a potential binding partner of CSFV NS4B. In this study, the interaction between host RPLP1 and CSFV NS4B was further characterized by co-immunoprecipitation (co-IP), glutathione S-transferase (GST) pulldown, and confocal microscopy. In addition, lentivirus-mediated shRNA knockdown of RPLP1 drastically attenuated CSFV growth, while stable overexpression of RPLP1 markedly enhanced CSFV production. Moreover, cellular RPLP1 expression was found to be significantly up-regulated along with CSFV infection. Dual-luciferase reporter assay showed that depletion of RPLP1 had no effects on the activity of CSFV internal ribosome entry site (IRES). In the first life cycle of CSFV, further studies revealed that RPLP1 depletion did not influence the intracellular viral RNA abundance but diminished the intracellular and extracellular progeny virus titers as well as the viral E2 protein expression, which indicates that RPLP1 is crucial for CSFV genome translation. In summary, this study demonstrated that RPLP1 interacts with CSFV NS4B and enhances virus production via promoting translation of viral genome.
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Affiliation(s)
- Longxiang Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jihui Lin
- School of Nursing, Southwest Medical University, Luzhou, Sichuan, China
| | - Maoyang Weng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Wen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Deng
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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26
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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27
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Boussaid I, Fontenay M. Translation defects in ribosomopathies. Curr Opin Hematol 2022; 29:119-125. [PMID: 35102070 DOI: 10.1097/moh.0000000000000705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Congenital or acquired ribosomopathies related to mutations or deletions in ribosomal proteins gene or ribosome-associated proteins exhibit defective ribosome biogenesis that expose the cell to translation defects. The mechanisms leading to low translation rate, loss-of-translation fidelity and translation selectivity are reviewed. RECENT FINDINGS New quantitative techniques to measure ribosome component stoichiometry reveal that the pool of ribosomes could be heterogeneous and/or decreased with a limited number of translationally competent ribosomes. During development or cell differentiation, the absence of specific ribosome components or their replacement by paralogs generate heterogeneous ribosomes that are specialized in the translation of specific mRNAs. Decreased ribosome content by defective biosynthesis of a subunit results in translation selectivity at the expense of short structured transcripts with high codon adaptation index. Activation of p53, as a witness of nucleolar stress associated with the hematological phenotype of ribosomopathies participates in translational reprogramming of the cell by interfering with cap-dependent translation. SUMMARY Translation selectivity is a common feature of ribosomopathies. p53 is more selectively activated in ribosomopathies with erythroid phenotype. The discovery of its dual role in regulating transcriptional and translational program supports new therapeutic perspectives.
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Affiliation(s)
- Ismael Boussaid
- Université de Paris, Laboratory of excellence for Red blood cells GR-Ex, and Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris, France
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28
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Zinani OQH, Keseroğlu K, Özbudak EM. Regulatory mechanisms ensuring coordinated expression of functionally related genes. Trends Genet 2022; 38:73-81. [PMID: 34376301 PMCID: PMC8678166 DOI: 10.1016/j.tig.2021.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023]
Abstract
Coordinated spatiotemporal expression of large sets of genes is required for the development and homeostasis of organisms. To achieve this goal, organisms use myriad strategies where they form operons, utilize bidirectional promoters, cluster genes, share enhancers among genes by DNA looping, and form topologically associated domains and transcriptional condensates. Coexpression achieved by these different strategies is hypothesized to have functional importance in minimizing gene expression variability, establishing dosage balance to ensure stoichiometry of protein complexes, and minimizing accumulation of toxic intermediate metabolites. By combining gene-editing tools with computational modeling, recent studies tested the advantages of adjacent genes located in pairs and clusters. We propose that with the advancement of gene editing, single-cell sequencing, and imaging tools, one could readily test the functional importance of different coexpression strategies in a variety of biological processes.
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Affiliation(s)
- Oriana Q H Zinani
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kemal Keseroğlu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M Özbudak
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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29
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Chen L, Li Z, Zeng T, Zhang YH, Zhang S, Huang T, Cai YD. Predicting Human Protein Subcellular Locations by Using a Combination of Network and Function Features. Front Genet 2021; 12:783128. [PMID: 34804131 PMCID: PMC8603309 DOI: 10.3389/fgene.2021.783128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Given the limitation of technologies, the subcellular localizations of proteins are difficult to identify. Predicting the subcellular localization and the intercellular distribution patterns of proteins in accordance with their specific biological roles, including validated functions, relationships with other proteins, and even their specific sequence characteristics, is necessary. The computational prediction of protein subcellular localizations can be performed on the basis of the sequence and the functional characteristics. In this study, the protein-protein interaction network, functional annotation of proteins and a group of direct proteins with known subcellular localization were used to construct models. To build efficient models, several powerful machine learning algorithms, including two feature selection methods, four classification algorithms, were employed. Some key proteins and functional terms were discovered, which may provide important contributions for determining protein subcellular locations. Furthermore, some quantitative rules were established to identify the potential subcellular localizations of proteins. As the first prediction model that uses direct protein annotation information (i.e., functional features) and STRING-based protein-protein interaction network (i.e., network features), our computational model can help promote the development of predictive technologies on subcellular localizations and provide a new approach for exploring the protein subcellular localization patterns and their potential biological importance.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, China
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, 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 Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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30
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Yang R, Chen X, Huang Q, Chen C, Rengasamy KRR, Chen J, Wan C(C. Mining RNA-Seq Data to Depict How Penicillium digitatum Shapes Its Transcriptome in Response to Nanoemulsion. Front Nutr 2021; 8:724419. [PMID: 34595200 PMCID: PMC8476847 DOI: 10.3389/fnut.2021.724419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Penicillium digitatum is the most severe pathogen that infects citrus fruits during storage. It can cause fruit rot and bring significant economic losses. The continuous use of fungicides has resulted in the emergence of drug-resistant strains. Consequently, there is a need to develop naturally and efficiently antifungal fungicides. Natural antimicrobial agents such as clove oil, cinnamon oil, and thyme oil can be extracted from different plant parts. They exhibited broad-spectrum antimicrobial properties and have great potential in the food industry. Here, we exploit a novel cinnamaldehyde (CA), eugenol (EUG), or carvacrol (CAR) combination antifungal therapy and formulate it into nanoemulsion form to overcome lower solubility and instability of essential oil. In this study, the antifungal activity evaluation and transcriptional profile of Penicillium digitatum exposed to compound nanoemulsion were evaluated. Results showed that compound nanoemulsion had a striking inhibitory effect on P. digitatum in a dose-dependent manner. According to RNA-seq analysis, there were 2,169 differentially expressed genes (DEGs) between control and nanoemulsion-treated samples, including 1,028 downregulated and 1,141 upregulated genes. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in intracellular organelle parts of cell component: cellular respiration, proton transmembrane transport of biological process, and guanyl nucleotide-binding molecular function. KEGG analysis revealed that metabolic pathway, biosynthesis of secondary metabolites, and glyoxylate and dicarboxylate metabolism were the most highly enriched pathways for these DEGs. Taken together, we can conclude the promising antifungal activity of nanoemulsion with multiple action sites against P. digitatum. These outcomes would deepen our knowledge of the inhibitory mechanism from molecular aspects and exploit naturally, efficiently, and harmlessly antifungal agents in the citrus postharvest industry.
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Affiliation(s)
- Ruopeng Yang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- College of Life Science and Technology, Honghe University, Mengzi, China
| | - Xiu Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Qiang Huang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Chuying Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Kannan R. R. Rengasamy
- Green Biotechnologies Research Centre of Excellence, University of Limpopo, Mankweng, South Africa
| | - Jinyin Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- College of Materials and Chemical Engineering, Pingxiang University, Pingxiang, China
| | - Chunpeng (Craig) Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
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31
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Alafari HA, Abd-Elgawad ME. Differential expression gene/protein contribute to heat stress-responsive in Tetraena propinqua in Saudi Arabia. Saudi J Biol Sci 2021; 28:5017-5027. [PMID: 34466077 PMCID: PMC8380999 DOI: 10.1016/j.sjbs.2021.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022] Open
Abstract
Within their natural habitat, plants are subjected to abiotic stresses that include heat stress. In the current study, the effect of 4 h, 24 h, and 48 h of heat stress on Tetraena propinqua ssp. migahidii seedling's protein profile and proteomic analyses were investigated. Total soluble protein SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) profile showed 18-protein bands, the newly synthesized protein band (with molecular weights 86.5, 30.2 and 31.4 KD) at 24 h of heat stress and 48 of normal conditions. Proteomic analysis showed that 81 and 930 targets are involved in gene and protein expression respectively. At 4 h, 57 genes and 110 proteins in C4 reached 56 genes and 173 proteins in T4. At 24 h, 63 genes and 180 proteins in C24 decreased to 54 genes and 151 protein in T24. After 48 h, 56 genes and 136 proteins in C48 increased to 64 genes and 180 proteins in T48. The genes and proteins involved in transcription, translation, photosynthesis, transport, and other unknown metabolic processes, were differentially expressed under treatments of heat stress. These findings provide insights into the molecular mechanisms related to heat stress, in addition to its influence on the physiological traits of T. propinqua seedlings. Heat stress-mediated differential regulation genes indicate a role in the development and stress response of T. propinqua. The candidate dual-specificity genes and proteins identified in this study paves way for more molecular analysis of up-and-down-regulation.
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Affiliation(s)
- Hayat Ali Alafari
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Magda Elsayed Abd-Elgawad
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- Botany Department, Faculty of Science, Fayoum University, Fayoum, Egypt
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32
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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Zhu Q, Tao B, Chen H, Shi H, Huang L, Chen J, Hu M, Lo LJ, Peng J. Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. Nucleic Acids Res 2021; 49:5743-5759. [PMID: 34019640 PMCID: PMC8191805 DOI: 10.1093/nar/gkab381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Yeast Rcl1 is a potential endonuclease that mediates pre-RNA cleavage at the A2-site to separate 18S rRNA from 5.8S and 25S rRNAs. However, the biological function of Rcl1 in opisthokonta is poorly defined. Moreover, there is no information regarding the exact positions of 18S pre-rRNA processing in zebrafish. Here, we report that zebrafish pre-rRNA harbours three major cleavage sites in the 5′ETS, namely –477nt (A′-site), –97nt (A0-site) and the 5′ETS and 18S rRNA link (A1-site), as well as two major cleavage regions within the ITS1, namely 208–218nt (site 2) and 20–33nt (site E). We also demonstrate that depletion of zebrafish Rcl1 mainly impairs cleavage at the A1-site. Phenotypically, rcl1–/– mutants exhibit a small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq analysis revealed that the most significant event in rcl1–/– mutants is the up-regulated expression of a cohort of genes related to ribosome biogenesis and tRNA production. Our data demonstrate that Rcl1 is essential for 18S rRNA maturation at the A1-site and for digestive organogenesis in zebrafish. Rcl1 deficiency, similar to deficiencies in other ribosome biogenesis factors, might trigger a common mechanism to upregulate the expression of genes responsible for ribosome biogenesis.
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Affiliation(s)
- Qinfang Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hong Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Hui Shi
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Ling Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Hu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, China
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Cao H, Duncan O, Islam S, Zhang J, Ma W, Millar AH. Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome. Mol Cell Proteomics 2021; 20:100097. [PMID: 34000434 PMCID: PMC8214148 DOI: 10.1016/j.mcpro.2021.100097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/15/2021] [Accepted: 05/11/2021] [Indexed: 11/24/2022] Open
Abstract
Introgression of a high-molecular-weight glutenin subunit (HMW-GS) allele, 1Ay21∗, into commercial wheat cultivars increased overall grain protein content and bread-making quality, but the role of proteins beyond this HMW-GS itself was unknown. In addition to increased abundance of 1Ay HMW-GS, 115 differentially accumulated proteins (DAPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines. Functional category analysis showed that the DAPs were predominantly other storage proteins and proteins involved in protein synthesis, protein folding, protein degradation, stress response, and grain development. Nearly half the genes encoding the DAPs showed strong coexpression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21∗ improves grain protein content but also directs selection of protein candidates for future wheat quality breeding programs.
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Affiliation(s)
- Hui Cao
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia; School of Molecular Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia; School of Molecular Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science Health Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia; Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, Western Australia, Australia
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science Health Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia; Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, Western Australia, Australia
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science Health Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia; Australia-China Joint Centre for Wheat Improvement, Murdoch University, Perth, Western Australia, Australia.
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia; School of Molecular Science, University of Western Australia, Crawley, Western Australia, Australia.
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35
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p53 activation during ribosome biogenesis regulates normal erythroid differentiation. Blood 2021; 137:89-102. [PMID: 32818241 DOI: 10.1182/blood.2019003439] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 08/03/2020] [Indexed: 12/22/2022] Open
Abstract
The role of ribosome biogenesis in erythroid development is supported by the recognition of erythroid defects in ribosomopathies in both Diamond-Blackfan anemia and 5q- syndrome. Whether ribosome biogenesis exerts a regulatory function on normal erythroid development is still unknown. In the present study, a detailed characterization of ribosome biogenesis dynamics during human and murine erythropoiesis showed that ribosome biogenesis is abruptly interrupted by the decline in ribosomal DNA transcription and the collapse of ribosomal protein neosynthesis. Its premature arrest by the RNA Pol I inhibitor CX-5461 targeted the proliferation of immature erythroblasts. p53 was activated spontaneously or in response to CX-5461, concomitant to ribosome biogenesis arrest, and drove a transcriptional program in which genes involved in cell cycle-arrested, negative regulation of apoptosis, and DNA damage response were upregulated. RNA Pol I transcriptional stress resulted in nucleolar disruption and activation of the ATR-CHK1-p53 pathway. Our results imply that the timing of ribosome biogenesis extinction and p53 activation is crucial for erythroid development. In ribosomopathies in which ribosome availability is altered by unbalanced production of ribosomal proteins, the threshold downregulation of ribosome biogenesis could be prematurely reached and, together with pathological p53 activation, prevents a normal expansion of erythroid progenitors.
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36
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Hsu PJ, Tan MC, Shen HL, Chen YH, Wang YY, Hwang SG, Chiang MH, Le QV, Kuo WS, Chou YC, Lin SY, Jauh GY, Cheng WH. The nucleolar protein SAHY1 is involved in pre-rRNA processing and normal plant growth. PLANT PHYSIOLOGY 2021; 185:1039-1058. [PMID: 33793900 PMCID: PMC8133687 DOI: 10.1093/plphys/kiaa085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/01/2020] [Indexed: 05/29/2023]
Abstract
Although the nucleolus is involved in ribosome biogenesis, the functions of numerous nucleolus-localized proteins remain unclear. In this study, we genetically isolated Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, pointed leaves, and sterility. SAHY1 encodes an uncharacterized protein that is predominantly expressed in root tips, early developing seeds, and mature pollen grains and is mainly restricted to the nucleolus. Dysfunction of SAHY1 primarily causes the accumulation of 32S, 18S-A3, and 27SB pre-rRNA intermediates. Coimmunoprecipitation experiments further revealed the interaction of SAHY1 with ribosome proteins and ribosome biogenesis factors. Moreover, sahy1 mutants are less sensitive to protein translation inhibitors and show altered expression of structural constituents of ribosomal genes and ribosome subunit profiles, reflecting the involvement of SAHY1 in ribosome composition and ribosome biogenesis. Analyses of ploidy, S-phase cell cycle progression, and auxin transport and signaling indicated the impairment of mitotic activity, translation of auxin transport carrier proteins, and expression of the auxin-responsive marker DR5::GFP in the root tips or embryos of sahy1 plants. Collectively, these data demonstrate that SAHY1, a nucleolar protein involved in ribosome biogenesis, plays critical roles in normal plant growth in association with auxin transport and signaling.
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Affiliation(s)
- Pei-jung Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chen Tan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hwei-Ling Shen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Huei Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ying Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - San-Gwang Hwang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hau Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Quang-Vuong Le
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Shuo Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Chan Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung County,Taiwan
| | - Shih-Yun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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37
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Gallegos KM, Patel JR, Llopis SD, Walker RR, Davidson AM, Zhang W, Zhang K, Tilghman SL. Quantitative Proteomic Profiling Identifies a Potential Novel Chaperone Marker in Resistant Breast Cancer. Front Oncol 2021; 11:540134. [PMID: 33718123 PMCID: PMC7951058 DOI: 10.3389/fonc.2021.540134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Development of aromatase inhibitor resistant breast cancer among postmenopausal women continues to be a major clinical obstacle. Previously, our group demonstrated that as breast cancer cells transition from hormone-dependent to hormone-independent, they are associated with increased growth factor signaling, enhanced cellular motility, and the epithelial to mesenchymal transition (EMT). Given the complexity of cancer stem cells (CSC) and their implications on endocrine resistance and EMT, we sought to understand their contribution towards the development of aromatase inhibitor resistant breast cancer. Cells cultured three dimensionally as mammospheres are enriched for CSCs and more accurately recapitulates tumors in vivo. Therefore, a global proteomic analysis was conducted using letrozole resistant breast cancer cells (LTLT-Ca) mammospheres and compared to their adherent counterparts. Results demonstrated over 1000 proteins with quantitative abundance ratios were identified. Among the quantified proteins, 359 were significantly altered (p < 0.05), where 173 were upregulated and 186 downregulated (p < 0.05, fold change >1.20). Notably, midasin, a chaperone protein required for maturation and nuclear export of the pre-60S ribosome was increased 35-fold. Protein expression analyses confirmed midasin is ubiquitously expressed in normal tissue but is overexpressed in lobular and ductal breast carcinoma tissue as well as ER+ and ER- breast cancer cell lines. Functional enrichment analyses indicated that 19 gene ontology terms and one KEGG pathway were over-represented by the down-regulated proteins and both were associated with protein synthesis. Increased midasin was strongly correlated with decreased relapse free survival in hormone independent breast cancer. For the first time, we characterized the global proteomic signature of CSC-enriched letrozole-resistant cells associated with protein synthesis, which may implicate a role for midasin in endocrine resistance.
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Affiliation(s)
- Karen M Gallegos
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Jankiben R Patel
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Shawn D Llopis
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Rashidra R Walker
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - A Michael Davidson
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Wensheng Zhang
- Division of Mathematical and Physical Sciences, Department of Computer Science, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA, United States
| | - Kun Zhang
- Division of Mathematical and Physical Sciences, Department of Computer Science, College of Arts and Sciences, Xavier University of Louisiana, New Orleans, LA, United States
| | - Syreeta L Tilghman
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
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38
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Hua Y, Song J, Peng C, Wang R, Ma Z, Zhang J, Zhang Z, Li N, Hou L. Advances in the Relationship Between Regulator of Ribosome Synthesis 1 (RRS1) and Diseases. Front Cell Dev Biol 2021; 9:620925. [PMID: 33718361 PMCID: PMC7947238 DOI: 10.3389/fcell.2021.620925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
A regulator of ribosome synthesis 1 (RRS1) was discovered in yeast and is mainly localized in the nucleolus and endoplasmic reticulum. It regulates ribosomal protein, RNA biosynthesis, and protein secretion and is closely involved in cellular senescence, cell cycle regulation, transcription, translation, oncogenic transformation etc., Mutations in the RRS1 gene are associated with the occurrence and development of Huntington’s disease and cancer, and overexpression of RRS1 promotes tumor growth and metastasis. In this review, the structure, function, and mechanisms of RRS1 in various diseases are discussed.
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Affiliation(s)
- Yanan Hua
- Department of Neurobiology, Basic Medical College, Qingdao University, Qingdao, China
| | - Jinlian Song
- Department of Laboratory, Women and Children's Hospital of Qingdao, Qingdao, China
| | - Cuixiu Peng
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Runze Wang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Zhongliang Ma
- Department of Breast Surgery, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jinyu Zhang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Zheng Zhang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Ning Li
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Lin Hou
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
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39
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Abstract
RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the cryo-EM structure of elongating human Pol I at 2.7 Å resolution. In the exit tunnel, we observe a double-stranded RNA helix that may support Pol I processivity. Our structure confirms that human Pol I consists of 13 subunits with only one subunit forming the Pol I stalk. Additionally, the structure of human Pol I in complex with the initiation factor RRN3 at 3.1 Å resolution reveals stalk flipping upon RRN3 binding. We also observe an inactivated state of human Pol I bound to an open DNA scaffold at 3.3 Å resolution. Lastly, the high-resolution structure of human Pol I allows mapping of disease-related mutations that can aid understanding of disease etiology.
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40
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Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2021; 12:647375. [PMID: 33777082 PMCID: PMC7994888 DOI: 10.3389/fpls.2021.647375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 05/14/2023]
Abstract
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Judith Fehrer,
| | - Renáta Slavíková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | | | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Patrik Mráz
- Department of Botany, Charles University, Prague, Czechia
| | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Charles University, Prague, Czechia
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41
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Lau B, Cheng J, Flemming D, La Venuta G, Berninghausen O, Beckmann R, Hurt E. Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome. Mol Cell 2020; 81:293-303.e4. [PMID: 33326748 DOI: 10.1016/j.molcel.2020.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A1, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis.
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Affiliation(s)
- Benjamin Lau
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Giuseppe La Venuta
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Otto Berninghausen
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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42
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Satturu V, Vattikuti JL, J DS, Kumar A, Singh RK, M SP, Zaw H, Jubay ML, Satish L, Rathore A, Mulinti S, Lakshmi VG I, Fiyaz R. A, Chakraborty A, Thirunavukkarasu N. Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper ( Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice. Vaccines (Basel) 2020; 8:vaccines8040608. [PMID: 33066559 PMCID: PMC7712083 DOI: 10.3390/vaccines8040608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.
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Affiliation(s)
- Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
- Correspondence: ; Tel.: +91-8186945838
| | - Jhansi Lakshmi Vattikuti
- Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India; (J.L.V.); (S.P.M.); (A.F.R.)
| | - Durga Sai J
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI)-South Asia Hub (SAH), Patancheru, Hyderabad 502324, India;
| | - Rakesh Kumar Singh
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
- Program Leader and Principal Scientist (Plant Breeding), Crop Diversification and Genetics, International Center for Biosaline Agriculture, Academic City, Dubai 14660, UAE
| | - Srinivas Prasad M
- Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India; (J.L.V.); (S.P.M.); (A.F.R.)
| | - Hein Zaw
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
- Department of Agriculture, Plant Biotechnology Center, Shwe Nanthar, Mingalardon Township, Yangon 11021, Myanmar
| | - Mona Liza Jubay
- Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines; (R.K.S.); (H.Z.); (M.L.J.)
| | - Lakkakula Satish
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Abhishek Rathore
- Agriculture Statistics Division, International Crops Research for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India;
| | - Sreedhar Mulinti
- MFPI-Quality Control Lab, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India;
| | - Ishwarya Lakshmi VG
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Abdul Fiyaz R.
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India; (D.S.J.); (I.L.V.)
| | - Animikha Chakraborty
- Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India; (A.C.); (N.T.)
| | - Nepolean Thirunavukkarasu
- Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India; (A.C.); (N.T.)
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Shigeoka T, Koppers M, Wong HHW, Lin JQ, Cagnetta R, Dwivedy A, de Freitas Nascimento J, van Tartwijk FW, Ströhl F, Cioni JM, Schaeffer J, Carrington M, Kaminski CF, Jung H, Harris WA, Holt CE. On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons. Cell Rep 2020; 29:3605-3619.e10. [PMID: 31825839 PMCID: PMC6915326 DOI: 10.1016/j.celrep.2019.11.025] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 09/30/2019] [Accepted: 11/06/2019] [Indexed: 01/19/2023] Open
Abstract
Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.
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Affiliation(s)
- Toshiaki Shigeoka
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Max Koppers
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Hovy Ho-Wai Wong
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Julie Qiaojin Lin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Roberta Cagnetta
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Asha Dwivedy
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | | | - Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Florian Ströhl
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Jean-Michel Cioni
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Julia Schaeffer
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Hosung Jung
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - William A Harris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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Hamzelou S, Kamath KS, Masoomi-Aladizgeh F, Johnsen MM, Atwell BJ, Haynes PA. Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought. Int J Mol Sci 2020; 21:ijms21175980. [PMID: 32825202 PMCID: PMC7504292 DOI: 10.3390/ijms21175980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Matthew M. Johnsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Correspondence:
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45
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Lin MH, Kuo PC, Chiu YC, Chang YY, Chen SC, Hsu CH. The crystal structure of protein-transporting chaperone BCP1 from Saccharomyces cerevisiae. J Struct Biol 2020; 212:107605. [PMID: 32805410 DOI: 10.1016/j.jsb.2020.107605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 11/25/2022]
Abstract
BCP1 is a protein enriched in the nucleus that is required for Mss4 nuclear export and identified as the chaperone of ribosomal protein Rpl23 in Saccharomyces cerevisiae. According to sequence homology, BCP1 is related to the mammalian BRCA2-interacting protein BCCIP and belongs to the BCIP protein family (PF13862) in the Pfam database. However, the BCIP family has no discernible similarity to proteins with known structure. Here, we report the crystal structure of BCP1, presenting an α/β fold in which the central antiparallel β-sheet is flanked by helices. Protein structural classification revealed that BCP1 has similarity to the GNAT superfamily but no conserved substrate-binding residues. Further modeling and protein-protein docking work provide a plausible model to explain the interaction between BCP1 and Rpl23. Our structural analysis presents the first structure of BCIP family and provides a foundation for understanding the molecular basis of BCP1 as a chaperone of Rpl23 for ribosome biosynthesis.
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Affiliation(s)
- Meng-Hsuan Lin
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Po-Chih Kuo
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chih Chiu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Sheng-Chia Chen
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.
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46
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Ellery A. How to Build a Biological Machine Using Engineering Materials and Methods. Biomimetics (Basel) 2020; 5:biomimetics5030035. [PMID: 32722540 PMCID: PMC7558640 DOI: 10.3390/biomimetics5030035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 01/09/2023] Open
Abstract
We present work in 3D printing electric motors from basic materials as the key to building a self-replicating machine to colonise the Moon. First, we explore the nature of the biological realm to ascertain its essence, particularly in relation to the origin of life when the inanimate became animate. We take an expansive view of this to ascertain parallels between the biological and the manufactured worlds. Life must have emerged from the available raw material on Earth and, similarly, a self-replicating machine must exploit and leverage the available resources on the Moon. We then examine these lessons to explore the construction of a self-replicating machine using a universal constructor. It is through the universal constructor that the actuator emerges as critical. We propose that 3D printing constitutes an analogue of the biological ribosome and that 3D printing may constitute a universal construction mechanism. Following a description of our progress in 3D printing motors, we suggest that this engineering effort can inform biology, that motors are a key facet of living organisms and illustrate the importance of motors in biology viewed from the perspective of engineering (in the Feynman spirit of “what I cannot create, I cannot understand”).
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Affiliation(s)
- Alex Ellery
- Space Exploration Engineering Group, Department of Mechanical & Aerospace Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada
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47
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Kalous J, Jansová D, Šušor A. Role of Cyclin-Dependent Kinase 1 in Translational Regulation in the M-Phase. Cells 2020; 9:cells9071568. [PMID: 32605021 PMCID: PMC7408968 DOI: 10.3390/cells9071568] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Cyclin dependent kinase 1 (CDK1) has been primarily identified as a key cell cycle regulator in both mitosis and meiosis. Recently, an extramitotic function of CDK1 emerged when evidence was found that CDK1 is involved in many cellular events that are essential for cell proliferation and survival. In this review we summarize the involvement of CDK1 in the initiation and elongation steps of protein synthesis in the cell. During its activation, CDK1 influences the initiation of protein synthesis, promotes the activity of specific translational initiation factors and affects the functioning of a subset of elongation factors. Our review provides insights into gene expression regulation during the transcriptionally silent M-phase and describes quantitative and qualitative translational changes based on the extramitotic role of the cell cycle master regulator CDK1 to optimize temporal synthesis of proteins to sustain the division-related processes: mitosis and cytokinesis.
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48
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Destefanis F, Manara V, Bellosta P. Myc as a Regulator of Ribosome Biogenesis and Cell Competition: A Link to Cancer. Int J Mol Sci 2020; 21:ijms21114037. [PMID: 32516899 PMCID: PMC7312820 DOI: 10.3390/ijms21114037] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
The biogenesis of ribosomes is a finely regulated multistep process linked to cell proliferation and growth-processes which require a high rate of protein synthesis. One of the master regulators of ribosome biogenesis is Myc, a well-known proto-oncogene that has an important role in ribosomal function and in the regulation of protein synthesis. The relationship between Myc and the ribosomes was first highlighted in Drosophila, where Myc's role in controlling Pol-I, II and III was evidenced by both microarrays data, and by the ability of Myc to control growth (mass), and cellular and animal size. Moreover, Myc can induce cell competition, a physiological mechanism through which cells with greater fitness grow better and thereby prevail over less competitive cells, which are actively eliminated by apoptosis. Myc-induced cell competition was shown to regulate both vertebrate development and tumor promotion; however, how these functions are linked to Myc's control of ribosome biogenesis, protein synthesis and growth is not clear yet. In this review, we will discuss the major pathways that link Myc to ribosomal biogenesis, also in light of its function in cell competition, and how these mechanisms may reflect its role in favoring tumor promotion.
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Affiliation(s)
- Francesca Destefanis
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
| | - Valeria Manara
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
- Department of Medicine, NYU Langone Medical Center, New York, NY 10016, USA
- Correspondence: ; Tel.: +39-0461-283070
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49
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Banerjee A, Kulkarni S, Mukherjee A. Herpes Simplex Virus: The Hostile Guest That Takes Over Your Home. Front Microbiol 2020; 11:733. [PMID: 32457704 PMCID: PMC7221137 DOI: 10.3389/fmicb.2020.00733] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Alpha (α)-herpesviruses (HSV-1 and HSV-2), like other viruses, are obligate intracellular parasites. They hijack the cellular machinery to survive and replicate through evading the defensive responses by the host. The viral genome of herpes simplex viruses (HSVs) contains viral genes, the products of which are destined to exploit the host apparatus for their own existence. Cellular modulations begin from the entry point itself. The two main gateways that the virus has to penetrate are the cell membrane and the nuclear membrane. Changes in the cell membrane are triggered when the glycoproteins of HSV interact with the surface receptors of the host cell, and from here, the components of the cytoskeleton take over. The rearrangement in the cytoskeleton components help the virus to enter as well as transport to the nucleus and back to the cell membrane to spread out to the other cells. The entire carriage process is also mediated by the motor proteins of the kinesin and dynein superfamily and is directed by the viral tegument proteins. Also, the virus captures the cell’s most efficient cargo carrying system, the endoplasmic reticulum (ER)–Golgi vesicular transport machinery for egress to the cell membrane. For these reasons, the host cell has its own checkpoints where the normal functions are halted once a danger is sensed. However, a cell may be prepared for the adversities from an invading virus, and it is simply commendable that the virus has the antidote to these cellular strategies as well. The HSV viral proteins are capable of limiting the use of the transcriptional and translational tools for the cell itself, so that its own transcription and translation pathways remain unhindered. HSV prefers to constrain any self-destruction process of the cell—be it autophagy in the lysosome or apoptosis by the mitochondria, so that it can continue to parasitize the cell for its own survival. This review gives a detailed account of the significance of compartmentalization during HSV pathogenesis. It also highlights the undiscovered areas in the HSV cell biology research which demand attention for devising improved therapeutics against the infection.
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Affiliation(s)
- Anwesha Banerjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Smita Kulkarni
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Anupam Mukherjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
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50
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Farias J, Holt CE, Sotelo JR, Sotelo-Silveira JR. Axon microdissection and transcriptome profiling reveals the in vivo RNA content of fully differentiated myelinated motor axons. RNA (NEW YORK, N.Y.) 2020; 26:595-612. [PMID: 32051223 PMCID: PMC7161357 DOI: 10.1261/rna.073700.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/31/2020] [Indexed: 05/23/2023]
Abstract
Axonal protein synthesis has been shown to play a role in developmental and regenerative growth, as well as in the maintenance of the axoplasm in a steady state. Recent studies have begun to identify the mRNAs localized in axons, which could be translated locally under different conditions. Despite that by now hundreds or thousands of mRNAs have been shown to be localized into the axonal compartment of cultured neurons in vitro, knowledge of which mRNAs are localized in mature myelinated axons is quite limited. With the purpose of characterizing the transcriptome of mature myelinated motor axons of peripheral nervous systems, we modified the axon microdissection method devised by Koenig, enabling the isolation of the axoplasm RNA to perform RNA-seq analysis. The transcriptome analysis indicates that the number of RNAs detected in mature axons is lower in comparison with in vitro data, depleted of glial markers, and enriched in neuronal markers. The mature myelinated axons are enriched for mRNAs related to cytoskeleton, translation, and oxidative phosphorylation. Moreover, it was possible to define core genes present in axons when comparing our data with transcriptomic data of axons grown in different conditions. This work provides evidence that axon microdissection is a valuable method to obtain genome-wide data from mature and myelinated axons of the peripheral nervous system, and could be especially useful for the study of axonal involvement in neurodegenerative pathologies of motor neurons such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophies (SMA).
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Affiliation(s)
- Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
- Departamento de Proteínas y Ácidos Nucléicos, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, United Kingdom
| | - José R Sotelo
- Departamento de Proteínas y Ácidos Nucléicos, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
| | - José R Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay
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