1
|
Martín-Villanueva S, Galmozzi CV, Ruger-Herreros C, Kressler D, de la Cruz J. The Beak of Eukaryotic Ribosomes: Life, Work and Miracles. Biomolecules 2024; 14:882. [PMID: 39062596 PMCID: PMC11274626 DOI: 10.3390/biom14070882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Ribosomes are not totally globular machines. Instead, they comprise prominent structural protrusions and a myriad of tentacle-like projections, which are frequently made up of ribosomal RNA expansion segments and N- or C-terminal extensions of ribosomal proteins. This is more evident in higher eukaryotic ribosomes. One of the most characteristic protrusions, present in small ribosomal subunits in all three domains of life, is the so-called beak, which is relevant for the function and regulation of the ribosome's activities. During evolution, the beak has transitioned from an all ribosomal RNA structure (helix h33 in 16S rRNA) in bacteria, to an arrangement formed by three ribosomal proteins, eS10, eS12 and eS31, and a smaller h33 ribosomal RNA in eukaryotes. In this review, we describe the different structural and functional properties of the eukaryotic beak. We discuss the state-of-the-art concerning its composition and functional significance, including other processes apparently not related to translation, and the dynamics of its assembly in yeast and human cells. Moreover, we outline the current view about the relevance of the beak's components in human diseases, especially in ribosomopathies and cancer.
Collapse
Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carla V. Galmozzi
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carmen Ruger-Herreros
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Dieter Kressler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland;
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| |
Collapse
|
2
|
Tang J, Sui Z, Li R, Xu Y, Xiang L, Fu S, Wei J, Cai X, Wu M, Zhang J, Chen W, Wei Y, Li G, Yang L. The Gβ-like protein Bcgbl1 regulates development and pathogenicity of the gray mold Botrytis cinerea via modulating two MAP kinase signaling pathways. PLoS Pathog 2023; 19:e1011839. [PMID: 38048363 PMCID: PMC10721196 DOI: 10.1371/journal.ppat.1011839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 12/14/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
The fungal Gβ-like protein has been reported to be involved in a variety of biological processes, such as mycelial growth, differentiation, conidiation, stress responses and infection. However, molecular mechanisms of the Gβ-like protein in regulating fungal development and pathogenicity are largely unknown. Here, we show that the Gβ-like protein gene Bcgbl1 in the gray mold fungus Botrytis cinerea plays a pivotal role in development and pathogenicity by regulating the mitogen-activated protein (MAP) kinases signaling pathways. The Bcgbl1 deletion mutants were defective in mycelial growth, sclerotial formation, conidiation, macroconidial morphogenesis, plant adhesion, and formation of infection cushions and appressorium-like structures, resulting in a complete loss of pathogenicity. Bcgbl1 interacted with BcSte50, the adapter protein of the cascade of MAP kinase (MAPK). Bcgbl1 mutants had reduced phosphorylation levels of two MAPKs, namely Bmp1 and Bmp3, thereby reducing infection. However, deletion of Bcgbl1 did not affect the intracellular cAMP level, and exogenous cAMP could not restore the defects. Moreover, Bcgbl1 mutants exhibited defects in cell wall integrity and oxidative stress tolerance. Transcriptional profiling revealed that Bcgbl1 plays a global role in regulation of gene expression upon hydrophobic surface induction. We further uncovered that three target genes encoding the hydrophobic surface binding proteins (HsbAs) contributed to the adhesion and virulence of B. cinerea. Overall, these findings suggest that Bcgbl1 had multiple functions and provided new insights for deciphering the Bcgbl1-mediated network for regulating development and pathogenicity of B. cinerea.
Collapse
Affiliation(s)
- Jiejing Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhe Sui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ronghui Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuping Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lixuan Xiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shiying Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfeng Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuan Cai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weidong Chen
- U.S. Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, Washington, United States of America
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
3
|
Chvalova V, Venkadasubramanian V, Klimova Z, Vojtova J, Benada O, Vanatko O, Vomastek T, Grousl T. Characterization of RACK1-depleted mammalian cells by a palette of microscopy approaches reveals defects in cell cycle progression and polarity establishment. Exp Cell Res 2023:113695. [PMID: 37393981 DOI: 10.1016/j.yexcr.2023.113695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/04/2023]
Abstract
The Receptor for Activated C Kinase 1 (RACK1) is an evolutionarily conserved scaffold protein involved in the regulation of numerous cellular processes. Here, we used CRISPR/Cas9 and siRNA to reduce the expression of RACK1 in Madin-Darby Canine Kidney (MDCK) epithelial cells and Rat2 fibroblasts, respectively. RACK1-depleted cells were examined using coherence-controlled holographic microscopy, immunofluorescence, and electron microscopy. RACK1 depletion resulted in decreased cell proliferation, increased cell area and perimeter, and in the appearance of large binucleated cells suggesting a defect in the cell cycle progression. Our results show that the depletion of RACK1 has a pleiotropic effect on both epithelial and mesenchymal cell lines and support its essential role in mammalian cells.
Collapse
Affiliation(s)
- Vera Chvalova
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Vignesh Venkadasubramanian
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Zuzana Klimova
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Jana Vojtova
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, 142 00, Prague, Czech Republic
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, 142 00, Prague, Czech Republic
| | - Ondrej Vanatko
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 00, Prague, Czech Republic; Second Faculty of Medicine, Charles University, 150 06, Prague, Czech Republic
| | - Tomas Vomastek
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Tomas Grousl
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic.
| |
Collapse
|
4
|
RACK1 Regulates Poxvirus Protein Synthesis Independently of Its Role in Ribosome-Based Stress Signaling. J Virol 2022; 96:e0109322. [PMID: 36098514 PMCID: PMC9517738 DOI: 10.1128/jvi.01093-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Receptor for activated C kinase 1 (RACK1) is a small ribosomal subunit protein that is phosphorylated by vaccinia virus (VacV) to maximize translation of postreplicative (PR) mRNAs that harbor 5' polyA leaders. However, RACK1 is a multifunctional protein that both controls translation directly and acts as a scaffold for signaling to and from the ribosome. This includes stress signaling that is activated by ribosome-associated quality control (RQC) and ribotoxic stress response (RSR) pathways. As VacV infection activates RQC and stress signaling, whether RACK1 influences viral protein synthesis through its effects on translation, signaling, or both remains unclear. Examining the effects of genetic knockout of RACK1 on the phosphorylation of key mitogenic and stress-related kinases, we reveal that loss of RACK1 specifically blunts the activation of c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) at late stages of infection. However, RACK1 was not required for JNK recruitment to ribosomes, and unlike RACK1 knockout, JNK inhibitors had no effect on viral protein synthesis. Moreover, reduced JNK activity during infection in RACK1 knockout cells contrasted with the absolute requirement for RACK1 in RSR-induced JNK phosphorylation. Comparing the effects of RACK1 knockout alongside inhibitors of late stage replication, our data suggest that JNK activation is only indirectly affected by the absence of RACK1 due to reduced viral protein accumulation. Cumulatively, our findings in the context of infection add further support for a model whereby RACK1 plays a specific and direct role in controlling translation of PR viral mRNAs that is independent of its role in ribosome-based stress signaling. IMPORTANCE Receptor for activated C kinase 1 (RACK1) is a multifunctional ribosomal protein that regulates translation directly and mediates signaling to and from the ribosome. While recent work has shown that RACK1 is phosphorylated by vaccinia virus (VacV) to stimulate translation of postreplicative viral mRNAs, whether RACK1 also contributes to VacV replication through its roles in ribosome-based stress signaling remains unclear. Here, we characterize the role of RACK1 in infected cells. In doing so, we find that RACK1 is essential for stress signal activation by ribotoxic stress responses but not by VacV infection. Moreover, although the loss of RACK1 reduces the level of stress-associated JNK activation in infected cells, this is an indirect consequence of RACK1's specific requirement for the synthesis of postreplicative viral proteins, the accumulation of which determines the level of cellular stress. Our findings reveal both the specific role of RACK1 and the complex downstream effects of its control of viral protein synthesis in the context of infection.
Collapse
|
5
|
Schmitt K, Kraft AA, Valerius O. A Multi-Perspective Proximity View on the Dynamic Head Region of the Ribosomal 40S Subunit. Int J Mol Sci 2021; 22:ijms222111653. [PMID: 34769086 PMCID: PMC8583833 DOI: 10.3390/ijms222111653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
A comparison of overlapping proximity captures at the head region of the ribosomal 40S subunit (hr40S) in Saccharomyces cerevisiae from four adjacent perspectives, namely Asc1/RACK1, Rps2/uS5, Rps3/uS3, and Rps20/uS10, corroborates dynamic co-localization of proteins that control activity and fate of both ribosomes and mRNA. Co-locating factors that associate with the hr40S are involved in (i) (de)ubiquitination of ribosomal proteins (Hel2, Bre5-Ubp3), (ii) clamping of inactive ribosomal subunits (Stm1), (iii) mRNA surveillance and vesicular transport (Smy2, Syh1), (iv) degradation of mRNA (endo- and exonucleases Ypl199c and Xrn1, respectively), (v) autophagy (Psp2, Vps30, Ykt6), and (vi) kinase signaling (Ste20). Additionally, they must be harmonized with translation initiation factors (eIF3, cap-binding protein Cdc33, eIF2A) and mRNA-binding/ribosome-charging proteins (Scp160, Sro9). The Rps/uS-BioID perspectives revealed substantial Asc1/RACK1-dependent hr40S configuration indicating a function of the β-propeller in context-specific spatial organization of this microenvironment. Toward resolving context-specific constellations, a Split-TurboID analysis emphasized the ubiquitin-associated factors Def1 and Lsm12 as neighbors of Bre5 at hr40S. These shuttling proteins indicate a common regulatory axis for the fate of polymerizing machineries for the biosynthesis of proteins in the cytoplasm and RNA/DNA in the nucleus.
Collapse
|
6
|
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1. PLoS Genet 2021; 17:e1009640. [PMID: 34214075 PMCID: PMC8282090 DOI: 10.1371/journal.pgen.1009640] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/15/2021] [Accepted: 06/02/2021] [Indexed: 12/31/2022] Open
Abstract
Heterotrimeric G proteins were originally discovered through efforts to understand the effects of hormones, such as glucagon and epinephrine, on glucose metabolism. On the other hand, many cellular metabolites, including glucose, serve as ligands for G protein-coupled receptors. Here we investigate the consequences of glucose-mediated receptor signaling, and in particular the role of a Gα subunit Gpa2 and a non-canonical Gβ subunit, known as Asc1 in yeast and RACK1 in animals. Asc1/RACK1 is of particular interest because it has multiple, seemingly unrelated, functions in the cell. The existence of such “moonlighting” operations has complicated the determination of phenotype from genotype. Through a comparative analysis of individual gene deletion mutants, and by integrating transcriptomics and metabolomics measurements, we have determined the relative contributions of the Gα and Gβ protein subunits to glucose-initiated processes in yeast. We determined that Gpa2 is primarily involved in regulating carbohydrate metabolism while Asc1 is primarily involved in amino acid metabolism. Both proteins are involved in regulating purine metabolism. Of the two subunits, Gpa2 regulates a greater number of gene transcripts and was particularly important in determining the amplitude of response to glucose addition. We conclude that the two G protein subunits regulate distinct but complementary processes downstream of the glucose-sensing receptor, as well as processes that lead ultimately to changes in cell growth and metabolism. Despite the societal importance of glucose fermentation in yeast, the mechanisms by which these cells detect and respond to glucose have remained obscure. Glucose detection requires a cell surface receptor coupled to a G protein that is comprised of two subunits, rather than the more typical heterotrimer: an α subunit Gpa2 and the β subunit Asc1 (or RACK1 in humans). Asc1/RACK1 also serves as a subunit of the ribosome, where it regulates the synthesis of proteins involved in glucose fermentation. This manuscript uses global metabolomics and transcriptomics to demonstrate the distinct roles of each G protein subunit in transmitting the glucose signal. Whereas Gpa2 is primarily involved in the metabolism of carbohydrates, Asc1/RACK1 contributes to production of amino acids necessary for protein synthesis and cell division. These findings reveal the initial steps of glucose signaling and several unique and complementary functions of the G protein subunits. More broadly, the integrated approach used here is likely to guide efforts to determine the topology of complex G protein and metabolic signaling networks in humans.
Collapse
|
7
|
Yan H, Shim WB. Characterization of non-canonical G beta-like protein FvGbb2 and its relationship with heterotrimeric G proteins in Fusarium verticillioides. Environ Microbiol 2019; 22:615-628. [PMID: 31760684 DOI: 10.1111/1462-2920.14875] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 11/29/2022]
Abstract
Fusarium verticillioides is a fungal pathogen that is responsible for maize ear rot and stalk rot diseases worldwide. The fungus also produces carcinogenic mycotoxins, fumonisins on infested maize. Unfortunately, we still lack clear understanding of how the pathogen responds to host and environmental stimuli to trigger fumonisin biosynthesis. The heterotrimeric G protein complex, consisting of canonical Gα, Gβ and Gγ subunits, is involved in transducing signals from external stimuli to regulate downstream signal transduction pathways. Previously, we demonstrated that Gβ protein FvGbb1 directly impacts fumonisin regulation but not other physiological aspects in F. verticillioides. In this study, we identified and characterized a RACK1 (Receptor for Activated C Kinase 1) homolog FvGbb2 as a putative Gβ-like protein in F. verticillioides. The mutant exhibited severe defects not only in fumonisin biosynthesis but also vegetative growth and conidiation. FvGbb2 was positively associated with carbon source utilization and stress agents but negatively regulated general amino acid control. While FvGbb2 does not interact with canonical G protein subunits, it may associate with diverse proteins in the cytoplasm to regulate vegetative growth, virulence, fumonisin biosynthesis and stress response in F. verticillioides.
Collapse
Affiliation(s)
- Huijuan Yan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
8
|
Schmitt K, Valerius O. yRACK1/Asc1 proxiOMICs-Towards Illuminating Ships Passing in the Night. Cells 2019; 8:cells8111384. [PMID: 31689955 PMCID: PMC6912217 DOI: 10.3390/cells8111384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/01/2023] Open
Abstract
Diverse signals and stress factors regulate the activity and homeostasis of ribosomes in all cells. The Saccharomyces cerevisiae protein Asc1/yRACK1 occupies an exposed site at the head region of the 40S ribosomal subunit (hr40S) and represents a central hub for signaling pathways. Asc1 strongly affects protein phosphorylation and is involved in quality control pathways induced by translation elongation arrest. Therefore, it is important to understand the dynamics of protein formations in the Asc1 microenvironment at the hr40S. We made use of the in vivo protein-proximity labeling technique Biotin IDentification (BioID). Unbiased proxiOMICs from two adjacent perspectives identified nucleocytoplasmic shuttling mRNA-binding proteins, the deubiquitinase complex Ubp3-Bre5, as well as the ubiquitin E3 ligase Hel2 as neighbors of Asc1. We observed Asc1-dependency of hr40S localization of mRNA-binding proteins and the Ubp3 co-factor Bre5. Hel2 and Ubp3-Bre5 are described to balance the mono-ubiquitination of Rps3 (uS3) during ribosome quality control. Here, we show that the absence of Asc1 resulted in massive exposure and accessibility of the C-terminal tail of its ribosomal neighbor Rps3 (uS3). Asc1 and some of its direct neighbors together might form a ribosomal decision tree that is tightly connected to close-by signaling modules.
Collapse
Affiliation(s)
- Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany.
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany.
| |
Collapse
|
9
|
Jung D, Seo JS, Nam J, Kim J. Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12. PLoS One 2019; 14:e0220137. [PMID: 31323064 PMCID: PMC6641207 DOI: 10.1371/journal.pone.0220137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022] Open
Abstract
Loc1 and Puf6, which are localized predominantly to the nucleus, are required for the localization and translational repression of the ASH1 mRNA in the yeast, Saccharomyces cerevisiae. During its transport to the daughter cell, the ASH1 mRNA is translationally repressed via associations with She2, Loc1, and Puf6. Here, we investigated the roles of Loc1 and Puf6 in the translation of mRNAs other than that encoding ASH1. In loc1 or puf6 deletion strains, expression of the mating-specific transcription factor, Ste12, was significantly increased at the post-transcriptional level. These phenotypes required the 5’ untranslated region (UTR) of STE12, which carries the putative Puf6-binding sequences. The RNA helicase, Dhh1, which is a known positive regulator for the translation of STE12 mRNA, was found to be functionally connected with Loc1 and Puf6 in the context of Ste12 expression. Our results collectively show that the phosphorylation of the N-terminal Thr16 residue of Dhh1 affects the protein interactions of Dhh1 with Loc1 or Puf6, and consequently regulates Ste12 expression.
Collapse
Affiliation(s)
- Daehee Jung
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jong Seok Seo
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jayoung Nam
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jinmi Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
| |
Collapse
|
10
|
Rollins MG, Jha S, Bartom ET, Walsh D. RACK1 evolved species-specific multifunctionality in translational control through sequence plasticity within a loop domain. J Cell Sci 2019; 132:jcs.228908. [PMID: 31118235 DOI: 10.1242/jcs.228908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/14/2019] [Indexed: 01/23/2023] Open
Abstract
Receptor of activated protein C kinase 1 (RACK1) is a highly conserved eukaryotic protein that regulates several aspects of mRNA translation; yet, how it does so, remains poorly understood. Here we show that, although RACK1 consists largely of conserved β-propeller domains that mediate binding to several other proteins, a short interconnecting loop between two of these blades varies across species to control distinct RACK1 functions during translation. Mutants and chimeras revealed that the amino acid composition of the loop is optimized to regulate interactions with eIF6, a eukaryotic initiation factor that controls 60S biogenesis and 80S ribosome assembly. Separately, phylogenetics revealed that, despite broad sequence divergence of the loop, there is striking conservation of negatively charged residues amongst protists and dicot plants, which is reintroduced to mammalian RACK1 by poxviruses through phosphorylation. Although both charged and uncharged loop mutants affect eIF6 interactions, only a negatively charged plant - but not uncharged yeast or human loop - enhances translation of mRNAs with adenosine-rich 5' untranslated regions (UTRs). Our findings reveal how sequence plasticity within the RACK1 loop confers multifunctionality in translational control across species.
Collapse
Affiliation(s)
- Madeline G Rollins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sujata Jha
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| |
Collapse
|
11
|
Collins JC, Ghalei H, Doherty JR, Huang H, Culver RN, Karbstein K. Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head. J Cell Biol 2018; 217:4141-4154. [PMID: 30348748 PMCID: PMC6279377 DOI: 10.1083/jcb.201804163] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/17/2018] [Accepted: 09/20/2018] [Indexed: 11/22/2022] Open
Abstract
Collins et al. use yeast genetics, biochemistry, and structure probing to dissect the role of the assembly factor Ltv1 in 40S ribosome maturation. Ribosomes from Ltv1-deficient cells have substoichiometric amounts of Rps10 and Asc1 and misfolded head rRNA, leading to defects in translational fidelity and ribosome-mediated RNA quality control, demonstrating a role for Ltv1 in chaperoning the assembly of the subunit head. The correct assembly of ribosomes from ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) is critical, as indicated by the diseases caused by RP haploinsufficiency and loss of RP stoichiometry in cancer cells. Nevertheless, how assembly of each RP is ensured remains poorly understood. We use yeast genetics, biochemistry, and structure probing to show that the assembly factor Ltv1 facilitates the incorporation of Rps3, Rps10, and Asc1/RACK1 into the small ribosomal subunit head. Ribosomes from Ltv1-deficient yeast have substoichiometric amounts of Rps10 and Asc1 and show defects in translational fidelity and ribosome-mediated RNA quality control. These defects provide a growth advantage under some conditions but sensitize the cells to oxidative stress. Intriguingly, relative to glioma cell lines, breast cancer cells have reduced levels of LTV1 and produce ribosomes lacking RPS3, RPS10, and RACK1. These data describe a mechanism to ensure RP assembly and demonstrate how cancer cells circumvent this mechanism to generate diverse ribosome populations that can promote survival under stress.
Collapse
Affiliation(s)
- Jason C Collins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Homa Ghalei
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Joanne R Doherty
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Haina Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Rebecca N Culver
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL
| |
Collapse
|
12
|
J Reschka E, Nordzieke S, Valerius O, Braus GH, Pöggeler S. A novel STRIPAK complex component mediates hyphal fusion and fruiting-body development in filamentous fungi. Mol Microbiol 2018; 110:513-532. [PMID: 30107058 DOI: 10.1111/mmi.14106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2018] [Indexed: 01/17/2023]
Abstract
The STRIPAK complex is involved in growth, cell fusion, development and signaling pathways, and thus malfunctions in the human STRIPAK complex often result in severe neuronal diseases and cancer. Despite the high degree of general conservation throughout the complex, several STRIPAK complex-associated small coiled-coil proteins of animals and yeasts are not conserved across species. As there are no data for filamentous ascomycetes, we addressed this through affinity purification with HA-tagged striatin ortholog PRO11 in Sordaria macrospora. Combining the method with liquid chromatography-mass spectrometry, we were able to co-purify STRIPAK complex interactor 1 (SCI1), the first STRIPAK-associated small coiled-coil protein in filamentous ascomycetes. Using yeast two-hybrid experiments, we identified SCI1 protein regions required for SCI1-PRO11 interaction, dimerization of SCI1 and interaction with other STRIPAK components. Further, both proteins PRO11 and SCI1 co-localize with the nuclear basket protein SmPOM152 at the nuclear envelope. Expression of the gene sci1 occurs during early developmental stages of S. macrospora, and the protein SCI1 in combination with PRO11 is required for cell fusion, vegetative growth and sexual development. The results of the present study will help to understand the underlying molecular mechanisms of STRIPAK signaling and function in cellular development and diseases in higher eukaryotes.
Collapse
Affiliation(s)
- Eva J Reschka
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany
| | - Steffen Nordzieke
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany
| | - Oliver Valerius
- Institute of Microbiology and Genetics, Department of Molecular Microbiology & Genetics, Georg-August University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Georg-August University, Göttingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics, Department of Molecular Microbiology & Genetics, Georg-August University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Georg-August University, Göttingen, Germany
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Georg-August University, Göttingen, Germany
| |
Collapse
|
13
|
Rogers DW, McConnell E, Miller EL, Greig D. Diminishing Returns on Intragenic Repeat Number Expansion in the Production of Signaling Peptides. Mol Biol Evol 2017; 34:3176-3185. [PMID: 28961820 PMCID: PMC5850478 DOI: 10.1093/molbev/msx243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Signaling peptides enable communication between cells, both within and between individuals, and are therefore key to the control of complex physiological and behavioral responses. Since their small sizes prevent direct transmission to secretory pathways, these peptides are often produced as part of a larger polyprotein comprising precursors for multiple related or identical peptides; the physiological and behavioral consequences of this unusual gene structure are not understood. Here, we show that the number of mature-pheromone-encoding repeats in the yeast α-mating-factor gene MFα1 varies considerably between closely related isolates of both Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus. Variation in repeat number has important phenotypic consequences: Increasing repeat number caused higher pheromone production and greater competitive mating success. However, the magnitude of the improvement decreased with increasing repeat number such that repeat amplification beyond that observed in natural isolates failed to generate more pheromone, and could actually reduce sexual fitness. We investigate multiple explanations for this pattern of diminishing returns and find that our results are most consistent with a translational trade-off: Increasing the number of encoded repeats results in more mature pheromone per translation event, but also generates longer transcripts thereby reducing the rate of translation—a phenomenon known as length-dependent translation. Length-dependent translation may be a powerful constraint on the evolution of genes encoding repetitive or modular proteins, with important physiological and behavioral consequences across eukaryotes.
Collapse
Affiliation(s)
- David W Rogers
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ellen McConnell
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eric L Miller
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Cambridge, United Kingdom
| | - Duncan Greig
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| |
Collapse
|
14
|
Heinisch JJ, Rodicio R. Protein kinase C in fungi—more than just cell wall integrity. FEMS Microbiol Rev 2017; 42:4562651. [DOI: 10.1093/femsre/fux051] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
|
15
|
Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O. Capturing the Asc1p/ Receptor for Activated C Kinase 1 (RACK1) Microenvironment at the Head Region of the 40S Ribosome with Quantitative BioID in Yeast. Mol Cell Proteomics 2017; 16:2199-2218. [PMID: 28982715 DOI: 10.1074/mcp.m116.066654] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 09/29/2017] [Indexed: 12/13/2022] Open
Abstract
The Asc1 protein of Saccharomyces cerevisiae is a scaffold protein at the head region of ribosomal 40S that links mRNA translation to cellular signaling. In this study, proteins that colocalize with Asc1p were identified with proximity-dependent Biotin IDentification (BioID), an in vivo labeling technique described here for the first time for yeast. Biotinylated Asc1p-birA*-proximal proteins were identified and quantitatively verified against controls applying SILAC and mass spectrometry. The mRNA-binding proteins Sro9p and Gis2p appeared together with Scp160p, each providing ribosomes with nuclear transcripts. The cap-binding protein eIF4E (Cdc33p) and the eIF3/a-subunit (Rpg1p) were identified reflecting the encounter of proteins involved in the initiation of mRNA translation at the head region of ribosomal 40S. Unexpectedly, a protein involved in ribosome preservation (the clamping factor Stm1p), the deubiquitylation complex Ubp3p-Bre5p, the RNA polymerase II degradation factor 1 (Def1p), and transcription factors (Spt5p, Mbf1p) colocalize with Asc1p in exponentially growing cells. For Asc1R38D, K40Ep, a variant considered to be deficient in binding to ribosomes, BioID revealed its predominant ribosome localization. Glucose depletion replaced most of the Asc1p colocalizing proteins for additional ribosomal proteins, suggesting a ribosome aggregation process during early nutrient limitation, possibly concomitant with ribosomal subunit clamping. Overall, the characterization of the Asc1p microenvironment with BioID confirmed and substantiated our recent findings that the β-propeller broadly contributes to signal transduction influencing phosphorylation of colocalizing proteins (e.g. of Bre5p), and by that might affect nuclear gene transcription and the fate of ribosomes.
Collapse
Affiliation(s)
- Nadine Opitz
- From the ‡Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Kerstin Schmitt
- From the ‡Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Verena Hofer-Pretz
- From the ‡Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Bettina Neumann
- §Department of Molecular Genetics, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Heike Krebber
- §Department of Molecular Genetics, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Gerhard H Braus
- From the ‡Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Oliver Valerius
- From the ‡Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany;
| |
Collapse
|
16
|
Li G, Zhang X, Tian H, Choi YE, Tao WA, Xu JR. MST50 is involved in multiple MAP kinase signaling pathways in Magnaporthe oryzae. Environ Microbiol 2017; 19:1959-1974. [PMID: 28244240 DOI: 10.1111/1462-2920.13710] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/17/2017] [Accepted: 02/19/2017] [Indexed: 12/31/2022]
Abstract
Appressorium formation plays a critical role in Magnaporthe oryzae. Mst50 is an adapter protein of the Mst11-Mst7-Pmk1 cascade that is essential for appressorium formation. To further characterize its functions, affinity purification was used to identify Mst50-interacting proteins (MIPs) in this study. Two of the MIPs are Mst11 and Mst7 that are known to interact with Mst50 for Pmk1 activation. Surprisingly, two other MIPs are Mck1 and Mkk2 that are the upstream kinases of the Mps1 pathway. Domain deletion analysis showed that the sterile alpha-motif of Mst50 but not the Ras-association domain was important for its interaction with Mck1 and responses to cell wall and oxidative stresses. The mst50 mutant was reduced in Mps1 activation under stress conditions. MIP11 encodes a RACK1 protein that also interacted with Mck1. Deletion of MIP11 resulted in defects in cell wall integrity, Mps1 phosphorylation and plant infection. Furthermore, Mst50 interacted with histidine kinase Hik1, and the mst50 mutant was reduced in Osm1 phosphorylation. These results indicated that Mst50 is involved in all three MAPK pathways in M. oryzae although its functions differ in each pathway. Several MIPs are conserved hypothetical proteins and may be involved in responses to various signals and crosstalk among signaling pathways.
Collapse
Affiliation(s)
- Guotian Li
- Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xue Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Huan Tian
- Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yoon-E Choi
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jin-Rong Xu
- Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
17
|
Nielsen MH, Flygaard RK, Jenner LB. Structural analysis of ribosomal RACK1 and its role in translational control. Cell Signal 2017; 35:272-281. [PMID: 28161490 DOI: 10.1016/j.cellsig.2017.01.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 12/28/2022]
Abstract
Receptor for Activated C-Kinase 1 (RACK1) belongs to the WD40 family of proteins, known to act as scaffolding proteins in interaction networks. Accordingly, RACK1 is found to have numerous interacting partners ranging from kinases and signaling proteins to membrane bound receptors and ion channels. Interestingly, RACK1 has also been identified as a ribosomal protein present in all eukaryotic ribosomes. Structures of eukaryotic ribosomes have shown RACK1 to be located at the back of the head of the small ribosomal subunit. This suggests that RACK1 could act as a ribosomal scaffolding protein recruiting regulators of translation to the ribosome, and several studies have in fact found RACK1 to play a role in regulation of translation. To fully understand the role of RACK1 we need to understand whether the many reported interaction partners of RACK1 bind to free or ribosomal RACK1. In this review we provide a structural analysis of ribosome-bound RACK1 to provide a basis for answering this fundamental question. Our analysis shows that RACK1 is tightly bound to the ribosome through highly conserved and specific interactions confirming RACK1 as an integral ribosomal protein. Furthermore, we have analyzed whether reported binding sites for RACK1 interacting partners with a proposed role in translational control are accessible on ribosomal RACK1. Our analysis shows that most of the interaction partners with putative regulatory functions have binding sites that are available on ribosomal RACK1, supporting the role of RACK1 as a ribosomal signaling hub. We also discuss the possible role for RACK1 in recruitment of ribosomes to focal adhesion sites and regulation of local translation during cell spreading and migration.
Collapse
Affiliation(s)
- Maja Holch Nielsen
- Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Aarhus University, Denmark
| | - Rasmus Kock Flygaard
- Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Aarhus University, Denmark
| | - Lasse Bohl Jenner
- Department of Molecular Biology and Genetics, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Aarhus University, Denmark
| |
Collapse
|
18
|
Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling. Mol Cell Biol 2017; 37:MCB.00279-16. [PMID: 27821475 DOI: 10.1128/mcb.00279-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
WD40 repeat proteins fold into characteristic β-propeller structures and control signaling circuits during cellular adaptation processes within eukaryotes. The RACK1 protein of Saccharomyces cerevisiae, Asc1p, consists exclusively of a single seven-bladed β-propeller that operates from the ribosomal base at the head region of the 40S subunit. Here we show that the R38D K40E ribosomal binding-compromised variant (Asc1DEp) is severely destabilized through mutation of phosphosite T143 to a dephosphorylation-mimicking alanine, probably through proteasomal degradation, leading to asc1- phenotypes. Phosphosite Y250 contributes to resistance to translational inhibitors but does not influence Asc1DEp stability. Beyond its own phosphorylation at T143, Y250, and other sites, Asc1p heavily influences the phosphorylation of as many as 90 proteins at 120 sites. Many of these proteins are regulators of fundamental processes ranging from mRNA translation to protein transport and turnover, cytoskeleton organization, and cellular signaling. Our data expose Asc1p/RACK1 as a key factor in phosphosignaling and manifest it as a control point at the head of the ribosomal 40S subunit itself regulated through posttranslational modification.
Collapse
|
19
|
Roles of Rack1 Proteins in Fungal Pathogenesis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4130376. [PMID: 27656651 PMCID: PMC5021465 DOI: 10.1155/2016/4130376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/16/2016] [Indexed: 01/21/2023]
Abstract
Pathogenic fungi cause diseases on various organisms. Despite their differences in life cycles, fungal pathogens use well-conserved proteins and pathways to regulate developmental and infection processes. In this review, we focus on Rack1, a multifaceted scaffolding protein involved in various biological processes. Rack1 is well conserved in eukaryotes and plays important roles in fungi, though limited studies have been conducted. To accelerate the study of Rack1 proteins in fungi, we review the functions of Rack1 proteins in model and pathogenic fungi and summarize recent progress on how Rack1 proteins are involved in fungal pathogenesis.
Collapse
|
20
|
Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin. BMC Genomics 2016; 17:417. [PMID: 27245696 PMCID: PMC4888481 DOI: 10.1186/s12864-016-2718-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
Background The trichothecene mycotoxins deoxynivalenol (DON) and trichothecin (TTC) are inhibitors of eukaryotic protein synthesis. Their effect on cellular homeostasis is poorly understood. We report a systematic functional investigation of the effect of DON and TTC on the yeast Saccharomyces cerevisiae using genetic array, network and microarray analysis. To focus the genetic analysis on intracellular consequences of toxin action we eliminated the PDR5 gene coding for a potent pleiotropic drug efflux protein potentially confounding results. We therefore used a knockout library with a pdr5Δ strain background. Results DON or TTC treatment creates a fitness bottleneck connected to ribosome efficiency. Genes isolated by systematic genetic array analysis as contributing to toxin resistance function in ribosome quality control, translation fidelity, and in transcription. Mutants in the E3 ligase Hel2, involved in ribosome quality control, and several members of the Rpd3 histone deacetylase complex were highly sensitive to DON. DON and TTC have similar genetic profiles despite their different toxic potency. Network analysis shows a coherent and tight network of genetic interactions among the DON and TTC resistance conferring gene products. The networks exhibited topological properties commonly associated with efficient processing of information. Many sensitive mutants have a "slow growth" gene expression signature. DON-exposed yeast cells increase transcripts of ribosomal protein and histone genes indicating an internal signal for growth enhancement. Conclusions The combination of gene expression profiling and analysis of mutants reveals cellular pathways which become bottlenecks under DON and TTC stress. These are generally directly or indirectly connected to ribosome biosynthesis such as the general secretory pathway, cytoskeleton, cell cycle delay, ribosome synthesis and translation quality control. Gene expression profiling points to an increased demand of ribosomal components and does not reveal activation of stress pathways. Our analysis highlights ribosome quality control and a contribution of a histone deacetylase complex as main sources of resistance against DON and TTC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2718-y) contains supplementary material, which is available to authorized users.
Collapse
|
21
|
Thompson MK, Rojas-Duran MF, Gangaramani P, Gilbert WV. The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs. eLife 2016; 5. [PMID: 27117520 PMCID: PMC4848094 DOI: 10.7554/elife.11154] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/21/2016] [Indexed: 02/06/2023] Open
Abstract
Translation is a core cellular process carried out by a highly conserved macromolecular machine, the ribosome. There has been remarkable evolutionary adaptation of this machine through the addition of eukaryote-specific ribosomal proteins whose individual effects on ribosome function are largely unknown. Here we show that eukaryote-specific Asc1/RACK1 is required for efficient translation of mRNAs with short open reading frames that show greater than average translational efficiency in diverse eukaryotes. ASC1 mutants in S. cerevisiae display compromised translation of specific functional groups, including cytoplasmic and mitochondrial ribosomal proteins, and display cellular phenotypes consistent with their gene-specific translation defects. Asc1-sensitive mRNAs are preferentially associated with the translational ‘closed loop’ complex comprised of eIF4E, eIF4G, and Pab1, and depletion of eIF4G mimics the translational defects of ASC1 mutants. Together our results reveal a role for Asc1/RACK1 in a length-dependent initiation mechanism optimized for efficient translation of genes with important housekeeping functions. DOI:http://dx.doi.org/10.7554/eLife.11154.001 Ribosomes are structures within cells that are responsible for making proteins. Molecules called messenger RNAs (or mRNAs), which contain genetic information derived from the DNA of a gene, pass through ribosomes that then “translate” that information to build proteins. Although all living cells contain ribosomes, the protein building blocks that make up the structure of the ribosome are not the same in all species. Furthermore, the exact roles that each building block plays during translation are not known. The ribosomes of plants, animals, and budding yeast contain the same protein, known as Asc1 in budding yeast and RACK1 in plants and animals. Thompson et al. have now explored the role of Asc1 in yeast cells by measuring translation in the absence of Asc1 using a technique called ribosome footprint profiling. This analysis revealed that cells lacking Asc1 translate fewer short mRNA molecules than normal cells. Short mRNAs encode small proteins that tend to play important ‘housekeeping’ roles in the cell — by forming the structural building blocks of ribosomes, for example. It has been observed previously that short mRNAs are translated at a higher rate than longer mRNAs on average, although the reasons behind this bias are still mysterious. The findings of Thompson et al. suggest that the ribosome itself may discriminate between short and long mRNAs and that the Asc1 protein is involved in calibrating the ribosome’s preference for short mRNAs. Cells need differing amounts of small proteins in different growth conditions. It will therefore be interesting to investigate whether mRNA length discrimination can be regulated by Asc1 and/or other components of the ribosome to tune gene expression to the environment. DOI:http://dx.doi.org/10.7554/eLife.11154.002
Collapse
Affiliation(s)
- Mary K Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Paritosh Gangaramani
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
22
|
Gallo S, Manfrini N. Working hard at the nexus between cell signaling and the ribosomal machinery: An insight into the roles of RACK1 in translational regulation. ACTA ACUST UNITED AC 2015; 3:e1120382. [PMID: 26824030 DOI: 10.1080/21690731.2015.1120382] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/19/2015] [Accepted: 11/09/2015] [Indexed: 02/08/2023]
Abstract
RACK1 is a ribosome-associated protein which functions as a receptor for activated PKCs. It also acts as a scaffold for many other proteins involved in diverse signaling pathways, e.g. Src, JNK, PDE4D and FAK signaling. With such a broad interactome, RACK1 has been suggested to function as a linker between cell signaling and the translation machinery. Accordingly, RACK1 modulates translation at different levels in several model organisms. For instance, it regulates ribosome stalling and mRNA quality control in yeasts and promotes translation efficiency downstream of specific cellular stimuli in mammals. However, the molecular mechanism by which RACK1 exerts these roles is widely uncharacterized. Moreover, the full list of ribosome-recruited RACK1 interactors still needs characterization. Here we discuss in vivo and in vitro findings to better delineate the roles of RACK1 in regulating ribosome function and translation.
Collapse
Affiliation(s)
- Simone Gallo
- Molecular Histology and Cell Growth Unit; National Institute of Molecular Genetics - INGM "Romeo and Enrica Invernizzi" ; Milan, Italy
| | - Nicola Manfrini
- Molecular Histology and Cell Growth Unit; National Institute of Molecular Genetics - INGM "Romeo and Enrica Invernizzi" ; Milan, Italy
| |
Collapse
|
23
|
Mendoza-Mendoza A, Steyaert J, Nieto-Jacobo MF, Holyoake A, Braithwaite M, Stewart A. Identification of growth stage molecular markers in Trichoderma sp. 'atroviride type B' and their potential application in monitoring fungal growth and development in soil. MICROBIOLOGY-SGM 2015; 161:2110-26. [PMID: 26341342 DOI: 10.1099/mic.0.000167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Several members of the genus Trichoderma are biocontrol agents of soil-borne fungal plant pathogens. The effectiveness of biocontrol agents depends heavily on how they perform in the complex field environment. Therefore, the ability to monitor and track Trichoderma within the environment is essential to understanding biocontrol efficacy. The objectives of this work were to: (a) identify key genes involved in Trichoderma sp. 'atroviride type B' morphogenesis; (b) develop a robust RNA isolation method from soil; and (c) develop molecular marker assays for characterizing morphogenesis whilst in the soil environment. Four cDNA libraries corresponding to conidia, germination, vegetative growth and conidiogenesis were created, and the genes identified by sequencing. Stage specificity of the different genes was confirmed by either Northern blot or quantitative reverse-transcriptase PCR (qRT-PCR) analysis using RNA from the four stages. con10, a conidial-specific gene, was observed in conidia, as well as one gene also involved in subsequent stages of germination (L-lactate/malate dehydrogenase encoding gene). The germination stage revealed high expression rates of genes involved in amino acid and protein biosynthesis, while in the vegetative-growth stage, genes involved in differentiation, including the mitogen-activated protein kinase kinase similar to Kpp7 from Ustilago maydis and the orthologue to stuA from Aspergillus nidulans, were preferentially expressed. Genes involved in cell-wall synthesis were expressed during conidiogenesis. We standardized total RNA isolation from Trichoderma sp. 'atroviride type B' growing in soil and then examined the expression profiles of selected genes using qRT-PCR. The results suggested that the relative expression patterns were cyclic and not accumulative.
Collapse
Affiliation(s)
- Artemio Mendoza-Mendoza
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Johanna Steyaert
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | | | - Andrew Holyoake
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Mark Braithwaite
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand
| | - Alison Stewart
- 1 Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln 7647, New Zealand 2 Marrone Bio Innovations, 1540 Drew Avenue, Davis, California 95618, USA
| |
Collapse
|
24
|
Choi J, Jung WH, Kronstad JW. The cAMP/protein kinase A signaling pathway in pathogenic basidiomycete fungi: Connections with iron homeostasis. J Microbiol 2015; 53:579-87. [PMID: 26231374 DOI: 10.1007/s12275-015-5247-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/03/2015] [Accepted: 07/03/2015] [Indexed: 12/26/2022]
Abstract
A number of pathogenic species of basidiomycete fungi are either life-threatening pathogens of humans or major economic pests for crop production. Sensing the host is a key aspect of pathogen proliferation during disease, and signal transduction pathways are critically important for detecting environmental conditions and facilitating adaptation. This review focuses on the contributions of the cAMP/protein kinase A (PKA) signaling pathway in Cryptococcus neoformans, a species that causes meningitis in humans, and Ustilago maydis, a model phytopathogen that causes a smut disease on maize. Environmental sensing by the cAMP/PKA pathway regulates the production of key virulence traits in C. neoformans including the polysaccharide capsule and melanin. For U. maydis, the pathway controls the dimorphic transition from budding growth to the filamentous cell type required for proliferation in plant tissue. We discuss recent advances in identifying new components of the cAMP/PKA pathway in these pathogens and highlight an emerging theme that pathway signaling influences iron acquisition.
Collapse
Affiliation(s)
- Jaehyuk Choi
- Division of Life Sciences, and Culture Collection and DNA Bank of Mushrooms, Incheon National University, Incheon, 406-772, Republic of Korea
| | | | | |
Collapse
|
25
|
Lu H, Zhu YF, Xiong J, Wang R, Jia Z. Potential extra-ribosomal functions of ribosomal proteins in Saccharomyces cerevisiae. Microbiol Res 2015. [PMID: 26211963 DOI: 10.1016/j.micres.2015.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ribosomal proteins (RPs), are essential components of the ribosomes, the molecular machines that turn mRNA blueprints into proteins, as they serve to stabilize the structure of the rRNA, thus improving protein biosynthesis. In addition, growing evidence suggests that RPs can function in other cellular roles. In the present review, we summarize several potential extra-ribosomal functions of RPs in ribosomal biogenesis, transcription activity, translation process, DNA repair, replicative life span, adhesive growth, and morphological transformation in Saccharomyces cerevisiae. However, the future in-depth studies are needed to identify these novel secondary functions of RPs in S. cerevisiae.
Collapse
Affiliation(s)
- Hui Lu
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Yi-Fei Zhu
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Juan Xiong
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Rong Wang
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China.
| | - Zhengping Jia
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China.
| |
Collapse
|
26
|
Wolf AS, Grayhack EJ. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA (NEW YORK, N.Y.) 2015; 21:935-45. [PMID: 25792604 PMCID: PMC4408800 DOI: 10.1261/rna.049080.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 05/09/2023]
Abstract
Quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. In yeast, ribosome stalling occurs at Arg CGA codon repeats, with even two consecutive CGA codons able to reduce translation by up to 50%. The conserved eukaryotic Asc1 protein limits translation through internal Arg CGA codon repeats. We show that, in the absence of Asc1 protein, ribosomes continue translating at CGA codons, but undergo substantial frameshifting with dramatically higher levels of frameshifting occurring with additional repeats of CGA codons. Frameshifting depends upon the slow or inefficient decoding of these codons, since frameshifting is suppressed by increased expression of the native tRNA(Arg(ICG)) that decodes CGA codons by wobble decoding. Moreover, the extent of frameshifting is modulated by the position of the CGA codon repeat relative to the translation start site. Thus, translation fidelity depends upon Asc1-mediated quality control.
Collapse
Affiliation(s)
- Andrew S Wolf
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| |
Collapse
|
27
|
Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. mBio 2015; 6:mBio.00427-15. [PMID: 25873380 PMCID: PMC4453552 DOI: 10.1128/mbio.00427-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.
Collapse
|
28
|
Daviel C, Carter PM, Nation CS, Pizarro JC, Guidry J, Aiyar A, Kelly BL. LACK, a RACK1 ortholog, facilitates cytochrome c oxidase subunit expression to promote Leishmania major fitness. Mol Microbiol 2015; 96:95-109. [PMID: 25582232 PMCID: PMC6055511 DOI: 10.1111/mmi.12924] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2015] [Indexed: 12/22/2022]
Abstract
Leishmania are kinetoplastid parasites that cause the sandfly-transmitted disease leishmaniasis. To maintain fitness throughout their infectious life cycle, Leishmania must undergo rapid metabolic adaptations to the dramatically distinct environments encountered during transition between sandfly and vertebrate hosts. We performed proteomic and immunoblot analyses of attenuated L. major strains deficient for LACK, the Leishmania ortholog of the mammalian receptor for activated c kinase (RACK1), that is important for parasite thermotolerance and virulence. This approach identified cytochrome c oxidase (LmCOX) subunit IV as a LACK-dependent fitness protein. Consistent with decreased levels of LmCOX subunit IV at mammalian temperature, and in amastigotes, LmCOX activity and mitochondrial function were also impaired in LACK-deficient L. major under these conditions. Importantly, overexpression of LmCOX subunit IV in LACK-deficient L. major restored thermotolerance and macrophage infectivity. Interestingly, overexpression of LmCOX subunit IV enhanced LmCOX subunit VI expression at mammalian temperature. Collectively, our data suggest LACK promotes Leishmania adaptation to the mammalian host environment by sustaining LmCOX subunit IV expression and hence energy metabolism in response to stress stimuli such as heat. These findings extend the repertoire of RACK1 protein utility to include a role in mitochondrial function.
Collapse
Affiliation(s)
- Cardenas Daviel
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Pamela M. Carter
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Catherine S. Nation
- Department of Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Juan C. Pizarro
- Department of Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Jessie Guidry
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ashok Aiyar
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ben L. Kelly
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| |
Collapse
|
29
|
Crystal structure of Gib2, a signal-transducing protein scaffold associated with ribosomes in Cryptococcus neoformans. Sci Rep 2015; 5:8688. [PMID: 25732347 PMCID: PMC4894404 DOI: 10.1038/srep08688] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/27/2015] [Indexed: 11/16/2022] Open
Abstract
The atypical Gβ-like/RACK1 Gib2 protein promotes cAMP signalling that plays a central role in regulating the virulence of Cryptococcus neoformans. Gib2 contains a seven-bladed β transducin structure and is emerging as a scaffold protein interconnecting signalling pathways through interactions with various protein partners. Here, we present the crystal structure of Gib2 at a 2.2-Å resolution. The structure allows us to analyse the association between Gib2 and the ribosome, as well as to identify the Gib2 amino acid residues involved in ribosome binding. Our studies not only suggest that Gib2 has a role in protein translation but also present Gib2 as a physical link at the crossroads of various regulatory pathways important for the growth and virulence of C. neoformans.
Collapse
|
30
|
González-Calixto C, Cázares-Raga FE, Cortés-Martínez L, Del Angel RM, Medina-Ramírez F, Mosso C, Ocádiz-Ruiz R, Valenzuela JG, Rodríguez MH, Hernández-Hernández FDLC. AealRACK1 expression and localization in response to stress in C6/36 HT mosquito cells. J Proteomics 2014; 119:45-60. [PMID: 25555378 DOI: 10.1016/j.jprot.2014.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 10/21/2014] [Accepted: 11/24/2014] [Indexed: 12/27/2022]
Abstract
UNLABELLED The Receptor for Activated C Kinase 1 (RACK1), a scaffold protein member of the tryptophan-aspartate (WD) repeat family, folds in a seven-bladed β-propeller structure that permits the association of proteins to form active complexes. Mosquitoes of the genus Aedes sp., are vectors of virus producing important diseases such as: dengue, chikungunya and yellow fever. Based on the highly conserved gene sequence of AeaeRACK1 of the mosquito Aedes aegypti we characterized the mRNA and protein of the homologous AealRACK1 from the Ae. albopictus-derived cell line C6/36 HT. Two protein species differing in MW/pI values were observed at 35kDa/8.0 and 36kDa/6.5. The behavior of AealRACK1 was studied inducing stress with serum deprivation and the glucocorticoid dexamethasone. Both stressors induced increase of the expression of AealRACK1 mRNA and proteins. In serum-deprived cells AealRACK1 protein was located cortically near the plasma membrane in contrast to dexamethasone-treated cells where the protein formed a dotted pattern in the cytoplasm. In addition, 33 protein partners were identified by immunoprecipitation and mass spectrometry. Most of the identified proteins were ribosomal, involved in signaling pathways and stress responses. Our results suggest that AealRACK1 in C6/36 HT cells respond to stress increasing its synthesis and producing phosphorylated activated form. BIOLOGICAL SIGNIFICANCE Insect cells adapt to numerous environmental stressors, including chemicals and invasion of pathogenic microorganisms among others, coordinating cellular and organismal responses. Individual cells sense the environment using receptors that trigger signaling pathways that regulate expression of specific effector proteins and/or cellular responses as movement or secretion. In the coordination of responses to stress, scaffold proteins are pivotal molecules that recruit other proteins forming active complexes. The Receptor for Activated C Kinase 1 (RACK1) is the best studied member of the conserved tryptophan-aspartate (WD) repeat family. RACK1 folds in a seven-bladed β-propeller structure and it could be activated during stress, participating in different signaling pathways. The presence and activities of RACK1 in mosquitoes had not been documented before, in this work the molecule is demonstrated in an Aedes albopictus-derived cell line and its reaction to stress is observed under the effect of serum deprivation and the presence of glucocorticoid analog dexamethasone, a chemical used to cause stress in vitro.
Collapse
Affiliation(s)
- Cecilia González-Calixto
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Febe E Cázares-Raga
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Leticia Cortés-Martínez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Rosa María Del Angel
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Fernando Medina-Ramírez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Clemente Mosso
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Ramón Ocádiz-Ruiz
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico
| | - Jesús G Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD 20852, USA
| | - Mario Henry Rodríguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, Cuernavaca, Morelos, Mexico
| | - Fidel de la Cruz Hernández-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional # 2508, San Pedro Zacatenco, 07360 México D.F., Mexico.
| |
Collapse
|
31
|
Tarnowski K, Fituch K, Szczepanowski RH, Dadlez M, Kaus-Drobek M. Patterns of structural dynamics in RACK1 protein retained throughout evolution: a hydrogen-deuterium exchange study of three orthologs. Protein Sci 2014; 23:639-51. [PMID: 24591271 DOI: 10.1002/pro.2448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/25/2014] [Accepted: 02/26/2014] [Indexed: 12/15/2022]
Abstract
RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation.
Collapse
Affiliation(s)
- Krzysztof Tarnowski
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, 02-106, Warsaw, Poland
| | | | | | | | | |
Collapse
|
32
|
Li D, Ellis EM. 4-Hydroxynonenal induces an increase in expression of Receptor for Activating C Kinase 1 (RACK1) in Chinese hamster V79-4 lung cells. Chem Biol Interact 2014; 213:13-20. [PMID: 24525193 DOI: 10.1016/j.cbi.2014.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/24/2014] [Accepted: 01/30/2014] [Indexed: 02/02/2023]
Abstract
4-Hydroxy-trans-2-nonenal (HNE) is a cytotoxic α,β-unsaturated aldehyde implicated in the pathology of several diseases that have an oxidative stress mechanism, including atherosclerosis, diabetes, alcohol-induced liver disease, and neurodegenerative disorders. As the most toxic aldehydic product of lipid peroxidation, HNE is known to exert a range of biological effects in a concentration-dependent manner. In this study, the effect of HNE on the levels of proteins in V79-4 Chinese hamster lung cells was investigated using two-dimensional electrophoresis and mass spectrometry. The results revealed that the expression of 23 proteins was increased by at least 2-fold and the expression of 19 proteins was decreased by at least 2-fold after exposure to 10 μM HNE for 24 h. Decreased proteins included the metabolic enzyme phosphoglycerate kinase 1 (PGK1), levels of which were decreased by 47%. Levels of the apoptotic indicator Lamin C were decreased by 33%. In contrast, levels of the scaffolding protein Receptor for Activating C Kinase 1 (RACK1) were increased by 2-fold after treatment with 10 μM HNE for 24h, and this was confirmed using quantitative PCR of reverse-transcribed mRNA and Western blots. The role of RACK1 in mediating the induction of apoptosis in response to 10 μM HNE was confirmed using RACK1-specific siRNA. The results from this study provide new information on the mechanism of adaptive stress response to HNE and also identify potential new biomarkers of exposure to HNE.
Collapse
Affiliation(s)
- Dan Li
- Department of Biopharmaceuticals, School of Pharmacy, China Medical University, Shenyang 110001, PR China; Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom.
| | - Elizabeth M Ellis
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| |
Collapse
|
33
|
Volta V, Beugnet A, Gallo S, Magri L, Brina D, Pesce E, Calamita P, Sanvito F, Biffo S. RACK1 depletion in a mouse model causes lethality, pigmentation deficits and reduction in protein synthesis efficiency. Cell Mol Life Sci 2013; 70:1439-50. [PMID: 23212600 PMCID: PMC11113757 DOI: 10.1007/s00018-012-1215-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 11/02/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
The receptor for activated C-kinase 1 (RACK1) is a conserved structural protein of 40S ribosomes. Strikingly, deletion of RACK1 in yeast homolog Asc1 is not lethal. Mammalian RACK1 also interacts with many nonribosomal proteins, hinting at several extraribosomal functions. A knockout mouse for RACK1 has not previously been described. We produced the first RACK1 mutant mouse, in which both alleles of RACK1 gene are defective in RACK1 expression (ΔF/ΔF), in a pure C57 Black/6 background. In a sample of 287 pups, we observed no ΔF/ΔF mice (72 expected). Dissection and genotyping of embryos at various stages showed that lethality occurs at gastrulation. Heterozygotes (ΔF/+) have skin pigmentation defects with a white belly spot and hypopigmented tail and paws. ΔF/+ have a transient growth deficit (shown by measuring pup size at P11). The pigmentation deficit is partly reverted by p53 deletion, whereas the lethality is not. ΔF/+ livers have mild accumulation of inactive 80S ribosomal subunits by polysomal profile analysis. In ΔF/+ fibroblasts, protein synthesis response to extracellular and pharmacological stimuli is reduced. These results highlight the role of RACK1 as a ribosomal protein converging signaling to the translational apparatus.
Collapse
Affiliation(s)
- Viviana Volta
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Anne Beugnet
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Simone Gallo
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Laura Magri
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Daniela Brina
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Elisa Pesce
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
- Environmental and Life Science Department (DISAV), University of Eastern Piedmont, Alessandria, Italy
| | - Piera Calamita
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Francesca Sanvito
- Department of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Biffo
- Laboratory of Molecular Histology and Cell Growth, Division of Oncology, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
- Environmental and Life Science Department (DISAV), University of Eastern Piedmont, Alessandria, Italy
| |
Collapse
|
34
|
Galvão FC, Rossi D, Silveira WDS, Valentini SR, Zanelli CF. The deoxyhypusine synthase mutant dys1-1 reveals the association of eIF5A and Asc1 with cell wall integrity. PLoS One 2013; 8:e60140. [PMID: 23573236 PMCID: PMC3613415 DOI: 10.1371/journal.pone.0060140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/21/2013] [Indexed: 11/19/2022] Open
Abstract
The putative eukaryotic translation initiation factor 5A (eIF5A) is a highly conserved protein among archaea and eukaryotes that has recently been implicated in the elongation step of translation. eIF5A undergoes an essential and conserved posttranslational modification at a specific lysine to generate the residue hypusine. The enzymes deoxyhypusine synthase (Dys1) and deoxyhypusine hydroxylase (Lia1) catalyze this two-step modification process. Although several Saccharomyces cerevisiae eIF5A mutants have importantly contributed to the study of eIF5A function, no conditional mutant of Dys1 has been described so far. In this study, we generated and characterized the dys1-1 mutant, which showed a strong depletion of mutated Dys1 protein, resulting in more than 2-fold decrease in hypusine levels relative to the wild type. The dys1-1 mutant demonstrated a defect in total protein synthesis, a defect in polysome profile indicative of a translation elongation defect and a reduced association of eIF5A with polysomes. The growth phenotype of dys1-1 mutant is severe, growing only in the presence of 1 M sorbitol, an osmotic stabilizer. Although this phenotype is characteristic of Pkc1 cell wall integrity mutants, the sorbitol requirement from dys1-1 is not associated with cell lysis. We observed that the dys1-1 genetically interacts with the sole yeast protein kinase C (Pkc1) and Asc1, a component of the 40S ribosomal subunit. The dys1-1 mutant was synthetically lethal in combination with asc1Δ and overexpression of TIF51A (eIF5A) or DYS1 is toxic for an asc1Δ strain. Moreover, eIF5A is more associated with translating ribosomes in the absence of Asc1 in the cell. Finally, analysis of the sensitivity to cell wall-perturbing compounds revealed a more similar behavior of the dys1-1 and asc1Δ mutants in comparison with the pkc1Δ mutant. These data suggest a correlated role for eIF5A and Asc1 in coordinating the translational control of a subset of mRNAs associated with cell integrity.
Collapse
Affiliation(s)
- Fabio Carrilho Galvão
- Department of Biological Sciences, Univ Estadual Paulista – UNESP, Araraquara-Saõ Paulo, Brazil
| | - Danuza Rossi
- Department of Biological Sciences, Univ Estadual Paulista – UNESP, Araraquara-Saõ Paulo, Brazil
| | | | | | | |
Collapse
|