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Yarullina L, Kalatskaja J, Tsvetkov V, Burkhanova G, Yalouskaya N, Rybinskaya K, Zaikina E, Cherepanova E, Hileuskaya K, Nikalaichuk V. The Influence of Chitosan Derivatives in Combination with Bacillus subtilis Bacteria on the Development of Systemic Resistance in Potato Plants with Viral Infection and Drought. PLANTS (BASEL, SWITZERLAND) 2024; 13:2210. [PMID: 39204646 PMCID: PMC11360750 DOI: 10.3390/plants13162210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Viral diseases of potatoes are among the main problems causing deterioration in the quality of tubers and loss of yield. The growth and development of potato plants largely depend on soil moisture. Prevention strategies require comprehensive protection against pathogens and abiotic stresses, including modeling the beneficial microbiome of agroecosystems combining microorganisms and immunostimulants. Chitosan and its derivatives have great potential for use in agricultural engineering due to their ability to induce plant immune responses. The effect of chitosan conjugate with caffeic acid (ChCA) in combination with Bacillus subtilis 47 on the transcriptional activity of PR protein genes and changes in the proteome of potato plants during potato virus Y (PVY) infection and drought was studied. The mechanisms of increasing the resistance of potato plants to PVY and lack of moisture are associated with the activation of transcription of genes encoding PR proteins: the main protective protein (PR-1), chitinase (PR-3), thaumatin-like protein (PR-5), protease inhibitor (PR-6), peroxidase (PR-9), and ribonuclease (PR-10), as well as qualitative and quantitative changes in the plant proteome. The revealed activation of the expression of marker genes of systemic acquired resistance and induced systemic resistance under the influence of combined treatment with B. subtilis and chitosan conjugate indicate that, in potato plants, the formation of resistance to viral infection in drought conditions proceeds synergistically. By two-dimensional electrophoresis of S. tuberosum leaf proteins followed by MALDI-TOF analysis, 10 proteins were identified, the content and composition of which differed depending on the experiment variant. In infected plants treated with ChCA, the synthesis of proteinaceous RNase P 1 and oxygen-evolving enhancer protein 2 was enhanced in conditions of normal humidity, and 20 kDa chaperonin and TMV resistance protein N-like was enhanced in conditions of lack of moisture. The virus coat proteins were detected, which intensively accumulated in the leaves of plants infected with potato Y-virus. ChCA treatment reduced the content of these proteins in the leaves, and in plants treated with ChCA in combination with Bacillus subtilis, viral proteins were not detected at all, both in conditions of normal humidity and lack of moisture, which suggests the promising use of chitosan derivatives in combination with B. subtilis bacteria in the regulation of plant resistance.
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Affiliation(s)
- Liubov Yarullina
- Institute of Biochemistry and Genetics, pr. Oktyabrya, 71, 450054 Ufa, Russia; (G.B.); (E.Z.); (E.C.)
| | - Joanna Kalatskaja
- Institute of Experimental Botany Named after V.F. Kuprevich, ul. Akademicheskaya, 27, 220072 Minsk, Belarus; (J.K.); (N.Y.); (K.R.)
| | - Vyacheslav Tsvetkov
- Department of Biochemistry and Biotechnology, Ufa University of Science and Technology, ul. Zaki Validi, 32, 450076 Ufa, Russia;
| | - Guzel Burkhanova
- Institute of Biochemistry and Genetics, pr. Oktyabrya, 71, 450054 Ufa, Russia; (G.B.); (E.Z.); (E.C.)
| | - Ninel Yalouskaya
- Institute of Experimental Botany Named after V.F. Kuprevich, ul. Akademicheskaya, 27, 220072 Minsk, Belarus; (J.K.); (N.Y.); (K.R.)
| | - Katerina Rybinskaya
- Institute of Experimental Botany Named after V.F. Kuprevich, ul. Akademicheskaya, 27, 220072 Minsk, Belarus; (J.K.); (N.Y.); (K.R.)
| | - Evgenia Zaikina
- Institute of Biochemistry and Genetics, pr. Oktyabrya, 71, 450054 Ufa, Russia; (G.B.); (E.Z.); (E.C.)
| | - Ekaterina Cherepanova
- Institute of Biochemistry and Genetics, pr. Oktyabrya, 71, 450054 Ufa, Russia; (G.B.); (E.Z.); (E.C.)
| | - Kseniya Hileuskaya
- Institute of Chemistry of New Materials, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (K.H.); (V.N.)
| | - Viktoryia Nikalaichuk
- Institute of Chemistry of New Materials, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (K.H.); (V.N.)
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Duan X, Wang H, Cao Z, Su N, Wang Y, Zheng Y. Deficiency of ValRS-m Causes Male Infertility in Drosophila melanogaster. Int J Mol Sci 2024; 25:7489. [PMID: 39000597 PMCID: PMC11242588 DOI: 10.3390/ijms25137489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Drosophila spermatogenesis involves the renewal of germline stem cells, meiosis of spermatocytes, and morphological transformation of spermatids into mature sperm. We previously demonstrated that Ocnus (ocn) plays an essential role in spermatogenesis. The ValRS-m (Valyl-tRNA synthetase, mitochondrial) gene was down-regulated in ocn RNAi testes. Here, we found that ValRS-m-knockdown induced complete sterility in male flies. The depletion of ValRS-m blocked mitochondrial behavior and ATP synthesis, thus inhibiting the transition from spermatogonia to spermatocytes, and eventually, inducing the accumulation of spermatogonia during spermatogenesis. To understand the intrinsic reason for this, we further conducted transcriptome-sequencing analysis for control and ValRS-m-knockdown testes. The differentially expressed genes (DEGs) between these two groups were selected with a fold change of ≥2 or ≤1/2. Compared with the control group, 4725 genes were down-regulated (dDEGs) and 2985 genes were up-regulated (uDEGs) in the ValRS-m RNAi group. The dDEGs were mainly concentrated in the glycolytic pathway and pyruvate metabolic pathway, and the uDEGs were primarily related to ribosomal biogenesis. A total of 28 DEGs associated with mitochondria and 6 meiosis-related genes were verified to be suppressed when ValRS-m was deficient. Overall, these results suggest that ValRS-m plays a wide and vital role in mitochondrial behavior and spermatogonia differentiation in Drosophila.
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Affiliation(s)
- Xin Duan
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Haolin Wang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Zhixian Cao
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Na Su
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Yufeng Wang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Ya Zheng
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
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Das AS, Basu A, Mukhopadhyay R. Ribosomal proteins: the missing piece in the inflammation puzzle? Mol Cell Biochem 2024:10.1007/s11010-024-05050-9. [PMID: 38951378 DOI: 10.1007/s11010-024-05050-9] [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: 03/26/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024]
Abstract
Ribosomal proteins (RPs) are constituents of macromolecular machinery, ribosome that translates genetic information into proteins. Besides ribosomal functions, RPs are now getting appreciated for their 'moonlighting'/extra-ribosomal functions modulating many cellular processes. Accumulating evidence suggests that a number of RPs are involved in inflammation. Though acute inflammation is a part of the innate immune response, uncontrolled inflammation is a driving factor for several chronic inflammatory diseases. An in-depth understanding of inflammation regulation has always been valued for the better management of associated diseases. Hence, this review first outlines the common livelihood of RPs and then provides a comprehensive account of five RPs that significantly contribute to the inflammation process. Finally, we discuss the possible therapeutic uses of RPs against chronic inflammatory diseases.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, 02912, USA.
| | - Anandita Basu
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, 02903, USA
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
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Aslam S, Aljawdah HM, Murshed M, Serrano GE. Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila. Sci Rep 2024; 14:13472. [PMID: 38866811 PMCID: PMC11169463 DOI: 10.1038/s41598-024-63555-1] [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: 12/31/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Waddlia chondrophila is a possible cause of fetal death in humans. This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses. Despite the years of efforts, the underlying mechanism behind the pathogenesis of W. chondrophila is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against W. chondrophila. At first, RNA polymerase sigma factor SigA and 3-deoxy-D-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with W. chondrophila; however, further research is required to ensure their safety.
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Affiliation(s)
- Sidra Aslam
- Banner Sun Health Research Institute, Sun City, AZ, USA.
| | - Hossam M Aljawdah
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Mutee Murshed
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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Buneeva OA, Fedchenko VI, Kaloshina SA, Zavyalova MG, Zgoda VG, Medvedev AE. Proteomic profiling of renal tissue of normo- and hypertensive rats with the renalase peptide RP220 as an affinity ligand. BIOMEDITSINSKAIA KHIMIIA 2024; 70:145-155. [PMID: 38940203 DOI: 10.18097/pbmc20247003145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Renalase (RNLS) is a recently discovered protein that plays an important role in the regulation of blood pressure by acting inside and outside cells. Intracellular RNLS is a FAD-dependent oxidoreductase that oxidizes isomeric forms of β-NAD(P)H. Extracellular renalase lacking its N-terminal peptide and cofactor FAD exerts various protective effects via non-catalytic mechanisms. Certain experimental evidence exists in the literature that the RP220 peptide (a 20-mer peptide corresponding to the amino acid sequence RNLS 220-239) reproduces a number of non-catalytic effects of this protein, acting on receptor proteins of the plasma membrane. The possibility of interaction of this peptide with intracellular proteins has not been studied. Taking into consideration the known role of RNLS as a possible antihypertensive factor, the aim of this study was to perform proteomic profiling of the kidneys of normotensive and hypertensive rats using RP220 as an affinity ligand. Proteomic (semi-quantitative) identification revealed changes in the relative content of about 200 individual proteins in the kidneys of hypertensive rats bound to the affinity sorbent as compared to the kidneys of normotensive animals. Increased binding of SHR renal proteins to RP220 over the normotensive control was found for proteins involved in the development of cardiovascular pathology. Decreased binding of the kidney proteins from hypertensive animals to RP220 was noted for components of the ubiquitin-proteasome system, ribosomes, and cytoskeleton.
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Affiliation(s)
- O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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Zhang K, Shen H, Wang Y, Shen H, Zhang C, Zou X, Yu Y, Tian X, Wang Y. Identification of End-Binding 1 Protein as Novel α-4 Giardin-Binding Partners in Giardia lamblia Trophozoites. Acta Parasitol 2024; 69:505-513. [PMID: 38206477 PMCID: PMC11001682 DOI: 10.1007/s11686-023-00774-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Giardia lamblia (syn. G. intestinalis, G. duodenalis) is a primitive opportunistic protozoon, and one of the earliest differentiated eukaryotes. Despite its primitive nature, G. lamblia has a sophisticated cytoskeleton system, which is closely related to its proliferation and pathogenicity. Meanwhile, α giardin is a G. lamblia-specific cytoskeleton protein, which belongs to the annexin superfamily. Interestingly, G. lamblia has 21 annexin-like α giardins, i.e., more than higher eukaryotes. The functional differences among α giardin members are not fully understood. METHODS We took α-4 giardin, a member of α giardin family, as a research object. A morpholino-mediated knockdown experiment was performed to identify the effect of α-4 giardin on G. lamblia trophozoites biological traits. A yeast two-hybrid cDNA library of G. lamblia strain C2 trophozoites was screened for interaction partners of α-4 giardin. Co-immunoprecipitation and fluorescent colocalization confirmed the relationship between G. lamblia EB1 (gEB1) and α-4 giardin. RESULTS α-4 Giardin could inhibit the proliferation and adhesion of G. lamblia trophozoites. In addition, it interacted with G. lamblia EB1 (gEB1). CONCLUSIONS α-4 Giardin was involved in proliferation and adhesion in G. lamblia trophozoites, and EB1, a crucial roles in mitosis, was an interacting partner of α-4 giardin.
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Affiliation(s)
- Kaiyue Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China
| | - Hai'e Shen
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China
| | - Yi Wang
- Department of Clinical Laboratory, North China University of Science and Technology Affiliated Hospital, Tangshan, 063000, China
| | - Hailin Shen
- The Second Hospital of Tangshan, Tangshan, 063000, China
| | - Chenshuo Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China
| | - Xu Zou
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China
| | - Yuan Yu
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China.
| | - Xifeng Tian
- College of Basic Medical Sciences, North China University of Science and Technology, Tangshan, 063000, China
| | - Yang Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063000, China.
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Liang WK, Zhang LB, Xu JL. Dietary steroids promote body weight growth and induce gametogenesis by increasing the expressions of genes related to cell proliferation of sea cucumber (Apostichopus japonicus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101191. [PMID: 38237259 DOI: 10.1016/j.cbd.2024.101191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/07/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024]
Abstract
Steroids play a vital role in animal survival, promoting growth and development when administered appropriate concentration exogenously. However, it remains unclear whether steroids can induce gonadal development and the underlying mechanism. This study assessed sea cucumber weights post-culturing, employing paraffin sections and RNA sequencing (RNA-seq) to explore gonadal changes and gene expression in response to exogenous steroid addition. Testosterone and cholesterol, dissolved in absolute ethanol, were incorporated into sea cucumber diets. After 30 days, testosterone and cholesterol significantly increased sea cucumber weights, with the total weight of experimental groups surpassing the control. The testosterone-fed group exhibited significantly higher eviscerated weight than the control group. In addition, dietary steroids influenced gonad morphology and upregulated genes related to cell proliferation,such as RPL35, PC, eLF-1, MPC2, ADCY10 and CYP2C18. Thees upregulated differentially expressed genes were significantly enriched in the organic system, metabolism, genetic information and environmental information categories. These findings imply that steroids may contribute to the growth and the process of genetic information translation and protein synthesis essential for gonadal development and gametogenesis.
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Affiliation(s)
- Wen-Ke Liang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li-Bin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Jia-Lei Xu
- Zhongke Tonhe (Shandong) Marine Technology Co., Ltd, Dongying 257200, China
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Das D, Mallick B, Sinha S, Ganguli S, Samanta D, Banerjee R, Roy D. Unearthing the inhibitory potential of phytochemicals from Lawsonia inermis L. and some drugs against dengue virus protein NS1: an in silico approach. J Biomol Struct Dyn 2023:1-18. [PMID: 38157248 DOI: 10.1080/07391102.2023.2298730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Dengue has received the status of an epidemic and endemic disease, with countless number of infections every year. Due to the unreliability of vaccines and non-specificity of drugs, it becomes necessary to find plant-based alternatives, with less harmful side effects. Lawsonia inermis L., is the sole source of dye, Mehendi. The rich repertoire of phytochemicals makes it useful, medicinally. The main objectives of the study are to explore the anti-dengue properties of the phytochemicals from Lawsonia inermis, and to shortlist potential candidates in curing the disease. Phytochemicals from the plant, and a set of drugs were screened and docked against NS1 protein, a less explored drug target, needed for maintenance of virus life cycle. Ligand screening and docking analysis concluded gallic acid, and chlorogenic acid to be good candidates, exhibiting high binding affinity and extensive interactions with the protein. From among the shortlisted drugs, only Vibegron showed effective binding affinity with NS1 protein with zero violations to the Lipinski's Rule of 5. Molecular dynamic simulations, executed for a time period of 100 nanoseconds, reveal the performance of a ligand within a solvated system. Chlorogenic and gallic acid, formed more stable and compact complexes with protein, with stable energy parameters and strong binding affinity. This was further validated with snapshots taken every 50 nanoseconds, showing no change in binding site between the ligand and protein, within the stipulated time frame. It was interesting to see that, a phenol (chlorogenic acid), served as a better drug candidate, against the NS1 protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debapriya Das
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Bidisha Mallick
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Suchita Sinha
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
| | - Sayak Ganguli
- Post Graduate Department of Biotechnology, St. Xaviers' College (Autonomous), Kolkata, India
| | - Dipu Samanta
- Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, India
| | - Rajat Banerjee
- Dr. BC Chandra Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Debleena Roy
- Post Graduate Department of Botany, Lady Brabourne College, Kolkata, India
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Lee SO, Kelliher JL, Song W, Tengler K, Sarkar A, Dray E, Leung JWC. UBA80 and UBA52 fine-tune RNF168-dependent histone ubiquitination and DNA repair. J Biol Chem 2023; 299:105043. [PMID: 37451480 PMCID: PMC10413357 DOI: 10.1016/j.jbc.2023.105043] [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: 12/24/2022] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
The ubiquitin signaling pathway is crucial for the DNA damage response pathway. More specifically, RNF168 is integral in regulating DNA repair proteins at damaged chromatin. However, the detailed mechanism by which RNF168 is regulated in cells is not fully understood. Here, we identify the ubiquitin-ribosomal fusion proteins UBA80 (also known as RPS27A) and UBA52 (also known as RPL40) as interacting proteins for H2A/H2AX histones and RNF168. Both UBA80 and UBA52 are recruited to laser-induced micro-irradiation DNA damage sites and are required for DNA repair. Ectopic expression of UBA80 and UBA52 inhibits RNF168-mediated H2A/H2AX ubiquitination at K13/15 and impairs 53BP1 recruitment to DNA lesions. Mechanistically, the C-terminal ribosomal fragments of UBA80 and UBA52, S27A and L40, respectively, limit RNF168-nucleosome engagement by masking the regulatory acidic residues at E143/E144 and the nucleosome acidic patch. Together, our results reveal that UBA80 and UBA52 antagonize the ubiquitination signaling pathway and fine-tune the spatiotemporal regulation of DNA repair proteins at DNA damage sites.
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Affiliation(s)
- Seong-Ok Lee
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jessica L Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Aradhan Sarkar
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.
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Protein-Coding Region Derived Small RNA in Exosomes from Influenza A Virus-Infected Cells. Int J Mol Sci 2023; 24:ijms24010867. [PMID: 36614310 PMCID: PMC9820831 DOI: 10.3390/ijms24010867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Exosomes may function as multifactorial mediators of cell-to-cell communication, playing crucial roles in both physiological and pathological processes. Exosomes released from virus-infected cells may contain RNA and proteins facilitating infection spread. The purpose of our study was to analyze how the small RNA content of exosomes is affected by infection with the influenza A virus (IAV). Exosomes were isolated by ultracentrifugation after hemadsorption of virions and their small RNA content was identified using high-throughput sequencing. As compared to mock-infected controls, 856 RNA transcripts were significantly differentially expressed in exosomes from IAV-infected cells, including fragments of 458 protein-coding (pcRNA), 336 small, 28 long intergenic non-coding RNA transcripts, and 33 pseudogene transcripts. Upregulated pcRNA species corresponded mainly to proteins associated with translation and antiviral response, and the most upregulated among them were RSAD2, CCDC141 and IFIT2. Downregulated pcRNA species corresponded to proteins associated with the cell cycle and DNA packaging. Analysis of differentially expressed pseudogenes showed that in most cases, an increase in the transcription level of pseudogenes was correlated with an increase in their parental genes. Although the role of exosome RNA in IAV infection remains undefined, the biological processes identified based on the corresponding proteins may indicate the roles of some of its parts in IAV replication.
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Liver Proteome Alterations in Red Deer ( Cervus elaphus) Infected by the Giant Liver Fluke Fascioloides magna. Pathogens 2022; 11:pathogens11121503. [PMID: 36558836 PMCID: PMC9786150 DOI: 10.3390/pathogens11121503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Liver fluke infections are recognised as diseases with worldwide distribution and considerable veterinary and public health importance. The giant liver fluke, Fascioloides magna, is an important non-native parasite which has been introduced to Europe, posing a threat to the survival of local wildlife populations such as red deer (Cervus elaphus). The aim of the study was to analyse differences in liver proteomes between F. magna-infected and control red deer groups using a label-based high-throughput quantitative proteomics approach. The proteomics analysis identified 234 proteins with differential abundance between the control and infected groups. Our findings showed that F. magna infection in this definitive host is associated with changes in the metabolism of proteins and fatty acids, oxidative stress, fibrosis, and signaling pathways. The identified proteins and associated biological pathways represent a valuable contribution to the understanding of host-parasite interactions and the pathogenesis of liver fluke infection.
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12
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Schneider M, Vedder L, Oyiga BC, Mathew B, Schoof H, Léon J, Naz AA. Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity. PLoS One 2022; 17:e0265981. [PMID: 36095002 PMCID: PMC9467324 DOI: 10.1371/journal.pone.0265981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley transcriptome and leaf chlorophyll content under 8h conditions, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. This might lead to a cascade of suspended sink-source activities, which ultimately delay organ development and differentiation in barley shoot meristems under short photoperiods.
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Affiliation(s)
- Michael Schneider
- University of Bonn, Institute of Crop Science and Resource Conservation, Plant Breeding, Bonn, Germany
| | - Lucia Vedder
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Bioinformatics, Bonn, Germany
| | - Benedict Chijioke Oyiga
- University of Bonn, Institute of Crop Science and Resource Conservation, Plant Breeding, Bonn, Germany
| | - Boby Mathew
- University of Bonn, Institute of Crop Science and Resource Conservation, Plant Breeding, Bonn, Germany
| | - Heiko Schoof
- University of Bonn, Institute of Crop Science and Resource Conservation, Crop Bioinformatics, Bonn, Germany
| | - Jens Léon
- University of Bonn, Institute of Crop Science and Resource Conservation, Plant Breeding, Bonn, Germany
| | - Ali Ahmad Naz
- University of Bonn, Institute of Crop Science and Resource Conservation, Plant Breeding, Bonn, Germany
- * E-mail:
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13
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Grunchec H, Deraze J, Dardalhon-Cuménal D, Ribeiro V, Coléno-Costes A, Dias K, Bloyer S, Mouchel-Vielh E, Peronnet F, Thomassin H. Single amino-acid mutation in a Drosoph ila melanogaster ribosomal protein: An insight in uL11 transcriptional activity. PLoS One 2022; 17:e0273198. [PMID: 35981051 PMCID: PMC9387862 DOI: 10.1371/journal.pone.0273198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/04/2022] [Indexed: 11/26/2022] Open
Abstract
The ribosomal protein uL11 is located at the basis of the ribosome P-stalk and plays a paramount role in translational efficiency. In addition, no mutant for uL11 is available suggesting that this gene is haplo-insufficient as many other Ribosomal Protein Genes (RPGs). We have previously shown that overexpression of Drosophila melanogaster uL11 enhances the transcription of many RPGs and Ribosomal Biogenesis genes (RiBis) suggesting that uL11 might globally regulate the level of translation through its transcriptional activity. Moreover, uL11 trimethylated on lysine 3 (uL11K3me3) interacts with the chromodomain of the Enhancer of Polycomb and Trithorax Corto, and both proteins co-localize with RNA Polymerase II at many sites on polytene chromosomes. These data have led to the hypothesis that the N-terminal end of uL11, and more particularly the trimethylation of lysine 3, supports the extra-ribosomal activity of uL11 in transcription. To address this question, we mutated the lysine 3 codon using a CRISPR/Cas9 strategy and obtained several lysine 3 mutants. We describe here the first mutants of D. melanogaster uL11. Unexpectedly, the uL11K3A mutant, in which the lysine 3 codon is replaced by an alanine, displays a genuine Minute phenotype known to be characteristic of RPG deletions (longer development, low fertility, high lethality, thin and short bristles) whereas the uL11K3Y mutant, in which the lysine 3 codon is replaced by a tyrosine, is unaffected. In agreement, the rate of translation decreases in uL11K3A but not in uL11K3Y. Co-immunoprecipitation experiments show that the interaction between uL11 and the Corto chromodomain is impaired by both mutations. However, Histone Association Assays indicate that the mutant proteins still bind chromatin. RNA-seq analyses from wing imaginal discs show that Corto represses RPG expression whereas very few genes are deregulated in uL11 mutants. We propose that Corto, by repressing RPG expression, ensures that all ribosomal proteins are present at the correct stoichiometry, and that uL11 fine-tunes its transcriptional regulation of RPGs.
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Affiliation(s)
- Héloïse Grunchec
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Jérôme Deraze
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Delphine Dardalhon-Cuménal
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Valérie Ribeiro
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Anne Coléno-Costes
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Karine Dias
- Genomics Core Facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, Inserm, Université PSL, Paris, France
| | - Sébastien Bloyer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emmanuèle Mouchel-Vielh
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Frédérique Peronnet
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
| | - Hélène Thomassin
- Laboratoire de Biologie du développement (LBD), Institut de Biologie Paris Seine (IBPS), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Paris, France
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14
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Hurtado-Rios JJ, Carrasco-Navarro U, Almanza-Pérez JC, Ponce-Alquicira E. Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials. Int J Mol Sci 2022; 23:ijms23169123. [PMID: 36012387 PMCID: PMC9409020 DOI: 10.3390/ijms23169123] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
Moonlighting proteins are those capable of performing more than one biochemical or biophysical function within the same polypeptide chain. They have been a recent focus of research due to their potential applications in the health, pharmacological, and nutritional sciences. Among them, some ribosomal proteins involved in assembly and protein translation have also shown other functionalities, including inhibiting infectious bacteria, viruses, parasites, fungi, and tumor cells. Therefore, they may be considered antimicrobial peptides (AMPs). However, information regarding the mechanism of action of ribosomal proteins as AMPs is not yet fully understood. Researchers have suggested that the antimicrobial activity of ribosomal proteins may be associated with an increase in intracellular reactive oxidative species (ROS) in target cells, which, in turn, could affect membrane integrity and cause their inactivation and death. Moreover, the global overuse of antibiotics has resulted in an increase in pathogenic bacteria resistant to common antibiotics. Therefore, AMPs such as ribosomal proteins may have potential applications in the pharmaceutical and food industries in the place of antibiotics. This article provides an overview of the potential roles of ribosomes and AMP ribosomal proteins in conjunction with their potential applications.
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Affiliation(s)
- Jessica J. Hurtado-Rios
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Ulises Carrasco-Navarro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Julio Cesar Almanza-Pérez
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Edith Ponce-Alquicira
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
- Correspondence: ; Tel.: +52-55-58044600 (ext. 2676)
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15
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Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23116174. [PMID: 35682850 PMCID: PMC9181716 DOI: 10.3390/ijms23116174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
A number of mutations in the RPS20 gene encoding the ribosomal protein uS10 have been found to be associated with a predisposition to hereditary non-polyposis colorectal carcinoma (CRC). We transfected HEK293T cells with constructs carrying the uS10 minigene with mutations identical to those mentioned above and examined the effects of the produced proteins on the cellular transcriptome. We showed that uS10 with mutations p.V50SfsX23 or p.L61EfsX11 cannot be incorporated into 40S ribosomal subunits, while the protein with the missense mutation p.V54L functionally replaces the respective endogenous protein in the 40S subunit assembly and the translation process. The comparison of RNA-seq data obtained from cells producing aberrant forms of uS10 with data for those producing the wild-type protein revealed overlapping sets of upregulated and downregulated differently expressed genes (DEGs) related to several pathways. Among the limited number of upregulated DEGs, there were genes directly associated with the progression of CRC, e.g., PPM1D and PIGN. Our findings indicate that the accumulation of the mutant forms of uS10 triggers a cascade of cellular events, similar to that which is triggered when the cell responds to a large number of erroneous proteins, suggesting that this may increase the risk of cancer.
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16
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Short AK, Thai CW, Chen Y, Kamei N, Pham AL, Birnie MT, Bolton JL, Mortazavi A, Baram TZ. Single-Cell Transcriptional Changes in Hypothalamic Corticotropin-Releasing Factor-Expressing Neurons After Early-Life Adversity Inform Enduring Alterations in Vulnerabilities to Stress. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 3:99-109. [PMID: 36712559 PMCID: PMC9874075 DOI: 10.1016/j.bpsgos.2021.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Mental health and vulnerabilities to neuropsychiatric disorders involve the interplay of genes and environment, particularly during sensitive developmental periods. Early-life adversity (ELA) and stress promote vulnerabilities to stress-related affective disorders, yet it is unknown how transient ELA dictates lifelong neuroendocrine and behavioral reactions to stress. The population of hypothalamic corticotropin-releasing factor (CRF)-expressing neurons that regulate stress responses is a promising candidate to mediate the long-lasting influences of ELA on stress-related behavioral and hormonal responses via enduring transcriptional and epigenetic mechanisms. Methods Capitalizing on a well-characterized model of ELA, we examined ELA-induced changes in gene expression profiles of CRF-expressing neurons in the hypothalamic paraventricular nucleus of developing male mice. We used single-cell RNA sequencing on isolated CRF-expressing neurons. We determined the enduring functional consequences of transcriptional changes on stress reactivity in adult ELA mice, including hormonal responses to acute stress, adrenal weights as a measure of chronic stress, and behaviors in the looming shadow threat task. Results Single-cell transcriptomics identified distinct and novel CRF-expressing neuronal populations, characterized by both their gene expression repertoire and their neurotransmitter profiles. ELA-provoked expression changes were selective to specific subpopulations and affected genes involved in neuronal differentiation, synapse formation, energy metabolism, and cellular responses to stress and injury. Importantly, these expression changes were impactful, apparent from adrenal hypertrophy and augmented behavioral responses to stress in adulthood. Conclusions We uncover a novel repertoire of stress-regulating CRF cell types differentially affected by ELA and resulting in augmented stress vulnerability, with relevance to the origins of stress-related affective disorders.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Christina W. Thai
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California
| | - Yuncai Chen
- Department of Pediatrics, University of California Irvine, Irvine, California
| | - Noriko Kamei
- Department of Pediatrics, University of California Irvine, Irvine, California
| | - Aidan L. Pham
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Matthew T. Birnie
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Jessica L. Bolton
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California,Department of Pediatrics, University of California Irvine, Irvine, California,Department of Neurology, University of California Irvine, Irvine, California,Address correspondence to Tallie Z. Baram, M.D., Ph.D.
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17
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Zou Q, Yang L, Shi R, Qi Y, Zhang X, Qi H. Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis. iScience 2021; 24:103396. [PMID: 34825148 PMCID: PMC8605100 DOI: 10.1016/j.isci.2021.103396] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 01/03/2023] Open
Abstract
Maintaining proteostasis is important for animal development. How proteostasis influences spermatogenesis that generates male gametes, spermatozoa, is not clear. We show that testis-specific paralog of ribosomal large subunit protein RPL39, RPL39L, is required for mouse spermatogenesis. Deletion of Rpl39l in mouse caused reduced proliferation of spermatogonial stem cells, malformed sperm mitochondria and flagella, leading to sub-fertility in males. Biochemical analyses revealed that lack of RPL39L deteriorated protein synthesis and protein quality control in spermatogenic cells, partly due to reduced biogenesis of ribosomal subunits and ribosome homeostasis. RPL39/RPL39L is likely assembled into ribosomes via H/ACA domain containing NOP10 complex early in ribosome biogenesis pathway. Furthermore, Rpl39l null mice exhibited compromised regenerative spermatogenesis after chemical insult and early degenerative spermatogenesis in aging mice. These data demonstrate that maintaining proteostasis is important for spermatogenesis, of which ribosome homeostasis maintained by ribosomal proteins coordinates translation machinery to the regulation of cellular growth. Rpl39l deletion causes reduced spermatogenesis and subfertility in male mice SSC proliferation, mitochondria and sperm flagella compromised in Rpl39l–/– mice Rpl39l deletion affects ribosomal LSU formation and protein quality control Aberrant proteostasis affects spermatogenesis and regeneration
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Affiliation(s)
- Qianxing Zou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lele Yang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Yuling Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou 510630, China
| | - Huayu Qi
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510630, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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18
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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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In Leishmania major, the Homolog of the Oncogene PES1 May Play a Critical Role in Parasite Infectivity. Int J Mol Sci 2021; 22:ijms222212592. [PMID: 34830469 PMCID: PMC8618447 DOI: 10.3390/ijms222212592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 01/09/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease caused by Leishmania spp. The improvement of existing treatments and the discovery of new drugs remain ones of the major goals in control and eradication of this disease. From the parasite genome, we have identified the homologue of the human oncogene PES1 in Leishmania major (LmjPES). It has been demonstrated that PES1 is involved in several processes such as ribosome biogenesis, cell proliferation and genetic transcription. Our phylogenetic studies showed that LmjPES encodes a highly conserved protein containing three main domains: PES N-terminus (shared with proteins involved in ribosomal biogenesis), BRCT (found in proteins related to DNA repair processes) and MAEBL-type domain (C-terminus, related to erythrocyte invasion in apicomplexan). This gene showed its highest expression level in metacyclic promastigotes, the infective forms; by fluorescence microscopy assay, we demonstrated the nuclear localization of LmjPES protein. After generating mutant parasites overexpressing LmjPES, we observed that these clones displayed a dramatic increase in the ratio of cell infection within macrophages. Furthermore, BALB/c mice infected with these transgenic parasites exhibited higher footpad inflammation compared to those inoculated with non-overexpressing parasites.
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20
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Wu W, Yu N, Li F, Gao P, Lin S, Zhu Y. RPL35 promotes neuroblastoma progression via the enhanced aerobic glycolysis. Am J Cancer Res 2021; 11:5701-5714. [PMID: 34873488 PMCID: PMC8640819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023] Open
Abstract
Neuroblastoma (NB) is an rare type of tumor that almost affects children age 5 or younger due to its rapid proliferation ability. The overall survival rate of patients with advanced NB is not satisfactory. Ribosomal proteins (RPs) play a critical role in the development and progress of cancer. However, the contribution of RPL35 in NB has not been proven. In this study, we reveal that RPL35 is upregulated in NB tissues and the upregulation of RPL35 promotes proliferation and migration of NB while RPL35 knockdown significantly restrained the proliferation of NB cells. In terms of mechanism, glycolysis was decreased and the mitochondrial respiration was increased with knockdown of RPL35 in NB cells, indicating that RPL35 function as a positive regulator in aerobic glycolysis. Importantly, our data indicated that RPL35 deficiency decreased HIF1α expression both in mRNA and protein levels. Western blot analysis showed that RPL35 knockdown has a negative regulatory effect on the ERK pathway, and RPL35 modulated aerobic glycolysis in part through its regulation of the RPL35/ERK/HIF1α axis. Overall, RPL35 functions as a positive regulator of aerobic glycolysis, and the RPL35/ERK/HIF1α axis could be a potential therapeutic target for the therapy of NB.
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Affiliation(s)
- Weidong Wu
- Department of Thoracic Surgery, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China,Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
| | - Nanding Yu
- Department of Thoracic Surgery, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China,Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
| | - Feng Li
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medical and Health Key Laboratory of NeurosurgeryJinan 250014, Shandong, China
| | - Pengqiang Gao
- Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
| | - Shiyu Lin
- Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
| | - Yong Zhu
- Department of Thoracic Surgery, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China,Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical UniversityFuzhou 350122, Fujian, China
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21
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Webster MW, Weixlbaumer A. Macromolecular assemblies supporting transcription-translation coupling. Transcription 2021; 12:103-125. [PMID: 34570660 DOI: 10.1080/21541264.2021.1981713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Coordination between the molecular machineries that synthesize and decode prokaryotic mRNAs is an important layer of gene expression control known as transcription-translation coupling. While it has long been known that translation can regulate transcription and vice-versa, recent structural and biochemical work has shed light on the underlying mechanistic basis. Complexes of RNA polymerase linked to a trailing ribosome (expressomes) have been structurally characterized in a variety of states at near-atomic resolution, and also directly visualized in cells. These data are complemented by recent biochemical and biophysical analyses of transcription-translation systems and the individual components within them. Here, we review our improved understanding of the molecular basis of transcription-translation coupling. These insights are discussed in relation to our evolving understanding of the role of coupling in cells.
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Affiliation(s)
- Michael W Webster
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
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Fang Y, Zong Q, He Z, Liu C, Wang YF. Knockdown of RpL36 in testes impairs spermatogenesis in Drosophila melanogaster. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:417-430. [PMID: 33734578 DOI: 10.1002/jez.b.23040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/06/2021] [Accepted: 02/27/2021] [Indexed: 01/03/2023]
Abstract
Many ribosomal proteins (RPs) not only play essential roles in ribosome biogenesis, but also have "extraribosomal" functions in various cellular processes. RpL36 encodes ribosomal protein L36, a component of the 60S subunit of ribosomes in Drosophila melanogaster. We report here that RpL36 is required for spermatogenesis in D. melanogaster. After showing the evolutionary conservation of RpL36 sequences in animals, we revealed that the RpL36 expression level in fly testes was significantly higher than in ovaries. Knockdown RpL36 in fly testes resulted in a significantly decreased egg hatch rate when these males mated with wild-type females. Furthermore, 76.67% of the RpL36 knockdown fly testes were much smaller in comparison to controls. Immunofluorescence staining exhibited that in the RpL36 knockdown testis hub cell cluster was enlarged, while the number of germ cells, including germ stem cells, was reduced. Knockdown of RpL36 in fly testis caused much fewer or no mature sperms in seminal vesicles. The terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) signal was stronger in RpL36 knockdown fly testes than in the control testes, but the TUNEL-positive cells could not be stained by Vasa antibody, indicating that apoptotic cells are not germ cells. The percentage of pH3-positive cells among the Vasa-positive cells was significantly reduced. The expression of genes involved in cell death, cell cycle progression, and JAK/STAT signaling pathway was significantly changed by RpL36 knockdown in fly testes. These results suggest that RpL36 plays an important role in spermatogenesis, likely through JAK/STAT pathway, thus resulting in defects in cell-cycle progression and cell death in D. melanogaster testes.
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Affiliation(s)
- Yang Fang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Qiong Zong
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Zhen He
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
| | - Chen Liu
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Yu-Feng Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, China
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23
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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24
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Abstract
Production and expression of RNA requires the action of multiple RNA-binding proteins (RBPs). New RBPs are most often created by novel combinations of dedicated RNA-binding modules. However, recruiting existing genes to create new RBPs is also an important evolutionary strategy. In this report, we analyzed the eight-member uL18 ribosomal protein family in Arabidopsis uL18 proteins share a short structurally conserved domain that binds the 5S ribosomal RNA (rRNA) and allows its incorporation into ribosomes. Our results indicate that Arabidopsis uL18-Like proteins are targeted to either mitochondria or chloroplasts. While two members of the family are found in organelle ribosomes, we show here that two uL18-type proteins function as factors necessary for the splicing of certain mitochondrial and plastid group II introns. These two proteins do not cosediment with mitochondrial or plastid ribosomes but instead associate with the introns whose splicing they promote. Our study thus reveals that the RNA-binding capacity of uL18 ribosomal proteins has been repurposed to create factors that facilitate the splicing of organellar introns.
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25
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Yang Z, Wang M, Zeng X, Wan ATY, Tsui SKW. In silico analysis of proteins and microRNAs related to human African trypanosomiasis in tsetse fly. Comput Biol Chem 2020; 88:107347. [PMID: 32745971 DOI: 10.1016/j.compbiolchem.2020.107347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 04/10/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Human African trypanosomiasis (HAT), also known as sleeping sickness, causes millions of deaths worldwide. HAT is primarily transmitted by the vector tsetse fly (Glossina morsitans). Early diagnosis remains a key objective for treating this disease. MicroRNAs (miRNAs) are evolutionarily conserved small non-coding RNAs that play key roles in vector-borne diseases. To date, the roles of proteins and miRNAs in HAT disease have not been thoroughly elucidated. In this study, we have re-annotated the function of protein-coding genes and identified several miRNAs based on a series of bioinformatics tools. A batch of 81.1 % of tsetse fly proteins could be determined homology in mosquito genome, suggesting their probable similar mechanisms in vector-borne diseases. A set of 11 novel salivary proteins and 14 midgut proteins were observed in the tsetse fly, which could be applied to the development of vaccine candidates for the control of HAT disease. In addition, 35 novel miRNAs were identified, among which 10 miRNAs were found to be unique in tsetse fly. Pathway analysis of these 10 miRNAs indicated that targets of miR-15a-5p were significantly enriched in the HAT-related neurotrophin signaling pathway. Besides, topological analysis of the miRNA-gene network indicated that miR-619-5p and miR-2490-3p targeted several genes that respond to trypanosome infection, including thioester-containing protein Tep1 and heat shock protein Hsp60a. In conclusion, our work helps to elucidate the function of miRNAs in tsetse fly and establishes a foundation for further investigations into the molecular regulatory mechanisms of HAT disease.
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Affiliation(s)
- Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, PR China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong.
| | - Mingqiang Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Xi Zeng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Angel Tsz-Yau Wan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
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26
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Li C, Ge M, Chen D, Sun T, Jiang H, Xie Y, Lu H, Zhang B, Han L, Chen J, Zhu J. RPL21 siRNA Blocks Proliferation in Pancreatic Cancer Cells by Inhibiting DNA Replication and Inducing G1 Arrest and Apoptosis. Front Oncol 2020; 10:1730. [PMID: 33014855 PMCID: PMC7509406 DOI: 10.3389/fonc.2020.01730] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our previous study showed that the ribosomal protein L21 (RPL21) may play an important role in the development and survival of pancreatic cancer. In this article, RNA interference (RNAi) experiments were performed with RPL21-specific small interfering RNA (siRNA) to elucidate the mechanism by which RPL21 controls PC PANC-1 and BxPC-3 cell proliferation. Methods In the present study, PANC-1, BxPC-3 cells, and BALB/c nude mice were used to investigate antitumor effect and mechanism by which RPL21 controls cell proliferation and apoptosis in vitro and in vivo. The effects of RPL21 knockdown on PANC-1 and BxPC-3 cell proliferation, cell cycle and cell apoptosis in vitro were determined using 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assays and flow cytometry assay. The mechanism of RPL21 regulating cell proliferation was investigated using transcriptome sequencing analysis and luciferase reporter assay. The effects of RPL21 knockdown on PANC-1 and BxPC-3 cell proliferation in vivo were determined using BALB/c nude mice tumor model. Results In PANC-1 and BxPC-3 cells, the knockdown of RPL21 expression with corresponding siRNA suppressed cell proliferation in vitro and in vivo, inhibited DNA replication, and induced arrests in the G1 phase of the cell cycle. Further results showed that the mini-chromosome maintenance (MCM) protein family (MCM2-7), CCND1 and CCNE1 were down-regulated significantly in PANC-1 and BxPC-3 cells after transfected with RPL21 siRNA, which suggests that the suppression of DNA replication is due to the reduced expression of MCM2-7 family, and the induction of G1 arrest is correlated with the inhibition of CCND1 and CCNE1. Luciferase reporter assay showed that RPL21 controls the DNA replication and G1-S phase progression possibly through the regulation of E2F1 transcription factor in PC cells. Moreover, RPL21 siRNA showed an apoptosis-inducing effect only in BxPC-3 and PANC-1 cells but not in normal HPDE6-C7 cells. The increase of caspase-8 activities and the loss of mitochondrial membrane potential after RPL21 silencing indicates that the RPL21 gene may be involved in caspase-8-related mitochondrial apoptosis. Conclusion Our findings suggest that siRNA against the RPL21 gene possesses a potential anti-cancer activity for PC cells by inhibiting their proliferation and DNA replication, as well as inducing cell cycle G1 arrest and cell apoptosis.
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Affiliation(s)
- Chaodong Li
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Jecho Biopharmaceuticals Co., Ltd., Tianjin, China
| | - Mei Ge
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Daijie Chen
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,China State Institute of Pharmaceutical Industry, Shanghai, China
| | - Tao Sun
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Jiang
- Jecho Laboratories, Inc., Frederick, MD, United States
| | - Yueqing Xie
- Jecho Laboratories, Inc., Frederick, MD, United States
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Baohong Zhang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Han
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Jecho Biopharmaceuticals Co., Ltd., Tianjin, China
| | - Junsheng Chen
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Jecho Biopharmaceuticals Co., Ltd., Tianjin, China.,Jecho Laboratories, Inc., Frederick, MD, United States
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27
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Qian J, Xu L, Yu W, Gu X, Zuo Y, Chen Y, Xie F, Wei L. Ribosomal protein L34 is a potential prognostic biomarker and therapeutic target in hilar cholangiocarcinoma. Cell Biosci 2020. [DOI: 10.1186/s13578-020-00463-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Ribosomal protein 34 (RPL34) is a highly conserved protein belonging to the 60S large subunit of mammalian ribosomes that has been found to be dysregulated in a variety of human tumors. However, there are limited results that illuminate the role and expression profiles of RPL34 in hilar cholangiocarcinoma (HCCA).
Methods
RPL34 expression was detected in human HCCA by immunohistochemistry. The relationship of RPL34 expression with clinical outcomes was evaluated by univariate and multivariate analyses. The effect of RPL34 on cell migration and tumor growth was detected after silencing endogenous RPL34 expression.
Results
RPL34 was overexpressed in HCCA compared with normal tissue samples and correlated significantly with regional lymph node metastasis and poorly/undifferentiated tumors. Patients with high RPL34 expression had a shorter time to recur and a poorer outcome than those without RPL34 expression. Silencing RPL34 inhibited cell proliferation and migration in vitro and upregulated E-cadherin. Silencing RPL34 also attenuated tumor growth in vivo.
Conclusions
Our findings suggested that RPL34 might serve as a promising prognostic biomarker and a potential therapeutic target for the treatment of HCCA.
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28
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Gershman BW, Pritchard CE, Chaney KP, Ware VC. Tissue-specific expression of ribosomal protein paralogue eRpL22-like in Drosophila melanogaster eye development. Dev Dyn 2020; 249:1147-1165. [PMID: 32353187 PMCID: PMC8109839 DOI: 10.1002/dvdy.185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Differences in core or tissue-specific ribosomal protein (Rp) composition within ribosomes contribute to ribosome heterogeneity and functional variability. Yet, the degree to which ribosome heterogeneity modulates development is unknown. The Drosophila melanogaster eRpL22 family contains structurally diverse paralogues, eRpL22 and eRpL22-like. Unlike ubiquitously expressed eRpL22, eRpL22-like expression is tissue-specific, notably within the male germline and the eye. We investigated expression within the developing eye to uncover tissue/cell types where specific paralogue roles might be defined. RESULTS Immunohistochemistry analysis confirms ubiquitous eRpL22 expression throughout eye development. In larvae, eRpL22-like is ubiquitously expressed, but highly enriched in the peripodial epithelium (PE). In early pupae, eRpL22-like is broadly distributed in multiple cell types, but later, is primarily enriched in interommatidial hair cells (IoHC). Adult patterns include the ring of accessory cells around ommatidia. Adult retinae IoHC patterning phenotypes (shown by scanning electron microscopy) may be linked to RNAi-mediated eRpL22-like depletion within larval PE. Immunoblots and polysome profile analyses show multiple variants of eRpL22-like across development, with the variant at the expected molecular mass co-sedimenting with active ribosomes. CONCLUSION Our data reveal differential patterns of eRpL22-like expression relative to eRpL22 and suggest a specific role for eRpL22-like in developmental patterning of the eye.
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Affiliation(s)
- Brett W. Gershman
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | | | - Kenneth P. Chaney
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
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29
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Petelski AA, Slavov N. Analyzing Ribosome Remodeling in Health and Disease. Proteomics 2020; 20:e2000039. [PMID: 32820594 PMCID: PMC7501214 DOI: 10.1002/pmic.202000039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Indexed: 12/24/2022]
Abstract
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, evidence is reviewed demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus protein remodeling of ribosomes should be investigated by methods that allow direct quantification of RPs, ideally of isolated ribosomes. Such methods are reviewed, focusing on mass spectrometry and emphasizing method-specific biases and approaches to control these biases. It is argued that using multiple complementary methods can help reduce the danger of interpreting reproducible systematic biases as evidence for ribosome remodeling.
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Affiliation(s)
- Aleksandra A Petelski
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
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30
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Zafar A, Jabbar M, Manzoor Y, Gulzar H, Hassan SG, Nazir MA, Ain-ul-Haq, Mustafa G, Sahar R, Masood A, Iqbal A, Hussain M, Hasan M. Quantifying Serum Derived Differential Expressed and Low Molecular Weight Protein in Breast Cancer Patients. Protein Pept Lett 2020; 27:658-673. [DOI: 10.2174/0929866527666200110155609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/29/2022]
Abstract
Background:Searching the biomarker from complex heterogeneous material for early detection of disease is a challenging task in the field of biomedical sciences.Objective:The study has been arranged to explore the proteomics serum derived profiling of the differential expressed and low molecular weight protein in breast cancer patient.Methods:Quantitative proteome was analyzed using the Nano LC/Mass and Bioinformatics tool.Results:This quantification yields 239 total protein constituting 29% of differentially expressed protein, with 82% downregulated differential protein and 18% up-regulated differential protein. While 12% of total protein were found to be cancer inducing proteins. Gene Ontology (GO) described that the altered proteins with 0-60 kDa mass in nucleus, cytosol, ER, and mitochondria were abundant that chiefly controlled the RNA, DNA, ATP, Ca ion and receptor bindings.Conclusion:The study demonstrate that the organelle specific, low molecular weighted proteins are significantly important biomarker. That act as strong agents in the prognosis and diagnosis of breast cancer at early stage.
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Affiliation(s)
- Ayesha Zafar
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Maryum Jabbar
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasmeen Manzoor
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Huma Gulzar
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Shahzad Gul Hassan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Muniba Anum Nazir
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Ain-ul-Haq
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Ghazala Mustafa
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Romana Sahar
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Aqeel Masood
- Bahawal Victoria Hospital, Bahawalpur (BVH), Pakistan
| | | | - Mulazim Hussain
- Department of Pediatrician, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Murtaza Hasan
- Department of Biochemistry & Biotechnology (Baghdad-ul-Jadeed Campus), Faculty of Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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31
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Molavi G, Samadi N, Hashemzadeh S, Halimi M, Hosseingholi EZ. Moonlight human ribosomal protein L13a downregulation is associated with p53 and HER2/neu expression in breast cancer. J Appl Biomed 2020; 18:46-53. [PMID: 34907725 DOI: 10.32725/jab.2020.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common malignancy among females worldwide. Recent studies have shown extra-ribosomal roles of the moonlight ribosomal proteins in the development of human cancers. Accurate quantification of the gene expression level is based on the selection of the reference genes whose expression is independent of cancer properties and patient's characteristics. The aim of this study was the evaluation of the expression level of a previously proposed ribosomal protein as moonlight, L13a (RPL13A), in breast cancer samples and their adjacent tissues. Its association with genes of known roles in developing cancers was also investigated. Traditionally used housekeeping genes were selected and their expression was analyzed in 80 surgically excised breast tissue specimens (40 tumors and 40 tumor-adjacent tissues) by applying three software tools including GeNorm, NormFinder, and BestKeeper to select the most stable reference genes. Then, mRNA expression levels of RPL13A and p53 were evaluated. Additionally, protein expression levels of RPL13A were measured. It was demonstrated that PUM1 and ACTB are the most reliable reference genes and RPL13A is the least stable gene. There was a positive correlation between RPL13A and p53 mRNA expression levels in all the tumor samples. Moreover, significant downregulation of RPL13A expression levels was revealed in HER2+ tumor samples compared to HER2- ones. There was also a marked decrease in p53 mRNA expression levels in HER2+ tumor subtypes. Our results suggest that there is a probable relationship between RPL13A decreased expression with p53 and HER2/neu expression in the breast cancer.
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Affiliation(s)
- Ghader Molavi
- Tabriz University of Medical Sciences, Drug Applied Research Center, Tabriz, Iran.,Tabriz University of Medical Sciences, Faculty of Advanced Medical Sciences, Department of Molecular Medicine, Tabriz, Iran
| | - Nasser Samadi
- Tabriz University of Medical Sciences, Drug Applied Research Center, Tabriz, Iran.,Tabriz University of Medical Sciences, Faculty of Advanced Medical Sciences, Department of Molecular Medicine, Tabriz, Iran.,Tabriz University of Medical Sciences, Faculty of Medicine, Department of Biochemistry, Tabriz, Iran
| | - Shahriar Hashemzadeh
- Tabriz University of Medical Sciences, Tuberculosis and Lung Disease Research Center, Tabriz, Iran.,Tabriz University of Medical Sciences, Imam Reza Hospital, General and Vascular Surgery Department, Tabriz, Iran
| | - Monireh Halimi
- Tabriz University of Medical Sciences, School of Medicine, Department of Pathology, Tabriz, Iran
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32
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Tsuchimatsu T, Kakui H, Yamazaki M, Marona C, Tsutsui H, Hedhly A, Meng D, Sato Y, Städler T, Grossniklaus U, Kanaoka MM, Lenhard M, Nordborg M, Shimizu KK. Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana. Nat Commun 2020; 11:2885. [PMID: 32514036 PMCID: PMC7280297 DOI: 10.1038/s41467-020-16679-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/19/2020] [Indexed: 11/08/2022] Open
Abstract
The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures of selection, indicating polygenic selection. We isolate the gene REDUCED POLLEN NUMBER1 (RDP1) at the locus with the strongest association. We validate its effect using a quantitative complementation test with CRISPR/Cas9-generated null mutants in nonstandard wild accessions. In contrast to pleiotropic null mutants, only pollen numbers are significantly affected by natural allelic variants. These data support theoretical predictions that reduced investment in male gametes is advantageous in predominantly selfing species.
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Affiliation(s)
- Takashi Tsuchimatsu
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
- Department of Biology, Chiba University, Chiba, 263-8522, Japan
- Department of Biological Sciences, University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Misako Yamazaki
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
| | - Cindy Marona
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Hiroki Tsutsui
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, 464-8602, Japan
| | - Afif Hedhly
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Yutaka Sato
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Thomas Städler
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland.
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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Banerjee A, Kulkarni S, Mukherjee A. Herpes Simplex Virus: The Hostile Guest That Takes Over Your Home. Front Microbiol 2020; 11:733. [PMID: 32457704 PMCID: PMC7221137 DOI: 10.3389/fmicb.2020.00733] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Alpha (α)-herpesviruses (HSV-1 and HSV-2), like other viruses, are obligate intracellular parasites. They hijack the cellular machinery to survive and replicate through evading the defensive responses by the host. The viral genome of herpes simplex viruses (HSVs) contains viral genes, the products of which are destined to exploit the host apparatus for their own existence. Cellular modulations begin from the entry point itself. The two main gateways that the virus has to penetrate are the cell membrane and the nuclear membrane. Changes in the cell membrane are triggered when the glycoproteins of HSV interact with the surface receptors of the host cell, and from here, the components of the cytoskeleton take over. The rearrangement in the cytoskeleton components help the virus to enter as well as transport to the nucleus and back to the cell membrane to spread out to the other cells. The entire carriage process is also mediated by the motor proteins of the kinesin and dynein superfamily and is directed by the viral tegument proteins. Also, the virus captures the cell’s most efficient cargo carrying system, the endoplasmic reticulum (ER)–Golgi vesicular transport machinery for egress to the cell membrane. For these reasons, the host cell has its own checkpoints where the normal functions are halted once a danger is sensed. However, a cell may be prepared for the adversities from an invading virus, and it is simply commendable that the virus has the antidote to these cellular strategies as well. The HSV viral proteins are capable of limiting the use of the transcriptional and translational tools for the cell itself, so that its own transcription and translation pathways remain unhindered. HSV prefers to constrain any self-destruction process of the cell—be it autophagy in the lysosome or apoptosis by the mitochondria, so that it can continue to parasitize the cell for its own survival. This review gives a detailed account of the significance of compartmentalization during HSV pathogenesis. It also highlights the undiscovered areas in the HSV cell biology research which demand attention for devising improved therapeutics against the infection.
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Affiliation(s)
- Anwesha Banerjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Smita Kulkarni
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
| | - Anupam Mukherjee
- Division of Virology, Indian Council of Medical Research-National AIDS Research Institute, Pune, India
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de Lima PM, Vieira JCS, Cavecci-Mendonça B, Fleuri LF, de Lima Leite A, Buzalaf MAR, Pezzato LE, Braga CP, de Magalhães Padilha P. Identification of Zinc Absorption Biomarkers in Muscle Tissue of Nile Tilapia Fed with Organic and Inorganic Sources of Zinc Using Metallomics Analysis. Biol Trace Elem Res 2020; 194:259-272. [PMID: 31172428 DOI: 10.1007/s12011-019-01765-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/27/2019] [Indexed: 10/26/2022]
Abstract
The development of metallomics techniques has allowed for metallomics analysis of biological systems, enabling a better understanding of the response mechanisms for different stimuli, their relationship to metallic species, and the characterization of biomarkers. In this study, a metallomics analysis of the muscle tissue of Nile tilapia was used to aid the understanding of the molecular mechanisms involved in zinc absorption in this fish species when fed organic and/or inorganic sources of zinc and to identify possible biomarkers for the absorption of this micromineral. To accomplish this, the fish were separated into three groups of 24 g, 74 g, and 85 g initial weights, and each group, respectively, was fed a zinc-free diet (control group, G1), a diet containing zinc found in organic sources (treatment 1, G2), and a diet containing zinc from an inorganic source (treatment 2, G3). Two-dimensional polyacrylamide (2D PAGE) gel electrophoresis was used to separate the proteins of the muscle tissue. Subsequently, the expression profiles of protein spots in the samples where zinc was applied in different concentrations were compared, using the software ImageMaster 2D Platinum version 7.0, to identify proteins that were differentially expressed. The identified proteins were then exposed to atomic absorption spectrometry in a graphite furnace to determine zinc mapping and were subsequently characterized via electrospray ionization tandem mass spectrometry (ESI-MS/MS). The metallomic analysis identified 15 proteins differentially expressed and associated with zinc, leading to the conclusion that three metal-binding proteins presented as possible biomarkers of zinc absorption in fish.
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Affiliation(s)
- Paula Monteiro de Lima
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - José Cavalcante Souza Vieira
- Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
- Federal University of Mato Grosso do Sul (UFMS), Campo Grande, Brazil.
| | - Bruna Cavecci-Mendonça
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Aline de Lima Leite
- Biochemistry Department, São Paulo University (USP), Bauru, São Paulo, Brazil
| | | | - Luiz Edivaldo Pezzato
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Pedro de Magalhães Padilha
- School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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Gowda R, Robertson BM, Iyer S, Barry J, Dinavahi SS, Robertson GP. The role of exosomes in metastasis and progression of melanoma. Cancer Treat Rev 2020; 85:101975. [PMID: 32050108 DOI: 10.1016/j.ctrv.2020.101975] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022]
Abstract
The mechanisms of melanoma metastasis have been the subject of extensive research for decades. Improved diagnostic and therapeutic strategies are of increasing importance for the treatment of melanoma due to its high burden of mortality in the advanced stages of the disease. Intercellular communication is a critical event for the progression of cancer. Collective evidence suggests that exosomes, small extracellular membrane vesicles released by the cells, are important facilitators of intercellular communication between the cells and the surrounding environment. Although the emerging field of exosomes is rapidly gaining traction in the scientific community, there is limited knowledge regarding the role of exosomes in melanoma. This review discusses the multifaceted role of melanoma-derived exosomes in promoting the process of metastasis by modulating the invasive and angiogenic capacity of malignant cells. The future implications of exosome research and the therapeutic potential of exosomes are also discussed.
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Affiliation(s)
- Raghavendra Gowda
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Foreman Foundation for Melanoma Research, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Bailey M Robertson
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Soumya Iyer
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - John Barry
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Saketh S Dinavahi
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Gavin P Robertson
- Departments of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Departments of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Departments of Dermatology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Departments of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Penn State Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States; Foreman Foundation for Melanoma Research, The Pennsylvania State University College of Medicine, Hershey, PA 17033, United States.
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Sun W, Zhu Q, Yan L, Shao F. Mesenchymal stem cells alleviate acute kidney injury via miR-107-mediated regulation of ribosomal protein S19. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:765. [PMID: 32042781 DOI: 10.21037/atm.2019.11.89] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background The characteristics of mesenchymal stem cells (MSCs) in the repair of acute kidney injury (AKI) have been extensively studied. However, some potential molecular mechanisms remain indistinct. The aim of this study was to combine published microRNA (miRNA) transcriptional profiling with quantitative proteomic analyses to reveal specific miRNAs or genes for MSC-based therapy in AKI. Methods Transcriptome data containing significantly changed miRNAs in renal tissue from AKI mice treated with and without MSCs were downloaded. Proteomics resources were downloaded from a human proximal renal tubule cell line (HK-2) that served as a good in vitro model for AKI treated with MSCs. We connected the proteomics data with transcriptional records based on miRNA function. Differentially expressed genes (DEGs) were sorted. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted, and protein-protein interaction (PPI) chains were formed. The genes identified in the analyses were verified in a cisplatin-induced AKI rat model and in HK-2 cells exposed to cisplatin and cocultured with MSCs. Results A total of 207 specific DEGs were sorted. The ribosomal pathway was identified in pathway enrichment, and ribosomal proteins were identified from the PPI network complex. The targeting of the microRNAs, miR-107 to RPS19, was directly verified by the dual-luciferase method. miR-107 knockdown induced RPS19 expression, protected HK-2 cells from cisplatin-induced apoptosis, and promoted cell proliferation. Conclusions By analyzing comprehensive bioinformatics data, we have confirmed the DEGs and pathways in AKI treated with MSCs. Bone marrow-derived MSCs reduce miR-107 expression and increase RPS19 expression by repressing the proliferation of cisplatin-induced AKI cells and initiating apoptosis.
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Affiliation(s)
- Weinan Sun
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Qing Zhu
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Lei Yan
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
| | - Fengmin Shao
- Department of Nephrology, People's Hospital of Zhengzhou University, He'nan Provincial People's Hospital, He'nan Provincial Key Laboratory of Kidney Disease and Immunology, Zhengzhou 450003, China
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Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging. Proc Natl Acad Sci U S A 2019; 116:22567-22572. [PMID: 31636180 DOI: 10.1073/pnas.1912060116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Across phyla, the ribosomes-the central molecular machines for translation of genetic information-exhibit an overall preserved architecture and a conserved functional core. The natural heterogeneity of the ribosome periodically phases a debate on their functional specialization and the tissue-specific variations of the ribosomal protein (RP) pool. Using sensitive differential proteomics, we performed a thorough quantitative inventory of the protein composition of ribosomes from 3 different mouse brain tissues, i.e., hippocampus, cortex, and cerebellum, across various ages, i.e., juvenile, adult, and middle-aged mouse groups. In all 3 brain tissues, in both monosomal and polysomal ribosome fractions, we detected an invariant set of 72 of 79 core RPs, RACK1 and 2 of the 8 RP paralogs, the stoichiometry of which remained constant across different ages. The amount of a few RPs punctually varied in either one tissue or one age group, but these fluctuations were within the tight bounds of the measurement noise. Further comparison with the ribosomes from a high-metabolic-rate organ, e.g., the liver, revealed protein composition identical to that of the ribosomes from the 3 brain tissues. Together, our data show an invariant protein composition of ribosomes from 4 tissues across different ages of mice and support the idea that functional heterogeneity may arise from factors other than simply ribosomal protein stoichiometry.
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Bi X, van Esse W, Mulki MA, Kirschner G, Zhong J, Simon R, von Korff M. CENTRORADIALIS Interacts with FLOWERING LOCUS T-Like Genes to Control Floret Development and Grain Number. PLANT PHYSIOLOGY 2019; 180:1013-1030. [PMID: 31004004 PMCID: PMC6548242 DOI: 10.1104/pp.18.01454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/08/2019] [Indexed: 05/20/2023]
Abstract
CENTRORADIALIS (CEN) is a key regulator of flowering time and inflorescence architecture in plants. Natural variation in the barley (Hordeum vulgare) homolog HvCEN is important for agricultural range expansion of barley cultivation, but its effects on shoot and spike architecture and consequently yield have not yet been characterized. Here, we evaluated 23 independent hvcen, also termed mat-c, mutants to determine the pleiotropic effects of HvCEN on developmental timing and shoot and spike morphologies of barley under outdoor and controlled conditions. All hvcen mutants flowered early and showed a reduction in spikelet number per spike, tiller number, and yield in the outdoor experiments. Mutations in hvcen accelerated spikelet initiation and reduced axillary bud number in a photoperiod-independent manner but promoted floret development only under long days (LDs). The analysis of a flowering locus t3 (hvft3) hvcen double mutant showed that HvCEN interacts with HvFT3 to control spikelet initiation. Furthermore, early flowering3 (hvelf3) hvcen double mutants with high HvFT1 expression levels under short days suggested that HvCEN interacts with HvFT1 to repress floral development. Global transcriptome profiling in developing shoot apices and inflorescences of mutant and wild-type plants revealed that HvCEN controlled transcripts involved in chromatin remodeling activities, cytokinin and cell cycle regulation and cellular respiration under LDs and short days, whereas HvCEN affected floral homeotic genes only under LDs. Understanding the stage and organ-specific functions of HvCEN and downstream molecular networks will allow the manipulation of different shoot and spike traits and thereby yield.
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Affiliation(s)
- Xiaojing Bi
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Wilma van Esse
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mohamed Aman Mulki
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Gwendolyn Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Jinshun Zhong
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
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Li S. Regulation of Ribosomal Proteins on Viral Infection. Cells 2019; 8:E508. [PMID: 31137833 PMCID: PMC6562653 DOI: 10.3390/cells8050508] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Ribosomal proteins (RPs), in conjunction with rRNA, are major components of ribosomes involved in the cellular process of protein biosynthesis, known as "translation". The viruses, as the small infectious pathogens with limited genomes, must recruit a variety of host factors to survive and propagate, including RPs. At present, more and more information is available on the functional relationship between RPs and virus infection. This review focuses on advancements in my own understanding of critical roles of RPs in the life cycle of viruses. Various RPs interact with viral mRNA and proteins to participate in viral protein biosynthesis and regulate the replication and infection of virus in host cells. Most interactions are essential for viral translation and replication, which promote viral infection and accumulation, whereas the minority represents the defense signaling of host cells by activating immune pathway against virus. RPs provide a new platform for antiviral therapy development, however, at present, antiviral therapeutics with RPs involving in virus infection as targets is limited, and exploring antiviral strategy based on RPs will be the guides for further study.
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Affiliation(s)
- Shuo Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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Pawłowski K, Pires JAA, Faulconnier Y, Chambon C, Germon P, Boby C, Leroux C. Mammary Gland Transcriptome and Proteome Modifications by Nutrient Restriction in Early Lactation Holstein Cows Challenged with Intra-Mammary Lipopolysaccharide. Int J Mol Sci 2019; 20:E1156. [PMID: 30845783 PMCID: PMC6429198 DOI: 10.3390/ijms20051156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 11/27/2022] Open
Abstract
: The objective is to study the effects of nutrient restrictions, which induce a metabolic imbalance on the inflammatory response of the mammary gland in early lactation cows. The aim is to decipher the molecular mechanisms involved, by comparing a control, with a restriction group, a transcriptome and proteome, after an intra-mammary lipopolysaccharide challenge. Multi-parous cows were either allowed ad libitum intake of a lactation diet (n = 8), or a ration containing low nutrient density (n = 8; 48% barley straw and dry matter basis) for four days starting at 24 ± 3 days in milk. Three days after the initiation of their treatments, one healthy rear mammary quarter of 12 lactating cows was challenged with 50 µg of lipopolysaccharide (LPS). Transcriptomic and proteomic analyses were performed on mammary biopsies obtained 24 h after the LPS challenge, using bovine 44K microarrays, and nano-LC-MS/MS, respectively. Restriction-induced deficits in energy, led to a marked negative energy balance (41 versus 97 ± 15% of Net Energy for Lactation (NEL) requirements) and metabolic imbalance. A microarray analyses identified 25 differentially expressed genes in response to restriction, suggesting that restriction had modified mammary metabolism, specifically β-oxidation process. Proteomic analyses identified 53 differentially expressed proteins, which suggests that the modification of protein synthesis from mRNA splicing to folding. Under-nutrition influenced mammary gland expression of the genes involved in metabolism, thereby increasing β-oxidation and altering protein synthesis, which may affect the response to inflammation.
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Affiliation(s)
- Karol Pawłowski
- Université Clermont Auvergne,INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences,02-776 Warsaw, Poland.
| | - José A A Pires
- Université Clermont Auvergne,INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
| | - Yannick Faulconnier
- Université Clermont Auvergne,INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
| | - Christophe Chambon
- INRA, INRA, Plateforme d'Exploration du Métabolisme, composante protéomique PFEMcp), F-63122 Saint-Genès Champanelle, France.
| | - Pierre Germon
- INRA Val de Loire, UMR ISP, F-37380 Nouzilly, France.
| | - Céline Boby
- Université Clermont Auvergne,INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
| | - Christine Leroux
- Université Clermont Auvergne,INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France.
- Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA.
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Liu CW, Chi L, Tu P, Xue J, Ru H, Lu K. Quantitative proteomics reveals systematic dysregulations of liver protein metabolism in sucralose-treated mice. J Proteomics 2019; 196:1-10. [DOI: 10.1016/j.jprot.2019.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/26/2018] [Accepted: 01/13/2019] [Indexed: 12/19/2022]
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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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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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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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The uL10 protein, a component of the ribosomal P-stalk, is released from the ribosome in nucleolar stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:34-47. [DOI: 10.1016/j.bbamcr.2017.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 09/20/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
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QTL analysis of cocoon shell weight identifies BmRPL18 associated with silk protein synthesis in silkworm by pooling sequencing. Sci Rep 2017; 7:17985. [PMID: 29269837 PMCID: PMC5740181 DOI: 10.1038/s41598-017-18277-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 12/07/2017] [Indexed: 01/17/2023] Open
Abstract
Mechanisms that regulate silk protein synthesis provide the basis for silkworm variety breeding and silk gland bioreactor optimization. Here, using the pooling sequencing-based methodology, we deciphered the genetic basis for the varied silk production in different silkworm strains. We identified 8 SNPs, with 6 on chromosome 11 and 1 each on chromosomes 22 and 23, that were linked with silk production. After conducting an association analysis between gene expression pattern, silk gland development and cocoon shell weight (CSW), BMGN011620 was found to be regulating silk production. BMGN011620 encodes the 60S ribosomal protein, L18, which is an indispensable component of the 60S ribosomal subunit; therefore we named it BmRPL18. Moreover, the clustering of linked SNPs on chromosome 11 and the analysis of differentially expressed genes reported in previous Omics studies indicated that the genes regulating silk protein synthesis may exhibit a clustering distribution in the silkworm genome. These results collectively advance our understanding of the regulation of silk production, including the role of ribosomal proteins and the clustered distribution of genes involved in silk protein synthesis.
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Jiang P, Hou Z, Bolin JM, Thomson JA, Stewart R. RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations. Toxicol Sci 2017; 159:251-265. [PMID: 28903495 PMCID: PMC6372217 DOI: 10.1093/toxsci/kfx129] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lead (Pb) is a well-known toxicant, especially for the developing nervous system, albeit the mechanism is largely unknown. In this study, we use time series RNA-seq to conduct a genome-wide survey of the transcriptome response of human embryonic stem cell-derived neural progenitor cells to lead treatment. Using a dynamic time warping algorithm coupled with statistical tests, we find that lead can either accelerate or decelerate the expression of specific genes during the time series. We further show that lead disrupts a neuron- and brain-specific splicing factor NOVA1 regulated splicing network. Using lead induced transcriptome change signatures, we predict several known and novel disease risks under lead exposure. The findings in this study will allow a better understanding of the mechanism of lead toxicity, facilitate the development of diagnostic biomarkers and treatment for lead exposure, and comprise a highly valuable resource for environmental toxicology. Our study also demonstrates that a human (embryonic stem) cell-derived system can be used for studying the mechanism of toxicants, which can be useful for drug or compound toxicity screens and safety assessment.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - Zhonggang Hou
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - Jennifer M. Bolin
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
| | - James A. Thomson
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin 53706
- Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106
| | - Ron Stewart
- Regenerative Biology Laboratory, Morgridge Institute for Research, Madison, Wisconsin 53707
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Pseudomonas aeruginosa cells attached to a surface display a typical proteome early as 20 minutes of incubation. PLoS One 2017; 12:e0180341. [PMID: 28678862 PMCID: PMC5498041 DOI: 10.1371/journal.pone.0180341] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/14/2017] [Indexed: 12/21/2022] Open
Abstract
Biofilms are present in all environments and often result in negative effects due to properties of the biofilm lifestyle and especially antibiotics resistance. Biofilms are associated with chronic infections. Controlling bacterial attachment, the first step of biofilm formation, is crucial for fighting against biofilm and subsequently preventing the persistence of infection. Thus deciphering the underlying molecular mechanisms involved in attachment could allow discovering molecular targets from it would be possible to develop inhibitors against bacterial colonization and potentiate antibiotherapy. To identify the key components and pathways that aid the opportunistic pathogen Pseudomonas aeruginosa in attachment we performed for the first time a proteomic analysis as early as after 20 minutes of incubation using glass wool fibers as a surface. We compared the protein contents of the attached and unattached bacteria. Using mass spectrometry, 3043 proteins were identified. Our results showed that, as of 20 minutes of incubation, using stringent quantification criteria 616 proteins presented a modification of their abundance in the attached cells compared to their unattached counterparts. The attached cells presented an overall reduced gene expression and characteristics of slow-growing cells. The over-accumulation of outer membrane proteins, periplasmic folding proteins and O-antigen chain length regulators was also observed, indicating a profound modification of the cell envelope. Consistently the sigma factor AlgU required for cell envelope homeostasis was highly over-accumulated in attached cells. In addition our data suggested a role of alarmone (p)ppGpp and polyphosphate during the early attachment phase. Furthermore, almost 150 proteins of unknown function were differentially accumulated in the attached cells. Our proteomic analysis revealed the existence of distinctive biological features in attached cells as early as 20 minutes of incubation. Analysis of some mutants demonstrated the interest of this proteomic approach in identifying genes involved in the early phase of adhesion to a surface.
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Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM. HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma. Cancer Metab 2017; 5:5. [PMID: 28680592 PMCID: PMC5496173 DOI: 10.1186/s40170-017-0167-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/25/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND A key feature of clear cell renal cell carcinoma (ccRCC) is the inactivation of the von Hippel-Lindau tumour suppressor protein (pVHL) that leads to the activation of hypoxia-inducible factor (HIF) pathway also in well-oxygenated conditions. Important regulator of HIF-α, prolyl hydroxylase PHD3, is expressed in high amounts in ccRCC. Although several functions and downstream targets for PHD3 in cancer have been suggested, the role of elevated PHD3 expression in ccRCC is not clear. METHODS To gain insight into the functions of high PHD3 expression in ccRCC, we used PHD3 knockdown by siRNA in 786-O cells under normoxic and hypoxic conditions and performed discovery mass spectrometry (LC-MS/MS) of the purified peptide samples. The LC-MS/MS results were analysed by label-free quantification of proteome data using a peptide-level expression-change averaging procedure and subsequent gene ontology enrichment analysis. RESULTS Our data reveals an intriguingly widespread effect of PHD3 knockdown with 91 significantly regulated proteins. Under hypoxia, the response to PHD3 silencing was wider than under normoxia illustrated by both the number of regulated proteins and by the range of protein expression levels. The main cellular functions regulated by PHD3 expression were glucose metabolism, protein translation and messenger RNA (mRNA) processing. PHD3 silencing led to downregulation of most glycolytic enzymes from glucose transport to lactate production supported by the reduction in extracellular acidification and lactate production and increase in cellular oxygen consumption rate. Moreover, upregulation of mRNA processing-related proteins and alteration in a number of ribosomal proteins was seen as a response to PHD3 silencing. Further studies on upstream effectors of the translational machinery revealed a possible role for PHD3 in regulation of mTOR pathway signalling. CONCLUSIONS Our findings suggest crucial involvement of PHD3 in the maintenance of key cellular functions including glycolysis and protein synthesis in ccRCC.
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Affiliation(s)
- Petra Miikkulainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Heidi Högel
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Krista Rantanen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Tomi Suomi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Department of Information Technology, Faculty of Mathematics and Natural Sciences, University of Turku, Vesilinnantie 5, 20520 Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Laura L. Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | - Panu M. Jaakkola
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
- Department of Medical Biochemistry, Faculty of Medicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
- Department of Oncology and Radiotherapy, Turku University Hospital, Hämeentie 11, 20520 Turku, Finland
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Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors. Mol Cell Biol 2016; 36:3019-3032. [PMID: 27697862 DOI: 10.1128/mcb.00303-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/15/2016] [Indexed: 01/05/2023] Open
Abstract
Protein arginine methyltransferase 3 (PRMT3) forms a stable complex with 40S ribosomal protein S2 (RPS2) and contributes to ribosome biogenesis. However, the molecular mechanism by which PRMT3 influences ribosome biogenesis and/or function still remains unclear. Using quantitative proteomics, we identified human programmed cell death 2-like (PDCD2L) as a novel PRMT3-associated protein. Our data suggest that RPS2 promotes the formation of a conserved extraribosomal complex with PRMT3 and PDCD2L. We also show that PDCD2L associates with 40S subunit precursors that contain a 3'-extended form of the 18S rRNA (18S-E pre-rRNA) and several pre-40S maturation factors. PDCD2L shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner using a leucine-rich nuclear export signal that is sufficient to direct the export of a reporter protein. Although PDCD2L is not required for the biogenesis and export of 40S ribosomal subunits, we found that PDCD2L-null cells accumulate free 60S ribosomal subunits, which is indicative of a deficiency in 40S subunit availability. Our data also indicate that PDCD2L and its paralog, PDCD2, function redundantly in 40S ribosomal subunit production. Our findings uncover the existence of an extraribosomal complex consisting of PDCD2L, RPS2, and PRMT3 and support a role for PDCD2L in the late maturation of 40S ribosomal subunits.
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