1
|
Cristiano L. The pseudogenes of eukaryotic translation elongation factors (EEFs): Role in cancer and other human diseases. Genes Dis 2022; 9:941-958. [PMID: 35685457 PMCID: PMC9170609 DOI: 10.1016/j.gendis.2021.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
The eukaryotic translation elongation factors (EEFs), i.e. EEF1A1, EEF1A2, EEF1B2, EEF1D, EEF1G, EEF1E1 and EEF2, are coding-genes that play a central role in the elongation step of translation but are often altered in cancer. Less investigated are their pseudogenes. Recently, it was demonstrated that pseudogenes have a key regulatory role in the cell, especially via non-coding RNAs, and that the aberrant expression of ncRNAs has an important role in cancer development and progression. The present review paper, for the first time, collects all that published about the EEFs pseudogenes to create a base for future investigations. For most of them, the studies are in their infancy, while for others the studies suggest their involvement in normal cell physiology but also in various human diseases. However, more investigations are needed to understand their functions in both normal and cancer cells and to define which can be useful biomarkers or therapeutic targets.
Collapse
|
2
|
Noorabadi MT, Masiello M, Taherkhani K, Zare R, Torbati M, Haidukowski M, Somma S, Logrieco AF, Moretti A, Susca A. Phylogeny and mycotoxin profile of Fusarium species isolated from sugarcane in Southern Iran. Microbiol Res 2021; 252:126855. [PMID: 34455360 DOI: 10.1016/j.micres.2021.126855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/05/2021] [Accepted: 08/21/2021] [Indexed: 11/26/2022]
Abstract
Sugarcane is an important crop in Southern Iran for agri-food, energy, and pharmaceutical industries. Among the pathogens that colonize sugarcane, mycotoxigenic Fusarium species are reason of serious concern for both their pathogenicity on plants and ability to produce harmful mycotoxins to humans and animals. We studied 104 Fusarium strains, selected within a wider Fusarium set isolated from sugarcane in Southern Iran, for molecular identification, phylogeny and mycotoxin analyses. Most of Fusarium strains belonged to Fusarium fujikuroi Species Complex (FFSC) and identified mainly as F. proliferatum, at minor extent as F. sacchari, and rarely as F. thapsinum, and F. verticillioides. Moreover, 14 strains identified as FFSC could not be assigned to any known species, although they were phylogenetically closely related to F. andiyazi, likely representing a new phylogenetic species. A subset of FFSC strains were analyzed for in vitro production of fumonisins (FBs), beauvericin (BEA), and enniatins (ENNs). Fusarium proliferatum strains produced FBs at high amount, and, at a lesser extent, BEA, and ENNs; F.sacchari produced only BEA and B ENNs at very low level; Fusarium sp. strains produced only B ENNs. The paper provides new insights on the genetic diversity of Fusarium species and their mycotoxin profile occurring on sugarcane in Iran.
Collapse
Affiliation(s)
- Maryam Tavakol Noorabadi
- Department of Plant Protection, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Mario Masiello
- National Research Council, Institute of Sciences of Food Production, Bari, Italy.
| | - Kourosh Taherkhani
- Sugarcane Research and Training Institute for the Development of Industries in Khuzestan, Ahvaz, Iran
| | - Rasoul Zare
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran
| | - Mohsen Torbati
- Department of Plant Protection, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Miriam Haidukowski
- National Research Council, Institute of Sciences of Food Production, Bari, Italy
| | - Stefania Somma
- National Research Council, Institute of Sciences of Food Production, Bari, Italy
| | | | - Antonio Moretti
- National Research Council, Institute of Sciences of Food Production, Bari, Italy
| | - Antonia Susca
- National Research Council, Institute of Sciences of Food Production, Bari, Italy
| |
Collapse
|
3
|
Argüello RJ, Reverendo M, Mendes A, Camosseto V, Torres AG, Ribas de Pouplana L, van de Pavert SA, Gatti E, Pierre P. SunRiSE - measuring translation elongation at single-cell resolution by means of flow cytometry. J Cell Sci 2018; 131:jcs.214346. [PMID: 29700204 DOI: 10.1242/jcs.214346] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/04/2018] [Indexed: 12/30/2022] Open
Abstract
The rate at which ribosomes translate mRNAs regulates protein expression by controlling co-translational protein folding and mRNA stability. Many factors regulate translation elongation, including tRNA levels, codon usage and phosphorylation of eukaryotic elongation factor 2 (eEF2). Current methods to measure translation elongation lack single-cell resolution, require expression of multiple transgenes and have never been successfully applied ex vivo Here, we show, by using a combination of puromycilation detection and flow cytometry (a method we call 'SunRiSE'), that translation elongation can be measured accurately in primary cells in pure or heterogenous populations isolated from blood or tissues. This method allows for the simultaneous monitoring of multiple parameters, such as mTOR or S6K1/2 signaling activity, the cell cycle stage and phosphorylation of translation factors in single cells, without elaborated, costly and lengthy purification procedures. We took advantage of SunRiSE to demonstrate that, in mouse embryonic fibroblasts, eEF2 phosphorylation by eEF2 kinase (eEF2K) mostly affects translation engagement, but has a surprisingly small effect on elongation, except after proteotoxic stress induction.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Rafael J Argüello
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France
| | - Marisa Reverendo
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France
| | - Andreia Mendes
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France
| | - Voahirana Camosseto
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France
| | - Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain.,Catalan Institute for Research and Advanced Studies (ICREA), P/Lluis Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Serge A van de Pavert
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France
| | - Evelina Gatti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France.,Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288, Marseille Cedex 9, France .,Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| |
Collapse
|
4
|
Pisani C, Onori A, Gabanella F, Delle Monache F, Borreca A, Ammassari-Teule M, Fanciulli M, Di Certo MG, Passananti C, Corbi N. eEF1Bγ binds the Che-1 and TP53 gene promoters and their transcripts. J Exp Clin Cancer Res 2016; 35:146. [PMID: 27639846 PMCID: PMC5027090 DOI: 10.1186/s13046-016-0424-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/10/2016] [Indexed: 11/25/2022] Open
Abstract
Background We have previously shown that the eukaryotic elongation factor subunit 1B gamma (eEF1Bγ) interacts with the RNA polymerase II (pol II) alpha-like subunit “C” (POLR2C), alone or complexed, in the pol II enzyme. Moreover, we demonstrated that eEF1Bγ binds the promoter region and the 3’ UTR mRNA of the vimentin gene. These events contribute to localize the vimentin transcript and consequentially its translation, promoting a proper mitochondrial network. Methods With the intent of identifying additional transcripts that complex with the eEF1Bγ protein, we performed a series of ribonucleoprotein immunoprecipitation (RIP) assays using a mitochondria-enriched heavy membrane (HM) fraction. Results Among the eEF1Bγ complexed transcripts, we found the mRNA encoding the Che-1/AATF multifunctional protein. As reported by other research groups, we found the tumor suppressor p53 transcript complexed with the eEF1Bγ protein. Here, we show for the first time that eEF1Bγ binds not only Che-1 and p53 transcripts but also their promoters. Remarkably, we demonstrate that both the Che-1 transcript and its translated product localize also to the mitochondria and that eEF1Bγ depletion strongly perturbs the mitochondrial network and the correct localization of Che-1. In a doxorubicin (Dox)-induced DNA damage assay we show that eEF1Bγ depletion significantly decreases p53 protein accumulation and slightly impacts on Che-1 accumulation. Importantly, Che-1 and p53 proteins are components of the DNA damage response machinery that maintains genome integrity and prevents tumorigenesis. Conclusions Our data support the notion that eEF1Bγ, besides its canonical role in translation, is an RNA-binding protein and a key player in cellular stress responses. We suggest for eEF1Bγ a role as primordial transcription/translation factor that links fundamental steps from transcription control to local translation. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0424-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cinzia Pisani
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Annalisa Onori
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161, Rome, Italy
| | - Francesca Gabanella
- CNR -Institute of Cell Biology and Neurobiology, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesca Delle Monache
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161, Rome, Italy
| | - Antonella Borreca
- CNR -Institute of Cell Biology and Neurobiology, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Martine Ammassari-Teule
- CNR -Institute of Cell Biology and Neurobiology, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Maurizio Fanciulli
- Department of Research, Advanced Diagnostic, and Technological Innovation, SAFU Laboratory, Regina Elena Cancer Institute, Rome, Italy
| | - Maria Grazia Di Certo
- CNR -Institute of Cell Biology and Neurobiology, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Claudio Passananti
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161, Rome, Italy
| | - Nicoletta Corbi
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161, Rome, Italy.
| |
Collapse
|
5
|
Spirin V, Runnel K, Vlasák J, Miettinen O, Põldmaa K. Species diversity in the Antrodia crassa group (Polyporales, Basidiomycota). Fungal Biol 2015; 119:1291-1310. [PMID: 26615751 DOI: 10.1016/j.funbio.2015.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/06/2015] [Accepted: 09/25/2015] [Indexed: 01/19/2023]
Abstract
Antrodia is a polyphyletic genus, comprising brown-rot polypores with annual or short-lived perennial resupinate, dimitic basidiocarps. Here we focus on species that are closely related to Antrodia crassa, and investigate their phylogeny and species delimitation using geographic, ecological, morphological and molecular data (ITS and LSU rDNA, tef1). Phylogenetic analyses distinguished four clades within the monophyletic group of eleven conifer-inhabiting species (five described herein): (1)A. crassa s. str. (boreal Eurasia), Antrodia cincta sp. nova (North America) and Antrodia cretacea sp. nova (holarctic), all three being characterized by inamyloid skeletal hyphae that dissolve quickly in KOH solution; (2) Antrodia ignobilis sp. nova, Antrodia sitchensis and Antrodia sordida from North America, and Antrodia piceata sp. nova (previously considered conspecific with A. sitchensis) from Eurasia, possessing amyloid skeletal hyphae; (3) Antrodia ladiana sp. nova from the southern part of the USA, Antrodia pinea from East Asia, and Antrodia ferox - so far known from subtropical North America, but here reported also from Eurasia. These three species have inamyloid hyphae and narrow basidiospores; (4) the North American Antrodia pini-cubensis, sharing similar morphological characters with A. pinea, forming a separate clade. The habitat data indicate that several species are threatened by intensive forestry.
Collapse
Affiliation(s)
- Viacheslav Spirin
- Botanical Unit (Mycology), Finnish Museum of Natural History, University of Helsinki, Unioninkatu 44, 00170 Helsinki, Finland
| | - Kadri Runnel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51015 Tartu, Estonia.
| | - Josef Vlasák
- Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Otto Miettinen
- Botanical Unit (Mycology), Finnish Museum of Natural History, University of Helsinki, Unioninkatu 44, 00170 Helsinki, Finland
| | - Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51015 Tartu, Estonia
| |
Collapse
|
6
|
Rai MK, Tiwari VV, Irinyi L, Kövics GJ. Advances in taxonomy of genus phoma: polyphyletic nature and role of phenotypic traits and molecular systematics. Indian J Microbiol 2014; 54:123-8. [PMID: 25320410 PMCID: PMC4188486 DOI: 10.1007/s12088-013-0442-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 11/24/2013] [Indexed: 11/24/2022] Open
Abstract
Phoma is a highly polyphyletic genus with its unclear species boundaries. The conventional system of identification is functional but it has its limitations. Besides morphological studies, chemotaxonomy, secondary metabolite and protein profiling have been assessed for the classification and identification of these fungi. Molecular datasets have provided a better outlook towards the phylogenetic and evolutionary trends of Phoma. Molecular markers such as ITS-rDNA, tubulin, actin, translation elongation factor have been widely used by the taxonomists to demarcate species. However, outcomes gained up till now represent preliminary step towards the study of Phoma systematics and a combined approach would be beneficial in the understanding of this polyphyletic group members. Lately, on the base of molecular phylogeny of the type species of the seven Phoma sections a new teleomorph family, Didymellaceae has been established, besides the Phaeosphaeriaceae related to sect. Paraphoma anamorphs, and the Leptosphaeriaceae to sect. Heterospora anamorphs. The estimated ratio is about 70 % of the recognized Phoma-like species can be associated with the Didymellaceae ascomycetous family.
Collapse
Affiliation(s)
- Mahendra Kumar Rai
- />Department of Biotechnology, S. G. B. Amravati University, Amravati, 444 602 Maharashtra India
| | - Vaibhav V. Tiwari
- />Department of Biotechnology, S. G. B. Amravati University, Amravati, 444 602 Maharashtra India
| | - László Irinyi
- />Plant Protection Institute, Debrecen University, P.O. Box 36, Debrecen, 4015 Hungary
| | - György János Kövics
- />Plant Protection Institute, Debrecen University, P.O. Box 36, Debrecen, 4015 Hungary
| |
Collapse
|