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Ryu S, Nakashima H, Tanaka Y, Mukai R, Ishihara Y, Tominaga T, Ohshima T. Ribosomal Protein S4 X-Linked as a Novel Modulator of MDM2 Stability by Suppressing MDM2 Auto-Ubiquitination and SCF Complex-Mediated Ubiquitination. Biomolecules 2024; 14:885. [PMID: 39199272 PMCID: PMC11351588 DOI: 10.3390/biom14080885] [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: 06/13/2024] [Revised: 07/19/2024] [Accepted: 07/20/2024] [Indexed: 09/01/2024] Open
Abstract
Mouse double minute 2 (MDM2) is an oncoprotein that is frequently overexpressed in tumors and enhances cellular transformation. Owing to the important role of MDM2 in modulating p53 function, it is crucial to understand the mechanism underlying the regulation of MDM2 levels. We identified ribosomal protein S4X-linked (RPS4X) as a novel binding partner of MDM2 and showed that RPS4X promotes MDM2 stability. RPS4X suppressed polyubiquitination of MDM2 by suppressing homodimer formation and preventing auto-ubiquitination. Moreover, RPS4X inhibited the interaction between MDM2 and Cullin1, a scaffold protein of the Skp1-Cullin1-F-box protein (SCF) complex and an E3 ubiquitin ligase for MDM2. RPS4X expression in cells enhanced the steady-state level of MDM2 protein. RPS4X was associated not only with MDM2 but also with Cullin1 and then blocked the MDM2/Cullin1 interaction. This is the first report of an interaction between ribosomal proteins (RPs) and Cullin1. Our results contribute to the elucidation of the MDM2 stabilization mechanism in cancer cells, expanding our understanding of the new functions of RPs.
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Affiliation(s)
- Satsuki Ryu
- Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan; (S.R.); (H.N.); (T.T.)
| | - Hiroki Nakashima
- Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan; (S.R.); (H.N.); (T.T.)
| | - Yuka Tanaka
- Faculty of Science and Engineering, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan;
| | - Risa Mukai
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07101-1709, USA;
| | - Yasuhiro Ishihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan;
| | - Takashi Tominaga
- Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan; (S.R.); (H.N.); (T.T.)
| | - Takayuki Ohshima
- Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan; (S.R.); (H.N.); (T.T.)
- Faculty of Science and Engineering, Tokushima Bunri University, 1314-1 Shido, Sanuki 769-2193, Japan;
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Choi BM, Cheong JH, Ryu JI, Won YD, Min KW, Han MH. Significant Genes Associated with Mortality and Disease Progression in Grade II and III Glioma. Biomedicines 2024; 12:858. [PMID: 38672212 PMCID: PMC11048596 DOI: 10.3390/biomedicines12040858] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The Wnt/β-catenin pathway plays a critical role in the tumorigenesis and maintenance of glioma stem cells. This study aimed to evaluate significant genes associated with the Wnt/β-catenin pathway involved in mortality and disease progression in patients with grade II and III glioma, using the Cancer Genome Atlas (TCGA) database. METHODS We obtained clinicopathological information and mRNA expression data from 515 patients with grade II and III gliomas from the TCGA database. We performed a multivariate Cox regression analysis to identify genes independently associated with glioma prognosis. RESULTS The analysis of 34 genes involved in Wnt/β-catenin signaling demonstrated that four genes (CER1, FRAT1, FSTL1, and RPSA) related to the Wnt/β-catenin pathway were significantly associated with mortality and disease progression in patients with grade II and III glioma. We also identified additional genes related to the four significant genes of the Wnt/β-catenin pathway mentioned above. The higher expression of BMP2, RPL18A, RPL19, and RPS12 is associated with better outcomes in patients with glioma. CONCLUSIONS Using a large-scale open database, we identified significant genes related to the Wnt/β-catenin signaling pathway associated with mortality and disease progression in patients with grade II and III gliomas.
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Affiliation(s)
- Bo Mi Choi
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Kyueng-Whan Min
- Department of Pathology, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu 11759, Gyeonggi-do, Republic of Korea
| | - Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
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3
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Tzur Y, Dubnov S, Madrer N, Bar A, Nadorp B, Mishra N, Heppenstall P, Bennett ER, Greenberg DS, Winek K, Soreq H. Ribosomal protein L24 mediates mammalian microRNA processing in an evolutionarily conserved manner. Cell Mol Life Sci 2024; 81:55. [PMID: 38261097 PMCID: PMC10805976 DOI: 10.1007/s00018-023-05088-w] [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: 08/06/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
To investigate the mechanism(s) underlying the expression of primate-specific microRNAs (miRs), we sought DNA regulatory elements and proteins mediating expression of the primate-specific hsa-miR-608 (miR-608), which is located in the SEMA4G gene and facilitates the cholinergic blockade of inflammation by targeting acetylcholinesterase mRNA. 'Humanized' mice carrying pre-miR-608 flanked by 250 bases of endogenous sequences inserted into the murine Sema4g gene successfully expressed miR-608. Moreover, by flanking miR-608 by shortened fragments of its human genome region we identified an active independent promoter within the 150 nucleotides 5' to pre-miR-608, which elevated mature miR-608 levels by 100-fold in transfected mouse- and human-originated cells. This highlighted a regulatory role of the 5' flank as enabling miR-608 expression. Moreover, pull-down of the 150-base 5' sequence revealed its interaction with ribosomal protein L24 (RPL24), implicating an additional mechanism controlling miR-608 levels. Furthermore, RPL24 knockdown altered the expression of multiple miRs, and RPL24 immunoprecipitation indicated that up- or down-regulation of the mature miRs depended on whether their precursors bind RPL24 directly. Finally, further tests showed that RPL24 interacts directly with DDX5, a component of the large microprocessor complex, to inhibit miR processing. Our findings reveal that RPL24, which has previously been shown to play a role in miR processing in Arabidopsis thaliana, has a similar evolutionarily conserved function in miR biogenesis in mammals. We thus characterize a novel extra-ribosomal role of RPL24 in primate miR regulation.
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Affiliation(s)
- Yonat Tzur
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - Serafima Dubnov
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem, Israel
| | - Nimrod Madrer
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - Adi Bar
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - Bettina Nadorp
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
- , New York City, USA
| | - Nibha Mishra
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
- , Waltham, USA
| | | | - Estelle R Bennett
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - David S Greenberg
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - Katarzyna Winek
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem, Israel.
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstraße 11, 07745, Jena, Germany.
| | - Hermona Soreq
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem, Israel.
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Sun C, Luo F, You Y, Gu M, Yang W, Yi C, Zhang W, Feng Z, Wang J, Hu W. MicroRNA-1 targets ribosomal protein genes to regulate the growth, development and reproduction of Schistosoma japonicum. Int J Parasitol 2023; 53:637-649. [PMID: 37355197 DOI: 10.1016/j.ijpara.2023.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 06/26/2023]
Abstract
Eggs laid by mature female schistosomes are primarily responsible for the pathogenesis of schistosomiasis and critical for transmission. Consequently, elucidating the mechanism of sexual maturation as well as egg production may lead to new strategies for the control of schistosomiasis. MicroRNAs (miRNAs) are involved in multiple biological processes including reproduction in many organisms, yet their roles have not been well characterized in schistosomes. Here, we investigated microRNA-1 (miR-1), which was downregulated gradually in both male and female Schistosoma japonicum after they reached sexually maturity. The expression of miR-1, as shown with quantitative reverse transcription PCR (qRT-PCR), was lower in the reproductive organs of adult females compared with the somatic tissues. Overexpression of miR-1 in adult worms destroyed the morphological architecture of reproductive organs and reduced the subsequent oviposition, which may be due to the activation of apoptosis pathways. Through in silico analysis, 34 potential target genes of miR-1 were identified, including five ribosomal protein genes, called rp-s13, rp-l7ae, rp-l14, rp-l11 and rp-s24e. In vitro dual-luciferase reporter gene assays and miRNA overexpression experiments further validated that these ribosomal protein genes were directly regulated by miR-1. In contrast to the gene expression of miR-1, qRT-PCR and in situ hybridization experiments demonstrated these ribosomal protein genes were enriched in the sexual organs of adult females. Using RNA interference to silence the ribosomal protein genes in different developmental stages in a mouse model system, we demonstrated that these miR-1 target genes not only participated in the reproductive development of S. japonicum, but also were required for the growth and survival of the parasite in the early developmental stages. Taken together, our data suggested that miR-1 may affect the growth, reproduction and oviposition of S. japonicum by targeting the ribosomal protein genes, which provides insights for exploration of new anti-schistosome strategies.
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Affiliation(s)
- Chengsong Sun
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China; Anhui Provincial Institute of Parasitic Diseases, No. 12560 Fanhua Avenue, Shushan District, Hefei 230601, Anhui Province, China
| | - Fang Luo
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yanmin You
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Mengjie Gu
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Wenbin Yang
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Cun Yi
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Wei Zhang
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention and Fudan University, No.207 Ruijin Road II, Shanghai 200025, China
| | - Jipeng Wang
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
| | - Wei Hu
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention and Fudan University, No.207 Ruijin Road II, Shanghai 200025, China; College of Life Sciences, Inner Mongolia University, No. 235 Daxue West Road, Saihan District, Hohhot 010021, Inner Mongolia Autonomous Region, China.
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Loxha L, Ibrahim NK, Stasche AS, Cinar B, Dolgner T, Niessen J, Schreek S, Fehlhaber B, Forster M, Stanulla M, Hinze L. GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells. Int J Mol Sci 2023; 24:13260. [PMID: 37686063 PMCID: PMC10488213 DOI: 10.3390/ijms241713260] [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: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Amino acid availability is crucial for cancer cells' survivability. Leukemia and colorectal cancer cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed the Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. The inhibition of GSK3α halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability toward asparaginase therapy. However, resistance toward GSK3α-mediated protein breakdown can occur, whose underlying mechanism is poorly understood. Here, we set out to define the mechanisms driving dependence toward this degradation machinery upon asparagine starvation in cancer cells. We show the independence of known stress response pathways including the integrated stress response mediated with GCN2. Additionally, we demonstrate the independence of changes in cell cycle progression and expression levels of the asparagine-synthesizing enzyme ASNS. Instead, RNA sequencing revealed that GSK3α inhibition and asparagine starvation leads to the temporally dynamic downregulation of distinct ribosomal proteins, which have been shown to display anti-proliferative functions. Using a CRISPR/Cas9 viability screen, we demonstrate that the downregulation of these specific ribosomal proteins can rescue cell death upon GSK3α inhibition and asparagine starvation. Thus, our findings suggest the vital role of the previously unrecognized regulation of ribosomal proteins in bridging GSK3α activity and tolerance of asparagine starvation.
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Affiliation(s)
- Lorent Loxha
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Nurul Khalida Ibrahim
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Anna Sophie Stasche
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Büsra Cinar
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Tim Dolgner
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Julia Niessen
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Sabine Schreek
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Beate Fehlhaber
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Michael Forster
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany;
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
| | - Laura Hinze
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany; (L.L.); (N.K.I.); (A.S.S.); (B.C.); (T.D.); (J.N.); (S.S.); (B.F.); (M.S.)
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Shivam S, Ertl R, Sexl V, El-Matbouli M, Kumar G. Differentially expressed transcripts of Tetracapsuloides bryosalmonae (Cnidaria) between carrier and dead-end hosts involved in key biological processes: novel insights from a coupled approach of FACS and RNA sequencing. Vet Res 2023; 54:51. [PMID: 37365650 PMCID: PMC10291810 DOI: 10.1186/s13567-023-01185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Tetracapsuloides bryosalmonae is a malacosporean endoparasite that infects a wide range of salmonids and causes proliferative kidney disease (PKD). Brown trout serves as a carrier host whereas rainbow trout represents a dead-end host. We thus asked if the parasite adapts to the different hosts by changing molecular mechanisms. We used fluorescent activated cell sorting (FACS) to isolate parasites from the kidney of brown trout and rainbow trout following experimental infection with T. bryosalmonae. The sorted parasite cells were then subjected to RNA sequencing. By this approach, we identified 1120 parasite transcripts that were expressed differentially in parasites derived from brown trout and rainbow trout. We found elevated levels of transcripts related to cytoskeleton organisation, cell polarity, peptidyl-serine phosphorylation in parasites sorted from brown trout. In contrast, transcripts related to translation, ribonucleoprotein complex biogenesis and subunit organisation, non-membrane bounded organelle assembly, regulation of protein catabolic process and protein refolding were upregulated in rainbow trout-derived parasites. These findings show distinct molecular adaptations of parasites, which may underlie their distinct outcomes in the two hosts. Moreover, the identification of these differentially expressed transcripts may enable the identification of novel drug targets that may be exploited as treatment against T. bryosalmonae. We here also describe for the first time how FACS based isolation of T. bryosalmonae cells from infected kidney of fish fosters research and allows to define differentially expressed parasite transcripts in carrier and dead-end fish hosts.
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Affiliation(s)
- Saloni Shivam
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Karwar Regional Station of Indian Council of Agricultural Research, Central Marine Fisheries Research Institute, Karwar, Karnataka, India
| | - Reinhard Ertl
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mansour El-Matbouli
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo, Egypt
| | - Gokhlesh Kumar
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria.
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Keenum MC, Chatterjee P, Atalis A, Pandey B, Jimenez A, Roy K. Single-cell epitope-transcriptomics reveal lung stromal and immune cell response kinetics to nanoparticle-delivered RIG-I and TLR4 agonists. Biomaterials 2023; 297:122097. [PMID: 37001347 PMCID: PMC10192313 DOI: 10.1016/j.biomaterials.2023.122097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Lung-resident and circulatory lymphoid, myeloid, and stromal cells, expressing various pattern recognition receptors (PRRs), detect pathogen- and danger-associated molecular patterns (PAMPs/DAMPs), and defend against respiratory pathogens and injuries. Here, we report the early responses of murine lungs to nanoparticle-delivered PAMPs, specifically the retinoic acid-inducible gene I (RIG-I) agonist poly-U/UC (PUUC), with or without the TLR4 agonist monophosphoryl lipid A (MPLA). Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we characterized the responses at 4 and 24 h after intranasal administration. Within 4 h, ribosome-associated transcripts decreased in both stromal and immune cells, followed by widespread interferon-stimulated gene (ISG) expression. Using RNA velocity, we show that lung-neutrophils dynamically regulate the synthesis of cytokines like CXCL-10, IL-1α, and IL-1β. Co-delivery of MPLA and PUUC increased chemokine synthesis and upregulated antimicrobial binding proteins targeting iron, manganese, and zinc in many cell types, including fibroblasts, endothelial cells, and epithelial cells. Overall, our results elucidate the early PAMP-induced cellular responses in the lung and demonstrate that stimulation of the RIG-I pathway, with or without TLR4 agonists, induces a ubiquitous microbial defense state in lung stromal and immune cells. Nanoparticle-delivered combination PAMPs may have applications in intranasal antiviral and antimicrobial therapies and prophylaxis.
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Affiliation(s)
- M Cole Keenum
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Paramita Chatterjee
- Marcus Center for Therapeutic Cell Characterization and Manufacturing Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandra Atalis
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Bhawana Pandey
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Angela Jimenez
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA
| | - Krishnendu Roy
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta, GA, USA; Marcus Center for Therapeutic Cell Characterization and Manufacturing Georgia Institute of Technology, Atlanta, GA, USA; The Parker H. Petit Institute for Bioengineering and Biosciences Georgia Institute of Technology, Atlanta, GA, USA.
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8
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Li G, Li H, Chen Z. Identification of ribosomal protein family as immune-cell-related biomarkers of NAFLD by bioinformatics and experimental analyses. Front Endocrinol (Lausanne) 2023; 14:1161269. [PMID: 37274336 PMCID: PMC10235545 DOI: 10.3389/fendo.2023.1161269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Background Immune cells play an integral role in the development and progression of non-alcoholic fatty liver disease (NAFLD). This study was to identify immune-cell-related biomarkers for the diagnosis and treatment of NAFLD. Methods and findings First, we introduced human liver transcriptome data from the GEO database (GSE48452 and GSE126848) and performed a weighted gene co-expression network analysis (WGCNA) to screen out the modules related to immune cell infiltration and to identify immune-cell-related differentially expressed genes (ICR-DEGs) associated with NAFLD progression. Further, the protein-protein interaction (PPI) network of ICR-DEGs was established to obtain hub genes and subsequently, the expression trend analysis was conducted to identify immune-cell-related biomarkers of NAFLD. Finally, the mRNA expression of biomarkers was validated in a NAFLD mouse model induced by high-fat diet (HFD) feeding. In total, we identified 66 ICR-DEGs and 13 hub genes associated with NAFLD. Among them, 9 hub genes (CD247, CD74, FCGR2B, IL2RB, INPP5D, MRPL16, RPL35, RPS3A, RPS8) were correlated with the infiltrating immune cells by the Pearson correlation analysis. Subsequently, 4 immune-cell-related biomarkers (RPL35, RPS3A, RPS8, and MRPL16) with the same expression trends in GSE48452 and GSE126848 datasets were identified. These biomarkers were enriched in immune-related pathways and had a good ability to distinguish between NASH and healthy samples. Moreover, we constructed a competing endogenous RNA (ceRNA) network of biomarkers and predicted twenty potential therapeutic drugs targeting RPS3A such as taxifolin and sitagliptin. Finally, experimental validation indicated that the hepatic mRNA expression of Rpl35, Rps3A, and Rps8 was significantly decreased in NAFLD mice. Conclusions This study identified four ribosomal protein genes (RPL35, RPS3A, RPS8, and MRPL16) as immune-cell-related biomarkers of NAFLD, which may actively participate in the immune processes during NAFLD progression and could serve as potential targets for the diagnosis and treatment of NAFLD.
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Affiliation(s)
- Gerui Li
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Li
- Department of Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ze Chen
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
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9
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Rodríguez-Almonacid CC, Kellogg MK, Karamyshev AL, Karamysheva ZN. Ribosome Specialization in Protozoa Parasites. Int J Mol Sci 2023; 24:ijms24087484. [PMID: 37108644 PMCID: PMC10138883 DOI: 10.3390/ijms24087484] [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: 02/27/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.
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Affiliation(s)
| | - Morgana K Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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10
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Shen C, Chen Z, Zhang Y, Xu W, Peng R, Jiang J, Zuo W, Fan Y, Zheng B. Biochemical and clinical effects of RPS20 expression in renal clear cell carcinoma. Oncol Rep 2022; 49:22. [PMID: 36484407 PMCID: PMC9773015 DOI: 10.3892/or.2022.8459] [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: 07/27/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) remains one of the most lethal urinary tumors in East Asia despite great advancements in treatment strategies in recent years. Ribosomal protein S20 (RPS20) is considered a new oncogene; however, little information is available on its expression, regulation and biological function in patients with RCC. In the present study, 43 pairs of human RCC and neighboring normal renal tissues were examined for protein expression and immunohistochemistry examination of RPS20. Lentiviral transduction was also employed to create RPS20 knockdown cell lines for downstream cellular experiments. MTT, flow cytometry, wound healing, colony formation and invasion assays were used to examine how RPS20 affected kidney renal clear cell carcinoma (KIRC) cell behavior. Western blotting was used to detect cycle‑related proteins (CDK4 and cyclin D1), Wnt‑related proteins (N‑cadherin and E‑cadherin) and signaling proteins [phosphorylated (p)‑AKT and p‑ERK]. The functions of RPS20 in vivo were examined in 786‑O cells with RPS20 knockdown. RPS20 was significantly overexpressed in tumor tissues compared with its expression in the corresponding normal tissues. RPS20 expression was linked to tumor stage, differentiation grade, tumor size and lymph node metastasis, and it had an independent prognostic value in KIRC. Since RCC cell proliferation, migration and invasion were suppressed when RPS20 was knocked down, the formation of renal tumors in vivo was markedly slowed down. In RPS20 knockdown cell lines, CDK4, cyclin D1 and E‑cadherin were downregulated, while N‑cadherin expression was increased. RPS20 was also observed to be involved in controlling the activation of the ERK and mTOR signaling pathways. In summary, the present study showed that RPS20 increased cell proliferation in RCC by activating the AKT‑mTOR and ERK‑MAPK signaling pathways, which suggests that RPS20 may be a therapeutic and prognostic target for RCC.
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Affiliation(s)
- Cheng Shen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Zhan Chen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yong Zhang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Wei Xu
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Rui Peng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jie Jiang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Wenjing Zuo
- Department of Orthopedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, P.R. China,Dr Yihui Fan, Department of Pathogenic Biology, School of Medicine, Nantong University, 20 Xisi Road, Chongchuan District, Nantong, Jiangsu 226001, P.R. China, E-mail:
| | - Bing Zheng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Correspondence to: Dr Bing Zheng, Department of Urology, The Second Affiliated Hospital of Nantong University, 6 North Road, Haierxiang, Nantong, Jiangsu 226001, P.R. China, E-mail:
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11
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Bentz EJ, Ophir AG. Chromosome-scale genome assembly of the African giant pouched rat (Cricetomys ansorgei) and evolutionary analysis reveals evidence of olfactory specialization. Genomics 2022; 114:110521. [PMID: 36351561 DOI: 10.1016/j.ygeno.2022.110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The Southern giant pouched rat, Cricetomys ansorgei, is a large rodent best known for its ability to detect landmines using its impressive sense of smell. Their powerful chemosensory abilities enable subtle discrimination of chemical social signals, and female pouched rats demonstrate a unique reproductive physiology hypothesized to be mediated by pheromonal mechanisms. Thus, C. ansorgei represents a novel mammalian model for chemosensory physiology, social behavior, and pheromonal control of reproductive physiology. We present the first chromosome-scale genomic sequence of the pouched rat encoding 22,671 protein coding genes, including 1571 olfactory receptors, and provide a glance into the evolutionary history of this species. Functional enrichment analysis reveals genetic expansions specific to the pouched rat are enriched for functions related to olfactory specialization. Overall, this assembly is of reference-quality, and will serve as a useful and informative genomic sequence on which we can confidently base future molecular research involving the pouched rat.
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Affiliation(s)
- Ehren J Bentz
- Department of Psychology, Cornell University, Ithaca, NY, USA.
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12
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Berloco MF, Minervini CF, Moschetti R, Palazzo A, Viggiano L, Marsano RM. Evidence of the Physical Interaction between Rpl22 and the Transposable Element Doc5, a Heterochromatic Transposon of Drosophila melanogaster. Genes (Basel) 2021; 12:1997. [PMID: 34946947 PMCID: PMC8701128 DOI: 10.3390/genes12121997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022] Open
Abstract
Chromatin is a highly dynamic biological entity that allows for both the control of gene expression and the stabilization of chromosomal domains. Given the high degree of plasticity observed in model and non-model organisms, it is not surprising that new chromatin components are frequently described. In this work, we tested the hypothesis that the remnants of the Doc5 transposable element, which retains a heterochromatin insertion pattern in the melanogaster species complex, can be bound by chromatin proteins, and thus be involved in the organization of heterochromatic domains. Using the Yeast One Hybrid approach, we found Rpl22 as a potential interacting protein of Doc5. We further tested in vitro the observed interaction through Electrophoretic Mobility Shift Assay, uncovering that the N-terminal portion of the protein is sufficient to interact with Doc5. However, in situ localization of the native protein failed to detect Rpl22 association with chromatin. The results obtained are discussed in the light of the current knowledge on the extra-ribosomal role of ribosomal protein in eukaryotes, which suggests a possible role of Rpl22 in the determination of the heterochromatin in Drosophila.
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Affiliation(s)
- Maria Francesca Berloco
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Roberta Moschetti
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Antonio Palazzo
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
| | - Luigi Viggiano
- Department of Biology, University of Bari “Aldo Moro”, 70126 Bari, Italy; (M.F.B.); (R.M.); (A.P.)
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13
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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14
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Cho SM, Lee HJ, Karuso P, Kwon HJ. Daptomycin suppresses tumor migration and angiogenesis via binding to ribosomal protein S19 in humans. J Antibiot (Tokyo) 2021; 74:726-733. [PMID: 34253886 DOI: 10.1038/s41429-021-00446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
We have previously reported that daptomycin (DAP), a last resort antibiotic, binds to ribosomal protein S19 (RPS19) in humans and exhibits selective anti-cancer activity against MCF7 breast cancer cells. Here, we investigated the role of RPS19 in the anti-cancer effects of DAP and have found that DAP does not induce autophagy, apoptosis or cell viability but does reduce cell proliferation. Our results suggest that an extraribosomal function of RPS19 involves the regulation of vascular endothelial growth factor (VEGF) but not EGF, PDGF or FGF. Engagement of RPS19 by DAP was shown by CETSA and ITDRFCETSA assays, and knocking down of RPS19 with siRNA increased the potency of DAP in MCF7 cells. In addition, DAP suppressed the secretion of VEGF in cancer cells and thereby inhibited cell migration. Collectively, these data provide an outline of the underlying mechanism of how DAP exhibits anti-cancer activity and suggests that RPS19 could be a promising target for the development of new anticancer drugs.
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Affiliation(s)
- Sung Min Cho
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hwa Jung Lee
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Peter Karuso
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ho Jeong Kwon
- Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
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15
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Yang X, Wei Y, Shi Y, Han X, Chen S, Yang L, Li H, Sun B, Shi Y. Cucumber Ribosomal Protein CsRPS21 Interacts With P22 Protein of Cucurbit Chlorotic Yellows Virus. Front Microbiol 2021; 12:654697. [PMID: 33995313 PMCID: PMC8116660 DOI: 10.3389/fmicb.2021.654697] [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: 01/17/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
Cucurbit chlorotic yellows virus (CCYV) is a cucurbit-infecting crinivirus. RNA silencing can be initiated as a plant defense against viruses. Viruses encode various RNA silencing suppressors to counteract antiviral silencing. P22 protein encoded by RNA1 of CCYV is a silencing suppressor, but its mechanism of action remains unclear. In this study, the cucumber ribosomal-like protein CsRPS21 was found to interact with P22 protein in vitro and in vivo. A conserved CsRPS21 domain was indispensable for its nuclear localization and interaction with P22. Transient expression of CsRPS21 in Nicotiana benthamiana leaves interfered with P22 accumulation and inhibited P22 silencing suppressor activity. CsRPS21 expression in N. benthamiana protoplasts inhibited CCYV accumulation. Increasing numbers of ribosomal proteins are being found to be involved in viral infections of plants. We identified a P22-interacting ribosomal protein, CsRPS21, and uncovered its role in early viral replication and silencing suppressor activity. Our study increases knowledge of the function of ribosomal proteins during viral infection.
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Affiliation(s)
- Xue Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ying Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yajuan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyu Han
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Siyu Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Lingling Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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16
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Xiong W, Zhang J, Lan T, Kong W, Wang X, Liu L, Chen X, Mo B. High resolution RNA-seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana. PLANT DIRECT 2021; 5:e00320. [PMID: 34095740 PMCID: PMC8156134 DOI: 10.1002/pld3.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 05/12/2023]
Abstract
In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.
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Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
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Xiong W, Lan T, Mo B. Extraribosomal Functions of Cytosolic Ribosomal Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:607157. [PMID: 33968093 PMCID: PMC8096920 DOI: 10.3389/fpls.2021.607157] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/29/2021] [Indexed: 05/20/2023]
Abstract
Ribosomes are basic translational machines in all living cells. The plant cytosolic ribosome is composed of four rRNAs and approximately 81 ribosomal proteins (RPs). In addition to the fundamental functions of RPs in the messenger RNA decoding process as well as in polypeptide synthesis and ribosome assembly, extraribosomal functions of RPs that occur in the absence of the ribosome have been proposed and studied with respect to RPs' ability to interact with RNAs and non-ribosomal proteins. In a few cases, extraribosomal functions of several RPs have been demonstrated with solid evidences in plants, including microRNA biogenesis, anti-virus defenses, and plant immunity, which have fascinated biologists. We believe that the widespread duplication of RP genes in plants may increase the potential of extraribosomal functions of RPs and more extraribosomal functions of plant RPs will be discovered in the future. In this article we review the current knowledge concerning the extraribosomal functions of RPs in plants and described the prospects for future research in this fascinating area.
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Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Beixin Mo,
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Interactions between tumor-derived proteins and Toll-like receptors. Exp Mol Med 2020; 52:1926-1935. [PMID: 33299138 PMCID: PMC8080774 DOI: 10.1038/s12276-020-00540-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 12/23/2022] Open
Abstract
Damage-associated molecular patterns (DAMPs) are danger signals (or alarmins) alerting immune cells through pattern recognition receptors (PRRs) to begin defense activity. Moreover, DAMPs are host biomolecules that can initiate a noninflammatory response to infection, and pathogen-associated molecular pattern (PAMPs) perpetuate the inflammatory response to infection. Many DAMPs are proteins that have defined intracellular functions and are released from dying cells after tissue injury or chemo-/radiotherapy. In the tumor microenvironment, DAMPs can be ligands for Toll-like receptors (TLRs) expressed on immune cells and induce cytokine production and T-cell activation. Moreover, DAMPs released from tumor cells can directly activate tumor-expressed TLRs that induce chemoresistance, migration, invasion, and metastasis. Furthermore, DAMP-induced chronic inflammation in the tumor microenvironment causes an increase in immunosuppressive populations, such as M2 macrophages, myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs). Therefore, regulation of DAMP proteins can reduce excessive inflammation to create an immunogenic tumor microenvironment. Here, we review tumor-derived DAMP proteins as ligands of TLRs and discuss their association with immune cells, tumors, and the composition of the tumor microenvironment. Tumor cells killed by radiotherapy or chemotherapy release signaling molecules that stimulate both immune response and tumor aggressiveness; regulating these molecules could improve treatment efficacy. Tae Heung Kang, Yeong-Min Park, and co-workers at Konkuk University, Seoul, South Korea, have reviewed the role of damage-associated molecular patterns (DAMPs) in immunity and cancer. These signaling molecules act as danger signals, activating immune cells by binding to specific receptors. However, tumor cells have the same receptors, and DAMPs binding triggers chemoresistance and increases invasiveness. The researchers report that although DAMPs can trigger a helpful immune response, they can also cause chronic inflammation, which in turn promotes an immune suppression response, allowing tumors to escape immune detection. Improving our understanding of the functions of different DAMPs could improve our ability to boost the immune response and decrease tumor aggressiveness.
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Qiu Y, Li K, Zhao X, Liu S, Wang L, Yang X, Jiang Z. Fermented Feed Modulates Meat Quality and Promotes the Growth of Longissimus Thoracis of Late-Finishing Pigs. Animals (Basel) 2020; 10:E1682. [PMID: 32957692 PMCID: PMC7552782 DOI: 10.3390/ani10091682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
This study investigated the effect of fermented diet on growth performance, carcass traits, meat quality and growth of longissimus thoracis (LT) of finishing pigs. A total of 48 finishing pigs [Duroc × (Landrace × Large White), male, 126 ± 5-d-old] weighing 98.76 ± 1.27 kg were randomly assigned to two treatments (eight pens per treatment and three pigs per pen) for a 28-d feeding trial, including control diet and fermented diet. Fermented diet significantly increased the loin eye area and lean mass percentage, decreased backfat thickness and improved meat quality of LT by decreasing the shear force and drip loss at 48 h post slaughter and improving meat sensory characteristics compared with control diet. A fermented diet also significantly increased the abundance of insulin, insulin receptor (IR), myoblast determination protein (MyoD) and myosin heavy chain-I (MyHC-I) transcripts, and the phosphorylation levels of AKT, mTORC1, 4EBP1 and S6K1 in LT, while decreasing the expression of muscle atrophy F-box (MAFbx) and forkhead Box O1 (Foxo1) mRNA transcripts. Moreover, proteomic analysis revealed that differentially expressed proteins predominantly involved in protein synthesis and muscle development were modulated by fermented diet. Our results indicated that a fermented diet improved meat quality and enhanced LT growth of finishing pigs by increasing insulin/AKT/mTORC1 protein synthesis cascade and activating the Foxo1/MAFbx pathway, along with the regulation of ribosomal protein and proteins involved in muscle contraction and muscle hypertrophy.
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Affiliation(s)
- Yueqin Qiu
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
| | - Kebiao Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Xichen Zhao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
| | - Shilong Liu
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Li Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Xuefen Yang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Zongyong Jiang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.Q.); (K.L.); (S.L.); (L.W.); (Z.J.)
- State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China
- Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
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20
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Prakash C, Pandey M, Talwar S, Singh Y, Kanojiya S, Pandey AK, Kumar N. Extra-ribosomal functions of Mtb RpsB in imparting stress resilience and drug tolerance to mycobacteria. Biochimie 2020; 177:87-97. [PMID: 32828823 DOI: 10.1016/j.biochi.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 01/21/2023]
Abstract
Emerging observations suggest that ribosomal proteins (RPs) play important extra-ribosomal roles in maintenance of cellular homeostasis. However, the mechanistic insights into these processes have not been extensively explored, especially in pathogenic bacteria. Here, we present our findings on potential extra-ribosomal functions of Mycobacterium tuberculosis (Mtb) RPs. We observed that Mtb RpsB and RpsQ are differentially localized to cell wall fraction in M. tuberculosis (H37Rv), while their M. smegmatis (Msm) homologs are primarily cytosolic. Cellular fractionation of ectopically expressed Mtb RPs in surrogate host (M. smegmatis) also shows their association with cell membrane/cell wall without any gross changes in cell morphology. M. smegmatis expressing Mtb RpsB exhibited altered redox homeostasis, decreased drug-induced ROS, reduced cell wall permeability and increased tolerance to various proteotoxic stress (oxidative stress, SDS and starvation). Mtb RpsB expression was also associated with increased resistance specifically towards Isoniazid, Ethionamide and Streptomycin. The enhanced drug tolerance was specific to Mtb RpsB and not observed upon ectopic expression of M. smegmatis homolog (Msm RpsB). Interestingly, C-terminus deletion in Mtb RpsB affected its localization and reversed the stress-resilient phenotypes. We also observed that M. tuberculosis (H37Rv) with upregulated RpsB levels had higher intracellular survival in macrophage. All these observations hint towards existence of moonlighting roles of Mtb RpsB in imparting stress resilience to mycobacteria. This work open avenues for further exploration of alternative pathways associated with fitness and drug tolerance in mycobacteria.
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Affiliation(s)
- Chetan Prakash
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Manitosh Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India; Department of Life Sciences, ITM University, Gwalior 475001, Madhya Pradesh, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yatendra Singh
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Sanjeev Kanojiya
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Amit Kumar Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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21
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Rajamäki ML, Sikorskaite-Gudziuniene S, Sarmah N, Varjosalo M, Valkonen JPT. Nuclear proteome of virus-infected and healthy potato leaves. BMC PLANT BIOLOGY 2020; 20:355. [PMID: 32727361 PMCID: PMC7392702 DOI: 10.1186/s12870-020-02561-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/20/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Infection of plants by viruses interferes with expression and subcellular localization of plant proteins. Potyviruses comprise the largest and most economically damaging group of plant-infecting RNA viruses. In virus-infected cells, at least two potyviral proteins localize to nucleus but reasons remain partly unknown. RESULTS In this study, we examined changes in the nuclear proteome of leaf cells from a diploid potato line (Solanum tuberosum L.) after infection with potato virus A (PVA; genus Potyvirus; Potyviridae) and compared the data with that acquired for healthy leaves. Gel-free liquid chromatography-coupled to tandem mass spectrometry was used to identify 807 nuclear proteins in the potato line v2-108; of these proteins, 370 were detected in at least two samples of healthy leaves. A total of 313 proteins were common in at least two samples of healthy and PVA-infected leaves; of these proteins, 8 showed differential accumulation. Sixteen proteins were detected exclusively in the samples from PVA-infected leaves, whereas other 16 proteins were unique to healthy leaves. The protein Dnajc14 was only detected in healthy leaves, whereas different ribosomal proteins, ribosome-biogenesis proteins, and RNA splicing-related proteins were over-represented in the nuclei of PVA-infected leaves. Two virus-encoded proteins were identified in the samples of PVA-infected leaves. CONCLUSIONS Our results show that PVA infection alters especially ribosomes and splicing-related proteins in the nucleus of potato leaves. The data increase our understanding of potyvirus infection and the role of nucleus in infection. To our knowledge, this is the first study of the nuclear proteome of potato leaves and one of the few studies of changes occurring in nuclear proteomes in response to plant virus infection.
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Affiliation(s)
- Minna-Liisa Rajamäki
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland.
| | - Sidona Sikorskaite-Gudziuniene
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Street 30, Babtai, LT-54333, Kaunas District, Lithuania
| | - Nandita Sarmah
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014, Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
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22
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Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, Williams LD. Root of the Tree: The Significance, Evolution, and Origins of the Ribosome. Chem Rev 2020; 120:4848-4878. [PMID: 32374986 DOI: 10.1021/acs.chemrev.9b00742] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.
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Affiliation(s)
- Jessica C Bowman
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton S Petrov
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Petar I Penev
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Loren Dean Williams
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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23
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Ipr1 Regulation by Cyclic GMP-AMP Synthase/Interferon Regulatory Factor 3 and Modulation of Irgm1 Expression via p53. Mol Cell Biol 2020; 40:MCB.00471-19. [PMID: 31988106 DOI: 10.1128/mcb.00471-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/21/2020] [Indexed: 12/28/2022] Open
Abstract
Intracellular pathogen resistance 1 (Ipr1) has been found to be a mediator to integrate cyclic GMP-AMP synthase (cGAS)-interferon regulatory factor 3 (IRF3), activated by intracellular pathogens, with the p53 pathway. Previous studies have shown the process of Ipr1 induction by various immune reactions, including intracellular bacterial and viral infections. The present study demonstrated that Ipr1 is regulated by the cGAS-IRF3 pathway during pathogenic infection. IRF3 was found to regulate Ipr1 expression by directly binding the interferon-stimulated response element motif of the Ipr1 promoter. Knockdown of Ipr1 decreased the expression of immunity-related GTPase family M member 1 (Irgm1), which plays critical roles in autophagy initiation. Irgm1 promoter characterization revealed a p53 motif in front of the transcription start site. P53 was found to participate in regulation of Irgm1 expression and IPR1-related effects on P53 stability by affecting interactions between ribosomal protein L11 (RPL11) and transformed mouse 3T3 cell double minute 2 (MDM2). Our results indicate that Ipr1 integrates cGAS-IRF3 with p53-modulated Irgm1 expression.
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24
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Qin L, Wang X, Gao Y, Bi K, Wang W. Roles of EvpP in Edwardsiella piscicida-Macrophage Interactions. Front Cell Infect Microbiol 2020; 10:53. [PMID: 32117819 PMCID: PMC7033576 DOI: 10.3389/fcimb.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Edwardsiella piscicida is found to be an important facultative intracellular pathogen with a broad host range. These organisms can replicate and survive within host macrophages to escape from the subversion of the immune defense. E. piscicida-macrophage interaction is very important in determining the outcome of edwardsiellasis. As an effector protein of E. piscicida T6SS, EvpP has been determined to be a very important virulence factor for E. piscicida, although its precise role in E. piscicida-macrophage interactions is not yet clear. In this study, the roles of EvpP in E. piscicida-macrophage interactions were characterized. Here, we constructed the deletion mutants of evpP (ΔevpP) and complementation (ΔevpP-C) by the allelic exchange method. Compared to wild type strain (WT), ΔevpP was found to be attenuated for growth within macrophages. In line with this observation, we found its survival capacity was lower than WT under oxidative and acid stress in vitro, which simulate conditions encountered in host macrophages. Attenuation of ΔevpP also correlated with enhanced activation of macrophages, as reflected by augmented NO production in ΔevpP-treated macrophages. Moreover, compared to WT, ΔevpP induced markedly increased apoptosis of macrophages, characterized by increased Annexin V binding and the activation of cleaved caspase-3. These findings provided strong evidence that EvpP is involved in the process of E. piscicida-macrophage interactions and is required for its survival and replication in macrophages. Thus, we propose that EvpP might be an important factor that controlling the fate of E. piscicida inside macrophages. To further exploring the underlying mechanism of EvpP action, the cDNA library was constructed from E. piscicida-infected macrophages and a yeast two-hybrid screen was performed to search for cellular proteins interacting with EvpP. Ribosomal protein S5 (RPS5) was identified as a target of EvpP. Furthermore, the interaction was validated with co-immunoprecipitation assay. This result implies that the observed effect of EvpP on macrophages might be related to RPS5-mediated regulation, contributing to a better understanding of the mechanisms of EvpP involved in E. piscicida-macrophage interactions.
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Affiliation(s)
- Lei Qin
- Jiangsu Key Laboratory of Marine Biotechnology, College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Lianyungang, China
| | - Xingqiang Wang
- Jiangsu Key Laboratory of Marine Biotechnology, College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Yingli Gao
- Jiangsu Key Laboratory of Marine Biotechnology, College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Keran Bi
- Jiangsu Key Laboratory of Marine Biotechnology, College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Weixia Wang
- Jiangsu Key Laboratory of Marine Biotechnology, College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, China
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25
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Xiao R, Li L, Ma Y. A label-free proteomic approach differentiates between conventional and organic rice. J Food Compost Anal 2019. [DOI: 10.1016/j.jfca.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Chico V, Salvador-Mira ME, Nombela I, Puente-Marin S, Ciordia S, Mena MC, Perez L, Coll J, Guzman F, Encinar JA, Mercado L, Ortega-Villaizan MDM. IFIT5 Participates in the Antiviral Mechanisms of Rainbow Trout Red Blood Cells. Front Immunol 2019; 10:613. [PMID: 31040842 PMCID: PMC6476978 DOI: 10.3389/fimmu.2019.00613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/07/2019] [Indexed: 12/14/2022] Open
Abstract
Viral hemorrhagic septicemia virus (VHSV) infection appears to be halted in rainbow trout nucleated red blood cells (RBCs). Diverse mechanisms are thought to be related to the antiviral immune response of rainbow trout RBCs to VHSV. However, the specific rainbow trout RBC proteins that interact directly with VHSV are still unknown. In an attempt to identify VHSV-RBC protein interactions, we characterized the immunoprecipitated (IP) proteome of RBCs exposed to VHSV using an antibody against the N protein of VHSV. The IP proteomic characterization identified 31 proteins by mass spectrometry analysis. Among them, we identified interferon-induced protein with tetratricopeptide repeats 5 (IFIT5), a protein belonging to a family of proteins that are induced after the production of type I interferon. Importantly, IFIT5 has been implicated in the antiviral immune response. We confirmed the participation of IFIT5 in the rainbow trout RBC antiviral response by examining the expression profile of IFIT5 in RBCs after VHSV exposure at transcriptional and protein levels. We detected a correlation between the highest IFIT5 expression levels and the decline in VHSV replication at 6 h post-exposure. In addition, silencing ifit5 resulted in a significant increase in VHSV replication in RBCs. Moreover, an increase in VHSV replication was observed in RBCs when the IFIT5 RNA-binding pocket cavity was modulated by using a natural compound from the SuperNatural II database. We performed a proximity ligation assay and detected a significant increase in positive cells among VHSV-exposed RBCs compared to unexposed RBCs, indicating protein-protein colocalization between IFIT5 and the glycoprotein G of VHSV. In summary, these results suggest a possible role of IFIT5 in the antiviral response of RBCs against VHSV.
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Affiliation(s)
- Veronica Chico
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Maria Elizabhet Salvador-Mira
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Ivan Nombela
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Sara Puente-Marin
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Sergio Ciordia
- Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - María Carmen Mena
- Unidad de Proteómica, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Luis Perez
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Julio Coll
- Departamento de Biotecnología, Instituto Nacional de Investigaciones y Tecnologías Agrarias y Alimentarias (INIA), Madrid, Spain
| | - Fanny Guzman
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
| | - Jose Antonio Encinar
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso (PUCV), Valparaíso, Chile
| | - Maria Del Mar Ortega-Villaizan
- Departamento de Bioquímica y Biología Molecular, Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández (UMH), Elche, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto de Investigación, Desarrollo e Innovación en Biotecnologîa Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), Elche, Spain
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27
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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28
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Dionne KL, Bergeron D, Landry-Voyer AM, Bachand F. The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3-uS5 interaction. J Biol Chem 2018; 294:1944-1955. [PMID: 30530495 DOI: 10.1074/jbc.ra118.004928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/27/2018] [Indexed: 02/06/2023] Open
Abstract
Ribosomal (r)-proteins are generally viewed as ubiquitous, constitutive proteins that simply function to maintain ribosome integrity. However, findings in the past decade have led to the idea that r-proteins have evolved specialized functions beyond the ribosome. For example, the 40S ribosomal protein uS5 (RPS2) is known to form an extraribosomal complex with the protein arginine methyltransferase PRMT3 that is conserved from fission yeast to humans. However, the full scope of uS5's extraribosomal functions, including whether uS5 interacts with any other proteins, is not known. In this study, we identify the conserved zinc finger protein 277 (ZNF277) as a new uS5-associated protein by using quantitative proteomics approaches in human cells. As previously shown for PRMT3, we found that ZNF277 uses a C2H2-type zinc finger domain to recognize uS5. Analysis of protein-protein interactions in living cells indicated that the ZNF277-uS5 complex is found in the cytoplasm and the nucleolus. Furthermore, we show that ZNF277 and PRMT3 compete for uS5 binding, because overexpression of PRMT3 inhibited the formation of the ZNF277-uS5 complex, whereas depletion of cellular ZNF277 resulted in increased levels of uS5-PRMT3. Notably, our results reveal that ZNF277 recognizes nascent uS5 in the course of mRNA translation, suggesting cotranslational assembly of the ZNF277-uS5 complex. Our findings thus unveil an intricate network of evolutionarily conserved protein-protein interactions involving extraribosomal uS5, suggesting a key role for uS5 beyond the ribosome.
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Affiliation(s)
- Kiersten L Dionne
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Danny Bergeron
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Anne-Marie Landry-Voyer
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François Bachand
- From the RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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Gayraud-Morel B, Le Bouteiller M, Commere PH, Cohen-Tannoudji M, Tajbakhsh S. Notchless defines a stage-specific requirement for ribosome biogenesis during lineage progression in adult skeletal myogenesis. Development 2018; 145:145/23/dev162636. [PMID: 30478226 DOI: 10.1242/dev.162636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/02/2018] [Indexed: 11/20/2022]
Abstract
Cell fate decisions occur through the action of multiple factors, including signalling molecules and transcription factors. Recently, the regulation of translation has emerged as an important step for modulating cellular function and fate, as exemplified by ribosomes that play distinct roles in regulating cell behaviour. Notchless (Nle) is a conserved nuclear protein that is involved in a crucial step in ribosome biogenesis, and is required for the maintenance of adult haematopoietic and intestinal stem/progenitor cells. Here, we show that activated skeletal muscle satellite cells in conditional Nle mutant mice are arrested in proliferation; however, deletion of Nle in myofibres does not impair myogenesis. Furthermore, conditional deletion of Nle in satellite cells during homeostasis did not impact on their fate for up to 3 months. In contrast, loss of Nle function in primary myogenic cells blocked proliferation because of major defects in ribosome formation. Taken together, we show that muscle stem cells undergo a stage-specific regulation of ribosome biogenesis, thereby underscoring the importance of differential modulation of mRNA translation for controlling cell fate decisions.
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Affiliation(s)
- Barbara Gayraud-Morel
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France.,CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Marie Le Bouteiller
- CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France.,Early Mammalian Development and Stem Cell Biology, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Pierre-Henri Commere
- Plateforme de Cytometrie, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Michel Cohen-Tannoudji
- CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France.,Early Mammalian Development and Stem Cell Biology, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France .,CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
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30
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Ribosomal flavours: an acquired taste for specific mRNAs? Biochem Soc Trans 2018; 46:1529-1539. [PMID: 30420413 DOI: 10.1042/bst20180160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 12/20/2022]
Abstract
The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via multiple avenues, including heterogeneity at the level of both ribosomal proteins and ribosomal RNAs and their covalent modifications. Together, these variations provide the potential for hundreds, if not thousands, of flavours of ribosome, each of which could have idiosyncratic preferences for the translation of certain messenger RNAs. Indeed, perturbations to this heterogeneity appear to affect specific subsets of transcripts and manifest as cell-type-specific diseases. This review provides a historical perspective of the ribosomal code hypothesis, before outlining the various sources of heterogeneity, their regulation and functional consequences for the cell.
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31
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Stevens BM, Khan N, D'Alessandro A, Nemkov T, Winters A, Jones CL, Zhang W, Pollyea DA, Jordan CT. Characterization and targeting of malignant stem cells in patients with advanced myelodysplastic syndromes. Nat Commun 2018; 9:3694. [PMID: 30209285 PMCID: PMC6135858 DOI: 10.1038/s41467-018-05984-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a chronic hematologic disorder that frequently evolves to more aggressive stages and in some cases leads to acute myeloid leukemia (AML). MDS arises from mutations in hematopoietic stem cells (HSCs). Thus, to define optimal therapies, it is essential to understand molecular events driving HSC pathogenesis. In this study, we report that during evolution of MDS, malignant HSCs activate distinct cellular programs that render such cells susceptible to therapeutic intervention. Specifically, metabolic analyses of the MDS stem cell compartment show a profound activation of protein synthesis machinery and increased oxidative phosphorylation. Pharmacological targeting of protein synthesis and oxidative phosphorylation demonstrated potent and selective eradication of MDS stem cells in primary human patient specimens. Taken together, our findings indicate that MDS stem cells are reliant on specific metabolic events and that such properties can be targeted prior to the onset of clinically significant AML, during antecedent MDS.
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Affiliation(s)
- Brett M Stevens
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Nabilah Khan
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Amanda Winters
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Courtney L Jones
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Wei Zhang
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Daniel A Pollyea
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Craig T Jordan
- Division of Hematology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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32
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Sun WS, Chun JL, Kim DH, Ahn JS, Kim MK, Hwang IS, Kwon DJ, Hwang S, Lee JW. Molecular cloning and characterization of porcine ribosomal protein L21. J Vet Sci 2018; 18:531-540. [PMID: 28057907 PMCID: PMC5746447 DOI: 10.4142/jvs.2017.18.4.531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 10/12/2016] [Accepted: 11/23/2016] [Indexed: 11/20/2022] Open
Abstract
Ribosomal protein L21 (RPL21) is a structural component of the 60S subunit of the eukaryotic ribosome. This protein has an important role in protein synthesis and the occurrence of hereditary diseases. Pig is a common laboratory model, however, to the best of our knowledge, its RPL21 gene has not been cloned to date. In this study, we cloned and identified the full-length sequence of the pig RPL21 gene for the first time. In addition, we examined its expression pattern and function by using overexpression or knockdown approaches. As a result, we obtained a 604 bp segment that contains a 483 bp open reading frame encoding 160 amino acids. The pig RPL21 gene is located in the “+” strand of chromosome 11, which spans 2167 bp from 4199792 to 4201958. Pig RPL21 protein has nine strands and two helices in its secondary structure. Pig RPL21 is predominantly expressed in ovary and lung, at lower levels in kidney, small intestine, and skin, and at the lowest levels in heart and liver. Furthermore, RPL21 expression is closely connected with cell proliferation and cell cycle arrest. The results are intended to provide useful information for the further study of pig RPL21.
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Affiliation(s)
- Wu-Sheng Sun
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.,Department of Animal Science and Biotechnology, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea
| | - Ju-Lan Chun
- Department of Animal Science and Biotechnology, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea
| | - Dong-Hwan Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jin-Seop Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Min-Kyu Kim
- Department of Animal Science and Biotechnology, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju 55365, Korea
| | - Dae-Jin Kwon
- Animal Biotechnology Division, National Institute of Animal Science, Wanju 55365, Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Wanju 55365, Korea
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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33
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Li H, Smigocki AC. Transcriptome analysis of sugar beet root maggot (Tetanops myopaeformis) genes modulated by the Beta vulgaris host. INSECT SCIENCE 2018; 25:222-234. [PMID: 27696738 DOI: 10.1111/1744-7917.12409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/27/2016] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Sugar beet root maggot (SBRM, Tetanops myopaeformis von Röder) is a major but poorly understood insect pest of sugar beet (Beta vulgaris L.). The molecular mechanisms underlying plant defense responses are well documented, however, little information is available about complementary mechanisms for insect adaptive responses to overcome host resistance. To date, no studies have been published on SBRM gene expression profiling. Suppressive subtractive hybridization (SSH) generated more than 300 SBRM ESTs differentially expressed in the interaction of the pest with a moderately resistant (F1016) and a susceptible (F1010) sugar beet line. Blast2GO v. 3.2 search indicated that over 40% of the differentially expressed genes had known functions, primarily driven by fruit fly D. melanogaster genes. Expression patterns of 18 selected EST clones were confirmed by RT-PCR analysis. Gene Ontology (GO) analysis predicted a dominance of metabolic and catalytic genes involved in the interaction of SBRM with its host. SBRM genes functioning during development, regulation, cellular process, signaling and under stress conditions were annotated. SBRM genes that were common or unique in response to resistant or susceptible interactions with the host were identified and their possible roles in insect responses to the host are discussed.
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Affiliation(s)
- Haiyan Li
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
| | - Ann C Smigocki
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
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34
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Li S, Li X, Zhou Y. Ribosomal protein L18 is an essential factor that promote rice stripe virus accumulation in small brown planthopper. Virus Res 2018; 247:15-20. [DOI: 10.1016/j.virusres.2018.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/13/2018] [Accepted: 01/22/2018] [Indexed: 01/10/2023]
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35
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Guhr A, Horn MA, Weig AR. Vitamin B2 (riboflavin) increases drought tolerance of Agaricus bisporus. Mycologia 2018; 109:860-873. [DOI: 10.1080/00275514.2017.1414544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Alexander Guhr
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr. Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Alfons R. Weig
- Keylab of Genomics & Bioinformatics, BayCEER, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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36
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Russo A, Maiolino S, Pagliara V, Ungaro F, Tatangelo F, Leone A, Scalia G, Budillon A, Quaglia F, Russo G. Enhancement of 5-FU sensitivity by the proapoptotic rpL3 gene in p53 null colon cancer cells through combined polymer nanoparticles. Oncotarget 2018; 7:79670-79687. [PMID: 27835895 PMCID: PMC5346744 DOI: 10.18632/oncotarget.13216] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/14/2016] [Indexed: 01/09/2023] Open
Abstract
Colon cancer is one of the leading causes of cancer-related death worldwide and the therapy with 5-fluorouracil (5-FU) is mainly limited due to resistance. Recently, we have demonstrated that nucleolar stress upon 5-FU treatment leads to the activation of ribosome-free rpL3 (L3) as proapoptotic factor. In this study, we analyzed L3 expression profile in colon cancer tissues and demonstrated that L3 mRNA amount decreased with malignant progression and the intensity of its expression was inversely related to tumor grade and Bcl-2/Bax ratio. With the aim to develop a combined therapy of 5-FU plus plasmid encoding L3 (pL3), we firstly assessed the potentiation of the cytotoxic effect of 5-FU on colon cancer cells by L3. Next, 10 μM 5-FU and 2 μg of pL3 were encapsulated in biocompatible nanoparticles (NPs) chemically conjugated with HA to achieve active tumor-targeting ability in CD44 overexpressing cancer cells. We showed the specific intracellular accumulation of NPs in cells and a sustained release for 5-FU and L3. Analysis of cytotoxicity and apoptotic induction potential of combined NPs clearly showed that the 5-FU plus L3 were more effective in inducing apoptosis than 5-FU or L3 alone. Furthermore, we show that the cancer-specific chemosensitizer effect of combined NPs may be dependent on L3 ability to affect 5-FU efflux by controlling P-gp (P-glycoprotein) expression. These results led us to propose a novel combined therapy with the use of 5-FU plus L3 in order to establish individualized therapy by examining L3 profiles in tumors to yield a better clinical outcomes.
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Affiliation(s)
- Annapina Russo
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Sara Maiolino
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Valentina Pagliara
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Francesca Ungaro
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Fabiana Tatangelo
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | - Alessandra Leone
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | | | - Alfredo Budillon
- Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, 80131 Napoli, Italy
| | - Fabiana Quaglia
- Laboratory of Drug Delivery, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Russo
- Laboratory of Biochemistry, Department of Pharmacy, University of Napoli Federico II, 80131 Napoli, Italy
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37
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Li YH, Wang J, Liu Y, Qiu L, Li JZ, Hu HG, Hu ZL, Zhang W, Lu B, Zhang JP. Esculentoside A specifically binds to ribosomal protein S3a and impairs LPS-induced signaling in macrophages. Int Immunopharmacol 2018; 54:254-260. [DOI: 10.1016/j.intimp.2017.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/24/2023]
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38
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Kalinina NO, Makarova S, Makhotenko A, Love AJ, Taliansky M. The Multiple Functions of the Nucleolus in Plant Development, Disease and Stress Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:132. [PMID: 29479362 PMCID: PMC5811523 DOI: 10.3389/fpls.2018.00132] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
The nucleolus is the most conspicuous domain in the eukaryotic cell nucleus, whose main function is ribosomal RNA (rRNA) synthesis and ribosome biogenesis. However, there is growing evidence that the nucleolus is also implicated in many other aspects of cell biology, such as regulation of cell cycle, growth and development, senescence, telomerase activity, gene silencing, responses to biotic and abiotic stresses. In the first part of the review, we briefly assess the traditional roles of the plant nucleolus in rRNA synthesis and ribosome biogenesis as well as possible functions in other RNA regulatory pathways such as splicing, nonsense-mediated mRNA decay and RNA silencing. In the second part of the review we summarize recent progress and discuss already known and new hypothetical roles of the nucleolus in plant growth and development. In addition, this part will highlight studies showing new nucleolar functions involved in responses to pathogen attack and abiotic stress. Cross-talk between the nucleolus and Cajal bodies is also discussed in the context of their association with poly(ADP ribose)polymerase (PARP), which is known to play a crucial role in various physiological processes including growth, development and responses to biotic and abiotic stresses.
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Affiliation(s)
- Natalia O. Kalinina
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Natalia O. Kalinina
| | - Svetlana Makarova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Antonida Makhotenko
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Taliansky
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Michael Taliansky
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39
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Grinchuk OV, Yenamandra SP, Iyer R, Singh M, Lee HK, Lim KH, Chow PK, Kuznetsov VA. Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma. Mol Oncol 2017; 12:89-113. [PMID: 29117471 PMCID: PMC5748488 DOI: 10.1002/1878-0261.12153] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/03/2017] [Accepted: 10/16/2017] [Indexed: 12/18/2022] Open
Abstract
Currently, molecular markers are not used when determining the prognosis and treatment strategy for patients with hepatocellular carcinoma (HCC). In the present study, we proposed that the identification of common pro‐oncogenic pathways in primary tumors (PT) and adjacent non‐malignant tissues (AT) typically used to predict HCC patient risks may result in HCC biomarker discovery. We examined the genome‐wide mRNA expression profiles of paired PT and AT samples from 321 HCC patients. The workflow integrated differentially expressed gene selection, gene ontology enrichment, computational classification, survival predictions, image analysis and experimental validation methods. We developed a 24‐ribosomal gene‐based HCC classifier (RGC), which is prognostically significant in both PT and AT. The RGC gene overexpression in PT was associated with a poor prognosis in the training (hazard ratio = 8.2, P = 9.4 × 10−6) and cross‐cohort validation (hazard ratio = 2.63, P = 0.004) datasets. The multivariate survival analysis demonstrated the significant and independent prognostic value of the RGC. The RGC displayed a significant prognostic value in AT of the training (hazard ratio = 5.0, P = 0.03) and cross‐validation (hazard ratio = 1.9, P = 0.03) HCC groups, confirming the accuracy and robustness of the RGC. Our experimental and bioinformatics analyses suggested a key role for c‐MYC in the pro‐oncogenic pattern of ribosomal biogenesis co‐regulation in PT and AT. Microarray, quantitative RT‐PCR and quantitative immunohistochemical studies of the PT showed that DKK1 in PT is the perspective biomarker for poor HCC outcomes. The common co‐transcriptional pattern of ribosome biogenesis genes in PT and AT from HCC patients suggests a new scalable prognostic system, as supported by the model of tumor‐like metabolic redirection/assimilation in non‐malignant AT. The RGC, comprising 24 ribosomal genes, is introduced as a robust and reproducible prognostic model for stratifying HCC patient risks. The adjacent non‐malignant liver tissue alone, or in combination with HCC tissue biopsy, could be an important target for developing predictive and monitoring strategies, as well as evidence‐based therapeutic interventions, that aim to reduce the risk of post‐surgery relapse in HCC patients.
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Affiliation(s)
| | | | | | - Malay Singh
- Bioinformatics InstituteSingapore
- Department of Computer ScienceSchool of ComputingNational University of SingaporeSingapore
| | - Hwee Kuan Lee
- Bioinformatics InstituteSingapore
- Department of Computer ScienceSchool of ComputingNational University of SingaporeSingapore
| | - Kiat Hon Lim
- Division of Surgical OncologyNational Cancer CentreSingaporeSingapore
| | - Pierce Kah‐Hoe Chow
- Division of Surgical OncologyNational Cancer CentreSingaporeSingapore
- Office of Clinical SciencesDuke‐NUS Graduate Medical SchoolSingaporeSingapore
- Department of HPB and Transplantation SurgerySingapore General HospitalSingapore
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40
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Mo Y, Lin R, Liu P, Tan M, Xiong Y, Guan KL, Yuan HX. SIRT7 deacetylates DDB1 and suppresses the activity of the CRL4 E3 ligase complexes. FEBS J 2017; 284:3619-3636. [PMID: 28886238 DOI: 10.1111/febs.14259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/28/2017] [Accepted: 08/31/2017] [Indexed: 12/14/2022]
Abstract
Cullin 4 (CUL4) and small ring finger protein ROC1 assemble to form E3 ubiquitin ligase (CRL4) complexes. CUL4 interacts with WD-40 proteins through the adaptor protein DNA damage-binding protein 1 (DDB1) to target substrates for ubiquitylation. Very little is known on how the CUL4 and DDB1 interaction is regulated. Here, we show that DDB1 is acetylated and acetylation promotes DDB1 binding to CUL4. We also identify nucleolar sirtuin 7 (SIRT7) as a major deacetylase that negatively regulates DDB1-CUL4 interaction. Following inhibition of nucleolar function by actinomycin D or 5-fluorouracil treatment or knocking down the gene for the RNA polymerase I component UBF, SIRT7 is mobilized from the nucleolus to the nucleoplasm and promotes DDB1 deacetylation, leading to decreased DDB1-CUL4 association and CRL4 activity. This results in the accumulation or activation of CRL4 substrates including LATS1 and p73, which contribute to cell apoptosis induced by actinomycin D and 5-fluorouracil. Our study uncovers a novel regulation of CRL4 E3 ligase complexes.
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Affiliation(s)
- Yan Mo
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ran Lin
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng Liu
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yue Xiong
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
| | - Kun-Liang Guan
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Hai-Xin Yuan
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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41
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Youn H, Lee HK, Sohn HR, Park UH, Kim EJ, Youn B, Um SJ. RaRF confers RA resistance by sequestering RAR to the nucleolus and regulating MCL1 in leukemia cells. Oncogene 2017; 37:352-362. [PMID: 28945224 DOI: 10.1038/onc.2017.329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/10/2017] [Accepted: 08/06/2017] [Indexed: 01/10/2023]
Abstract
Retinoic acid (RA) has broad clinical applications for the treatment of various cancers, particularly acute promyelocytic leukemia. However, RA-based therapy is limited by relapse in patients associated with RA resistance, the mechanism of which is poorly understood. Here, we suggest a new molecular mechanism of RA resistance by a repressor, named RA resistance factor (RaRF). RaRF suppressed transcriptional activity of the RA receptor (RAR) by directly interacting with and sequestering RAR to the nucleolus in response to RA. RaRF was highly expressed in RA-resistant leukemia cells and its expression was strongly correlated with RA sensitivity. MCL1 was upregulated by RA treatment upon RaRF depletion, accompanying leukemic myeloblast differentiation, which is negatively regulated by ectopic RaRF expression. Collectively, we propose that RaRF may be a factor in the resistance mechanism and thus a potential target for leukemia therapy using RA.
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Affiliation(s)
- H Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - H-K Lee
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - H-R Sohn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - U-H Park
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
| | - E-J Kim
- Department of Molecular Biology, Dankook University, Cheonan-si, Chungnam, Korea
| | - B Youn
- Department of Biological Sciences, Pusan National University, Gumjeong-gu, Busan 46241, Republic of Korea
| | - S-J Um
- Department of Integrative Bioscience and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Korea
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42
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Chen Y, Zhi J, Zhang H, Li J, Zhao Q, Xu J. Transcriptome analysis of Phytolacca americana L. in response to cadmium stress. PLoS One 2017; 12:e0184681. [PMID: 28898278 PMCID: PMC5595333 DOI: 10.1371/journal.pone.0184681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/29/2017] [Indexed: 11/18/2022] Open
Abstract
Phytolacca americana L. (pokeweed) has metal phytoremediation potential, but little is known about its metal accumulation-related genes. In this study, the de novo sequencing of total RNA produced 53.15 million reads covering 10.63 gigabases of transcriptome raw data in cadmium (Cd)-treated and untreated pokeweed. Of the 97,502 assembled unigenes, 42,197 had significant matches in a public database and were annotated accordingly. An expression level comparison between the samples revealed 1515 differentially expressed genes (DEGs), 923 down- and 592 up-regulated under Cd treatment. A KEGG pathway enrichment analysis of DEGs revealed that they were involved in 72 metabolism pathways, with photosynthesis, phenylalanine metabolism, ribosome, phenylpropanoid biosynthesis, flavonoid biosynthesis and carbon fixation in photosynthetic organisms containing 24, 18, 72, 14, 7 and 15 genes, respectively. Genes related to heavy metal tolerance, absorption, transport and accumulation were also identified, including 11 expansins, 8 nicotianamine synthases, 6 aquaporins, 4 ZRT/IRT-like proteins, 3 ABC transporters and 3 metallothioneins. The gene expression results of 12 randomly selected DEGs were validated using quantitative real-time PCR, and showed different response patterns to Cd in their roots, stems and leaves. These results may be helpful in increasing our understanding of heavy metal hyperaccumulators and in future phytoremediation applications.
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Affiliation(s)
- Yongkun Chen
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Junkai Zhi
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Hao Zhang
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jian Li
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Qihong Zhao
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jichen Xu
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- * E-mail:
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Protein composition analysis of polyhedra matrix of Bombyx mori nucleopolyhedrovirus (BmNPV) showed powerful capacity of polyhedra to encapsulate foreign proteins. Sci Rep 2017; 7:8768. [PMID: 28821766 PMCID: PMC5562830 DOI: 10.1038/s41598-017-08987-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/14/2017] [Indexed: 11/23/2022] Open
Abstract
Polyhedra can encapsulate other proteins and have potential applications as protein stabilizers. The extremely stable polyhedra matrix may provide a platform for future engineered micro-crystal devices. However, the protein composition of the polyhedra matrix remains largely unknown. In this study, the occlusion-derived virus (ODV)-removed BmNPV polyhedra matrix fraction was subjected to SDS-PAGE and then an LC-ESI-MS/MS analysis using a Thermo Scientific Q Exactive mass spectrometer. In total, 28 host and 91 viral proteins were identified. The host components were grouped into one of six categories, i.e., chaperones, ubiquitin and related proteins, host helicases, cytoskeleton-related proteins, RNA-binding proteins and others, according to their predicted Pfam domain(s). Most viral proteins may not be essential for polyhedra assembly, as evidenced by studies in the literature showing that polyhedra formation occurs in the nucleus upon the disruption of individual genes. The structural role of these proteins in baculovirus replication will be of significant interest in future studies. The immobilization of enhanced green fluorescent protein (eGFP) into the polyhedra by fusing with the C-terminus of BM134 that is encoded by open reading frame (ORF) 134 suggested that the polyhedra had a powerful capacity to trap foreign proteins, and BM134 was a potential carrier for incorporating proteins of interest into the polyhedra.
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Hingston P, Chen J, Allen K, Truelstrup Hansen L, Wang S. Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes. PLoS One 2017; 12:e0180123. [PMID: 28662112 PMCID: PMC5491136 DOI: 10.1371/journal.pone.0180123] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/11/2017] [Indexed: 11/19/2022] Open
Abstract
The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA) profiling to characterize the bacterium's cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3×) were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431) and magnitude (>1,000-fold) of differentially expressed genes (>2-fold, p<0.05) in response to cold. A core set of 22 genes was upregulated at all growth phases, including nine genes required for branched-chain fatty acid (BCFA) synthesis, the osmolyte transporter genes opuCBCD, and the internalin A and D genes. Genes suppressed at 4°C were largely associated with cobalamin (B12) biosynthesis or the production/export of cell wall components. Antisense transcription accounted for up to 1.6% of total mapped reads with higher levels (2.5×) observed at 4°C than 20°C. The greatest number of upregulated antisense transcripts at 4°C occurred in early lag phase, however, at both temperatures, antisense expression levels were highest in late stationary-phase cells. Cold-induced FA membrane changes included a 15% increase in the proportion of BCFAs and a 15% transient increase in unsaturated FAs between lag and exponential phase. These increases probably reduced the membrane phase transition temperature until optimal levels of BCFAs could be produced. Collectively, this research provides new information regarding cold-induced membrane composition changes in L. monocytogenes, the growth-phase dependency of its cold-stress regulon, and the active roles of antisense transcripts in regulating its cold stress response.
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Affiliation(s)
- Patricia Hingston
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica Chen
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Allen
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Siyun Wang
- Department of Food, Nutrition, and Health, The University of British Columbia, Vancouver, British Columbia, Canada
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Rajamäki ML, Xi D, Sikorskaite-Gudziuniene S, Valkonen JPT, Whitham SA. Differential Requirement of the Ribosomal Protein S6 and Ribosomal Protein S6 Kinase for Plant-Virus Accumulation and Interaction of S6 Kinase with Potyviral VPg. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:374-384. [PMID: 28437137 DOI: 10.1094/mpmi-06-16-0122-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ribosomal protein S6 (RPS6) is an indispensable plant protein regulated, in part, by ribosomal protein S6 kinase (S6K) which, in turn, is a key regulator of plant responses to stresses and developmental cues. Increased expression of RPS6 was detected in Nicotiana benthamiana during infection by diverse plant viruses. Silencing of the RPS6 and S6K genes in N. benthamiana affected accumulation of Cucumber mosaic virus, Turnip mosaic virus (TuMV), and Potato virus A (PVA) in contrast to Turnip crinkle virus and Tobacco mosaic virus. In addition, the viral genome-linked protein (VPg) of TuMV and PVA interacted with S6K in plant cells, as detected by bimolecular fluorescence complementation assay. The VPg-S6K interaction was detected in cytoplasm, nucleus, and nucleolus, whereas the green fluorescent protein-tagged S6K alone showed cytoplasmic localization only. These results demonstrate that the requirement for RPS6 and S6K differs for diverse plant viruses with different translation initiation strategies and suggest that potyviral VPg-S6K interaction may affect S6K functions in both the cytoplasm and the nucleus.
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Affiliation(s)
- Minna-Liisa Rajamäki
- 1 Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Helsinki, Finland
| | - Dehui Xi
- 2 College of Life Science, Sichuan University, Chengdu, 610064, China; and
| | | | - Jari P T Valkonen
- 1 Department of Agricultural Sciences, P.O. Box 27, FI-00014 University of Helsinki, Helsinki, Finland
| | - Steven A Whitham
- 3 Department of Plant Pathology and Microbiology, Iowa State University, Ames 50011, U.S.A
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Lo CA, Greben AW, Chen BE. Generating stable cell lines with quantifiable protein production using CRISPR/Cas9-mediated knock-in. Biotechniques 2017; 62:165-174. [DOI: 10.2144/000114534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/17/2017] [Indexed: 11/23/2022] Open
Abstract
Cell lines expressing foreign genes have been widely used to produce a variety of recombinant proteins. However, generating recombinant protein–expressing cell lines is usually a lengthy process and the resulting protein expression levels are often inconsistent. Here, we describe an efficient method for making stable cell lines expressing any recombinant protein of interest in a controllable and quantifiable manner. We integrate transgenes into specific genomic loci using CRISPR/Cas9 such that transgene expression is driven by endogenous promoters to ensure consistent and predictable expression of the recombinant protein. Expression levels can be predetermined by selecting promoters from genes with the desired level of expression. To quantify recombinant protein expression, a protein quantitation reporter (PQR) is incorporated between the endogenous and foreign genes. The PQR allows equimolar production of the endogenous protein, the recombinant protein, and a fluorescent reporter. As a result, expression levels of both the endogenous and recombinant proteins can be continuously monitored using fluorescence.
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Affiliation(s)
- Chiu-An Lo
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre
- Departments of Medicine and Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Alexander W. Greben
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre
- Departments of Medicine and Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Brian Edwin Chen
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre
- Departments of Medicine and Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
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Ribosomal Proteins Control or Bypass p53 during Nucleolar Stress. Int J Mol Sci 2017; 18:ijms18010140. [PMID: 28085118 PMCID: PMC5297773 DOI: 10.3390/ijms18010140] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/12/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022] Open
Abstract
The nucleolus is the site of ribosome biogenesis, a complex process that requires the coordinate activity of all three RNA polymerases and hundreds of non-ribosomal factors that participate in the maturation of ribosomal RNA (rRNA) and assembly of small and large subunits. Nevertheless, emerging studies have highlighted the fundamental role of the nucleolus in sensing a variety of cellular stress stimuli that target ribosome biogenesis. This condition is known as nucleolar stress and triggers several response pathways to maintain cell homeostasis, either p53-dependent or p53-independent. The mouse double minute (MDM2)-p53 stress signaling pathways are activated by multiple signals and are among the most important regulators of cellular homeostasis. In this review, we will focus on the role of ribosomal proteins in p53-dependent and p53-independent response to nucleolar stress considering novel identified regulators of these pathways. We describe, in particular, the role of ribosomal protein uL3 (rpL3) in p53-independent nucleolar stress signaling pathways.
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Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences. DisoRDPbind provides accurate predictions and is sufficiently fast to make predictions for full genomes. Our method is implemented as a user-friendly webserver that is freely available at http://biomine.ece.ualberta.ca/DisoRDPbind/ . We overview our predictor, discuss how to run the webserver, and show how to interpret the corresponding results. We also demonstrate the utility of our method based on two case studies, human BRCA1 protein that binds various proteins and DNA, and yeast 60S ribosomal protein L4 that interacts with proteins and RNA.
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Deisenroth C, Franklin DA, Zhang Y. The Evolution of the Ribosomal Protein-MDM2-p53 Pathway. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026138. [PMID: 27908926 DOI: 10.1101/cshperspect.a026138] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The progression of our understanding of ribosomal proteins as static building blocks of the ribosome to highly integrated sensors of p53 surveillance and function has achieved a tremendous rate of growth over the past several decades. As the workhorse of the cell, ribosomes are responsible for translating the genetic code into the functional units that drive cell growth and proliferation. The seminal identification of ribosomal protein binding to MDM2, the negative regulator of p53, has evolved into a paradigm for ribosomal protein-MDM2-p53 signaling that extends into processes as diverse as energy metabolism to proliferation. The central core of signaling occurs when perturbations to rRNA synthesis, processing, and assembly modulate the rate of ribosome biogenesis, signaling a nucleolar stress response to p53. This has led to identification of a number of disease pathologies related to ribosomal protein dysfunction that are manifested as developmental disorders or cancer. Advancing research into the basic mechanics of ribosomal protein-MDM2-p53 signaling is paving the way for novel translational research into biomarker identification and therapeutic strategies for ribosome-related diseases.
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Affiliation(s)
- Chad Deisenroth
- The Hamner Institutes for Health Sciences, Institute for Chemical Safety Sciences, Research Triangle Park, North Carolina 27709
| | - Derek A Franklin
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Yanping Zhang
- Department of Radiation Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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50
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Fu Y, Li C, Tang Q, Tian S, Jin L, Chen J, Li M, Li C. Genomic analysis reveals selection in Chinese native black pig. Sci Rep 2016; 6:36354. [PMID: 27808243 PMCID: PMC5093412 DOI: 10.1038/srep36354] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/13/2016] [Indexed: 12/12/2022] Open
Abstract
Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.
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Affiliation(s)
- Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Jianhai Chen
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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