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McCain JSP, Tagliabue A, Susko E, Achterberg EP, Allen AE, Bertrand EM. Cellular costs underpin micronutrient limitation in phytoplankton. SCIENCE ADVANCES 2021; 7:7/32/eabg6501. [PMID: 34362734 PMCID: PMC8346223 DOI: 10.1126/sciadv.abg6501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/22/2021] [Indexed: 05/08/2023]
Abstract
Micronutrients control phytoplankton growth in the ocean, influencing carbon export and fisheries. It is currently unclear how micronutrient scarcity affects cellular processes and how interdependence across micronutrients arises. We show that proximate causes of micronutrient growth limitation and interdependence are governed by cumulative cellular costs of acquiring and using micronutrients. Using a mechanistic proteomic allocation model of a polar diatom focused on iron and manganese, we demonstrate how cellular processes fundamentally underpin micronutrient limitation, and how they interact and compensate for each other to shape cellular elemental stoichiometry and resource interdependence. We coupled our model with metaproteomic and environmental data, yielding an approach for estimating biogeochemical metrics, including taxon-specific growth rates. Our results show that cumulative cellular costs govern how environmental conditions modify phytoplankton growth.
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Affiliation(s)
- J Scott P McCain
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Eric P Achterberg
- GEOMAR Helmholtz Center for Ocean Research Kiel, Wischhofstrasse 1-3, 24148 Kiel, Germany
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome. Biochem J 2021; 477:3019-3032. [PMID: 32744327 PMCID: PMC7452503 DOI: 10.1042/bcj20200385] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/26/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Cytosolic 80S ribosomes contain proteins of the mature cytosolic ribosome (r-proteins) as well as proteins with roles in ribosome biogenesis, protein folding or modification. Here, we refined the core r-protein composition in Arabidopsis thaliana by determining the abundance of different proteins during enrichment of ribosomes from cell cultures using peptide mass spectrometry. The turnover rates of 26 40S subunit r-proteins and 29 60S subunit r-proteins were also determined, showing that half of the ribosome population is replaced every 3–4 days. Three enriched proteins showed significantly shorter half-lives; a protein annotated as a ribosomal protein uL10 (RPP0D, At1g25260) with a half-life of 0.5 days and RACK1b and c with half-lives of 1–1.4 days. The At1g25260 protein is a homologue of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role in the 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins; 26 were enriched more than 10-fold during ribosome enrichment. Some of these enriched proteins have known roles in translation, while others are newly proposed ribosome-associated factors in plants. This analysis provides an improved understanding of A. thaliana ribosome protein content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and how protein turnover can help identify r-proteins involved in ribosome biogenesis or regulation in plants.
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3
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Ibuot A, Webster RE, Williams LE, Pittman JK. Increased metal tolerance and bioaccumulation of zinc and cadmium in Chlamydomonas reinhardtii expressing a AtHMA4 C-terminal domain protein. Biotechnol Bioeng 2020; 117:2996-3005. [PMID: 32579250 DOI: 10.1002/bit.27476] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/05/2020] [Accepted: 06/23/2020] [Indexed: 02/03/2023]
Abstract
The use of microalgal biomass for metal pollutant bioremediation might be improved by genetic engineering to modify the selectivity or capacity of metal biosorption. A plant cadmium (Cd) and zinc (Zn) transporter (AtHMA4) was used as a transgene to increase the ability of Chlamydomonas reinhardtii to tolerate 0.2 mM Cd and 0.3 mM Zn exposure. The transgenic cells showed increased accumulation and internalization of both metals compared to wild-type. AtHMA4 was expressed either as the full-length (FL) protein or just the C-terminal (CT) tail, which is known to have metal-binding sites. Similar Cd and Zn tolerance and accumulation was observed with expression of either the FL protein or CT domain, suggesting that enhanced metal tolerance was mainly due to increased metal binding rather than metal transport. The effectiveness of the transgenic cells was further examined by immobilization in calcium alginate to generate microalgal beads that could be added to a metal contaminated solution. Immobilization maintained metal tolerance, while AtHMA4-expressing cells in alginate showed a concentration-dependent increase in metal biosorption that was significantly greater than alginate beads composed of wild-type cells. This demonstrates that expressing AtHMA4 FL or CT has great potential as a strategy for bioremediation using microalgal biomass.
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Affiliation(s)
- Aniefon Ibuot
- Department of Science Technology, Akwa Ibom State Polytechnic, Ikot Ekpene, Akwa Ibom, Nigeria
| | - Rachel E Webster
- The Manchester Museum, The University of Manchester, Manchester, UK
| | | | - Jon K Pittman
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, UK
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Lai YC, Chang CH, Chen CY, Chang JS, Ng IS. Towards protein production and application by using Chlorella species as circular economy. BIORESOURCE TECHNOLOGY 2019; 289:121625. [PMID: 31203183 DOI: 10.1016/j.biortech.2019.121625] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
In this study, productions of microalgal proteins were explored via a circular economy concept. First, production of proteins from Chlorella vulgaris FSP-E (CV) and Chlorella sorokiniana (CS) was optimized by using favorable cultivation conditions and strategies. The optimal CO2 concentration for the growth of both microalgae was 5% (v/v), while the optimal nitrogen source for CV and CS were 12 mM of NaNO3 and NH4Cl, respectively. Addition of 12 mg/L ammonium iron (III) citrate enhanced protein production. Next, semi-batch cultivation strategy was employed to achieve a protein production of 793.3 and 812.8 mg/L for CV and C S, representing a 4.86 and 2.77 fold increase, respectively, in protein productivity. The obtained microalgal proteins consist of 40% essential amino acids. The CV and CS proteins possess prebiotic activities as they enhanced the growth of Lactobacillus rhamnosus ZY by 48 and 74%, respectively, with a good antibacterial activity against predominant pathogens.
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Affiliation(s)
- Yu-Cheng Lai
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chien-Hsiang Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Yen Chen
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Circular Economy, National Cheng Kung University, Tainan 701, Taiwan; College of Engineering, Tunghai University, Taichung 407, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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5
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Villain J, Minguez L, Halm-Lemeille MP, Durrieu G, Bureau R. Acute toxicities of pharmaceuticals toward green algae. mode of action, biopharmaceutical drug disposition classification system and quantile regression models. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 124:337-343. [PMID: 26590695 DOI: 10.1016/j.ecoenv.2015.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 06/05/2023]
Abstract
The acute toxicities of 36 pharmaceuticals towards green algae were estimated from a set of quantile regression models representing the first global quantitative structure-activity relationships. The selection of these pharmaceuticals was based on their predicted environmental concentrations. An agreement between the estimated values and the observed acute toxicity values was found for several families of pharmaceuticals, in particular, for antidepressants. A recent classification (BDDCS) of drugs based on ADME properties (Absorption, Distribution, Metabolism and Excretion) was clearly correlated with the acute ecotoxicities towards algae. Over-estimation of toxicity from our QSAR models was observed for classes 2, 3 and 4 whereas our model results were in agreement for the class 1 pharmaceuticals. Clarithromycin, a class 3 antibiotic characterized by weak metabolism and high solubility, was the most toxic to algae (molecular stability and presence in surface water).
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Affiliation(s)
- Jonathan Villain
- UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), UPRES EA 4258-FR CNRS 3038 INC3M, Bd Becquerel, F-14032 Caen, France; Laboratoire de Mathématiques de Bretagne Atlantique, Université de Bretagne Sud et UMR CNRS 6205, Campus de Tohannic, 56017 Vannes, France
| | - Laetitia Minguez
- Normandie Univ., France; UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), UPRES EA 4258-FR CNRS 3038 INC3M, Bd Becquerel, F-14032 Caen, France
| | - Marie-Pierre Halm-Lemeille
- Normandie Univ., France; UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), UPRES EA 4258-FR CNRS 3038 INC3M, Bd Becquerel, F-14032 Caen, France
| | - Gilles Durrieu
- Laboratoire de Mathématiques de Bretagne Atlantique, Université de Bretagne Sud et UMR CNRS 6205, Campus de Tohannic, 56017 Vannes, France
| | - Ronan Bureau
- Normandie Univ., France; UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), UPRES EA 4258-FR CNRS 3038 INC3M, Bd Becquerel, F-14032 Caen, France.
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6
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Abstract
The proteome of cells is synthesized by ribosomes, complex ribonucleoproteins that in eukaryotes contain 79-80 proteins and four ribosomal RNAs (rRNAs) more than 5,400 nucleotides long. How these molecules assemble together and how their assembly is regulated in concert with the growth and proliferation of cells remain important unanswered questions. Here, we review recently emerging principles to understand how eukaryotic ribosomal proteins drive ribosome assembly in vivo. Most ribosomal proteins assemble with rRNA cotranscriptionally; their association with nascent particles is strengthened as assembly proceeds. Each subunit is assembled hierarchically by sequential stabilization of their subdomains. The active sites of both subunits are constructed last, perhaps to prevent premature engagement of immature ribosomes with active subunits. Late-assembly intermediates undergo quality-control checks for proper function. Mutations in ribosomal proteins that affect mostly late steps lead to ribosomopathies, diseases that include a spectrum of cell type-specific disorders that often transition from hypoproliferative to hyperproliferative growth.
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Affiliation(s)
- Jesus de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, E-41013 Sevilla, Spain
- Departamento de Genetica, Universidad de Sevilla, E-41013 Sevilla, Spain
| | - Katrin Karbstein
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida 33458
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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Maruyama S, Tokutsu R, Minagawa J. Transcriptional regulation of the stress-responsive light harvesting complex genes in Chlamydomonas reinhardtii. PLANT & CELL PHYSIOLOGY 2014; 55:1304-10. [PMID: 24850838 DOI: 10.1093/pcp/pcu068] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dissipating excess energy of light is critical for photosynthetic organisms to keep the photosynthetic apparatus functional and less harmful under stressful environmental conditions. In the green alga Chlamydomonas reinhardtii, efficient energy dissipation is achieved by a process called non-photochemical quenching (NPQ), in which a distinct member of light harvesting complex, LHCSR, is known to play a key role. Although it has been known that two very closely related genes (LHCSR3.1 and LHCSR3.2) encoding LHCSR3 protein and another paralogous gene LHCSR1 are present in the C. reinhardtii genome, it is unclear how these isoforms are differentiated in terms of transcriptional regulation and functionalization. Here, we show that transcripts of both of the isoforms, LHCSR3.1 and LHCSR3.2, are accumulated under high light stress. Reexamination of the genomic sequence and gene models along with survey of sequence motifs suggested that these two isoforms shared an almost identical but still distinct promoter sequence and a completely identical polypeptide sequence, with more divergent 3'-untranscribed regions. Transcriptional induction under high light condition of both isoforms was suppressed by treatment with a photosystem II inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), and a calmodulin inhibitor W7. Despite a similar response to high light, the inhibitory effects of DCMU and W7 to the LHCSR1 transcript accumulation were limited compared to LHCSR3 genes. These results suggest that the transcription of LHCSR paralogs in C. reinhardtii are regulated by light signal and differentially modulated via photosynthetic electron transfer and calmodulin-mediated calcium signaling pathway(s).
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Affiliation(s)
- Shinichiro Maruyama
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
| | - Ryutaro Tokutsu
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
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Wang B, Yu J, Zhu D, Chang Y, Zhao Q. Maize ZmRACK1 is involved in the plant response to fungal phytopathogens. Int J Mol Sci 2014; 15:9343-59. [PMID: 24865494 PMCID: PMC4100098 DOI: 10.3390/ijms15069343] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 04/25/2014] [Accepted: 05/13/2014] [Indexed: 01/17/2023] Open
Abstract
The receptor for activated C kinase 1 (RACK1) belongs to a protein subfamily containing a tryptophan-aspartic acid-domain (WD) repeat structure. Compelling evidence indicates that RACK1 can interact with many signal molecules and affect different signal transduction pathways. In this study, we cloned a maize RACK1 gene (ZmRACK1) by RT-PCR. The amino acid sequence of ZmRACK1 had seven WD repeats in which there were typical GH (glycine-histidine) and WD dipeptides. Comparison with OsRACK1 from rice revealed 89% identity at the amino acid level. Expression pattern analysis by RT-PCR showed that ZmRACK1 was expressed in all analyzed tissues of maize and that its transcription in leaves was induced by abscisic acid and jasmonate at a high concentration. Overexpression of ZmRACK1 in maize led to a reduction in symptoms caused by Exserohilum turcicum (Pass.) on maize leaves. The expression levels of the pathogenesis-related protein genes, PR-1 and PR-5, increased 2.5-3 times in transgenic maize, and reactive oxygen species production was more active than in the wild-type. Yeast two-hybrid assays showed that ZmRACK1 could interact with RAC1, RAR1 and SGT1. This study and previous work leads us to believe that ZmRACK1 may form a complex with regulators of plant disease resistance to coordinate maize reactions to pathogens.
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Affiliation(s)
- Baosheng Wang
- State Key Laboratory of Agribiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jingjuan Yu
- State Key Laboratory of Agribiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Dengyun Zhu
- State Key Laboratory of Agribiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Yujie Chang
- State Key Laboratory of Agribiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Qian Zhao
- State Key Laboratory of Agribiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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9
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Production of anti-cancer immunotoxins in algae: Ribosome inactivating proteins as fusion partners. Biotechnol Bioeng 2013; 110:2826-35. [DOI: 10.1002/bit.24966] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/03/2013] [Accepted: 05/24/2013] [Indexed: 12/27/2022]
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10
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Carroll AJ. The Arabidopsis Cytosolic Ribosomal Proteome: From form to Function. FRONTIERS IN PLANT SCIENCE 2013; 4:32. [PMID: 23459595 PMCID: PMC3585428 DOI: 10.3389/fpls.2013.00032] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/10/2013] [Indexed: 05/20/2023]
Abstract
The cytosolic ribosomal proteome of Arabidopsis thaliana has been studied intensively by a range of proteomics approaches and is now one of the most well characterized eukaryotic ribosomal proteomes. Plant cytosolic ribosomes are distinguished from other eukaryotic ribosomes by unique proteins, unique post-translational modifications and an abundance of ribosomal proteins for which multiple divergent paralogs are expressed and incorporated. Study of the A. thaliana ribosome has now progressed well beyond a simple cataloging of protein parts and is focused strongly on elucidating the functions of specific ribosomal proteins, their paralogous isoforms and covalent modifications. This review summarises current knowledge concerning the Arabidopsis cytosolic ribosomal proteome and highlights potentially fruitful areas of future research in this fast moving and important area.
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Affiliation(s)
- Adam J. Carroll
- Australian Research Council Centre of Excellence in Plant Energy Biology, Australian National UniversityCanberra, ACT, Australia
- *Correspondence: Adam J. Carroll, Australian Research Council Centre of Excellence in Plant Energy Biology, Australian National University, ACT 0200, Canberra, Australia. e-mail:
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Zhigailov AV, Babaylova ES, Polimbetova NS, Graifer DM, Karpova GG, Iskakov BK. Fragment of mRNA coding part complementary to region 1638–1650 of wheat 18S RNA functions as a translational enhancer. Mol Biol 2012. [DOI: 10.1134/s0026893312040164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Adams DR, Ron D, Kiely PA. RACK1, A multifaceted scaffolding protein: Structure and function. Cell Commun Signal 2011; 9:22. [PMID: 21978545 PMCID: PMC3195729 DOI: 10.1186/1478-811x-9-22] [Citation(s) in RCA: 324] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/06/2011] [Indexed: 12/17/2022] Open
Abstract
The Receptor for Activated C Kinase 1 (RACK1) is a member of the tryptophan-aspartate repeat (WD-repeat) family of proteins and shares significant homology to the β subunit of G-proteins (Gβ). RACK1 adopts a seven-bladed β-propeller structure which facilitates protein binding. RACK1 has a significant role to play in shuttling proteins around the cell, anchoring proteins at particular locations and in stabilising protein activity. It interacts with the ribosomal machinery, with several cell surface receptors and with proteins in the nucleus. As a result, RACK1 is a key mediator of various pathways and contributes to numerous aspects of cellular function. Here, we discuss RACK1 gene and structure and its role in specific signaling pathways, and address how posttranslational modifications facilitate subcellular location and translocation of RACK1. This review condenses several recent studies suggesting a role for RACK1 in physiological processes such as development, cell migration, central nervous system (CN) function and circadian rhythm as well as reviewing the role of RACK1 in disease.
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Affiliation(s)
- David R Adams
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland.
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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14
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Abstract
Proteomics of chloroplast ribosomes in spinach and Chlamydomonas revealed unique protein composition and structures of plastid ribosomes. These studies have suggested the presence of some ribosomal proteins unique to plastid ribosomes which may be involved in plastid-unique translation regulation. Considering the strong background of genetic analysis and molecular biology in Arabidopsis, the in-depth proteomic characterization of Arabidopsis plastid ribosomes would facilitate further understanding of plastid translation in higher plants. Here, I describe simple and rapid methods for the preparation of plastid ribosomes from Chlamydomonas and Arabidopsis using sucrose gradients. I also describe purity criteria and methods for yield estimation of the purified plastid ribosomes and subunits, methods for the preparation of plastid ribosomal proteins, as well as the identification of some Arabidopsis plastid ribosomal proteins by matrix-assisted laser desorption/ionization mass spectrometry.
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Guo J, Wang S, Valerius O, Hall H, Zeng Q, Li JF, Weston DJ, Ellis BE, Chen JG. Involvement of Arabidopsis RACK1 in protein translation and its regulation by abscisic acid. PLANT PHYSIOLOGY 2011; 155:370-83. [PMID: 21098678 PMCID: PMC3075769 DOI: 10.1104/pp.110.160663] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/18/2010] [Indexed: 05/20/2023]
Abstract
Earlier studies have shown that RACK1 functions as a negative regulator of abscisic acid (ABA) responses in Arabidopsis (Arabidopsis thaliana), but the molecular mechanism of the action of RACK1 in these processes remains elusive. Global gene expression profiling revealed that approximately 40% of the genes affected by ABA treatment were affected in a similar manner by the rack1 mutation, supporting the view that RACK1 is an important regulator of ABA responses. On the other hand, coexpression analysis revealed that more than 80% of the genes coexpressed with RACK1 encode ribosome proteins, implying a close relationship between RACK1's function and the ribosome complex. These results implied that the regulatory role for RACK1 in ABA responses may be partially due to its putative function in protein translation, which is one of the major cellular processes that mammalian and Saccharomyces cerevisiae RACK1 is involved in. Consistently, all three Arabidopsis RACK1 homologous genes, namely RACK1A, RACK1B, and RACK1C, complemented the growth defects of the S. cerevisiae cross pathway control2/rack1 mutant. In addition, RACK1 physically interacts with Arabidopsis Eukaryotic Initiation Factor6 (eIF6), whose mammalian homolog is a key regulator of 80S ribosome assembly. Moreover, rack1 mutants displayed hypersensitivity to anisomycin, an inhibitor of protein translation, and displayed characteristics of impaired 80S functional ribosome assembly and 60S ribosomal subunit biogenesis in a ribosome profiling assay. Gene expression analysis revealed that ABA inhibits the expression of both RACK1 and eIF6. Taken together, these results suggest that RACK1 may be required for normal production of 60S and 80S ribosomes and that its action in these processes may be regulated by ABA.
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16
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Chen M, Zhao L, Sun YL, Cui SX, Zhang LF, Yang B, Wang J, Kuang TY, Huang F. Proteomic analysis of hydrogen photoproduction in sulfur-deprived Chlamydomonas cells. J Proteome Res 2010; 9:3854-66. [PMID: 20509623 DOI: 10.1021/pr100076c] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The green alga Chlamydomonas reinhardtii is a model organism to study H(2) metabolism in photosynthetic eukaryotes. To understand the molecular mechanism of H(2) metabolism, we used 2-DE coupled with MALDI-TOF and MALDI-TOF/TOF-MS to investigate proteomic changes of Chlamydomonas cells that undergo sulfur-depleted H(2) photoproduction process. In this report, we obtained 2-D PAGE soluble protein profiles of Chlamydomonas at three time points representing different phases leading to H(2) production. We found over 105 Coomassie-stained protein spots, corresponding to 82 unique gene products, changed in abundance throughout the process. Major changes included photosynthetic machinery, protein biosynthetic apparatus, molecular chaperones, and 20S proteasomal components. A number of proteins related to sulfate, nitrogen and acetate assimilation, and antioxidative reactions were also changed significantly. Other proteins showing alteration during the sulfur-depleted H(2) photoproduction process were proteins involved in cell wall and flagella metabolisms. In addition, among these differentially expressed proteins, 11 were found to be predicted proteins without functional annotation in the Chlamydomonas genome database. The results of this proteomic analysis provide new insight into molecular basis of H(2) photoproduction in Chlamydomonas under sulfur depletion.
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Affiliation(s)
- Mei Chen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Evangelisti AM, Conant GC. Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling. Genome Biol Evol 2010; 2:826-34. [PMID: 20966100 PMCID: PMC2988524 DOI: 10.1093/gbe/evq067] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are less evident among the synonymous positions and noncoding regulatory elements. This result suggests a potential explanation for the somewhat puzzling fact that duplicated RP genes are not functionally redundant despite their very high protein sequence identity. An analysis of the patterns of regulatory network evolution after genome duplication also indicates that the duplicated proteins have diverged considerably in expression despite their similar protein sequences.
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18
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Bailey-Serres J, Sorenson R, Juntawong P. Getting the message across: cytoplasmic ribonucleoprotein complexes. TRENDS IN PLANT SCIENCE 2009; 14:443-53. [PMID: 19616989 DOI: 10.1016/j.tplants.2009.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 05/29/2009] [Accepted: 05/29/2009] [Indexed: 05/20/2023]
Abstract
mRNA-ribonucleoprotein (mRNP) complexes mediate post-transcriptional control mechanisms in the cell nucleus and cytoplasm. Transcriptional control is paramount to gene expression but is followed by regulated nuclear pre-mRNA maturation and quality control processes that culminate in the export of a functional transcript to the cytoplasm. Once in the cytosol, mRNPs determine the activity of individual mRNAs through regulation of localization, translation, sequestration and turnover. Here, we review how quantitative assessment of mRNAs in distinct cytoplasmic mRNPs, such as polyribosomes (polysomes), has provided new perspectives on post-transcriptional regulation from the global to gene-specific level. In addition, we explore recent genetic and biochemical studies of cytoplasmic mRNPs that have begun to expose RNA-binding proteins in an integrated network that fine-tunes gene expression.
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Affiliation(s)
- J Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
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19
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Baecker JJ, Sneddon JC, Hollingsworth MJ. Efficient translation in chloroplasts requires element(s) upstream of the putative ribosome binding site from atpI. AMERICAN JOURNAL OF BOTANY 2009; 96:627-636. [PMID: 21628219 DOI: 10.3732/ajb.0800259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Thousands of proteins make up a chloroplast, but fewer than 100 are encoded by the chloroplast genome. Despite this low number, expression of chloroplast-encoded genes is essential for plant survival. Every chloroplast has its own gene expression system with a major regulatory point at the initiation of protein synthesis (translation). In chloroplasts, most protein-encoding genes contain elements resembling the ribosome binding sites (RBS) found in prokaryotes. In vitro, these putative chloroplast ribosome binding sequences vary in their ability to support translation. Here we report results from an investigation into effects of the predicted RBS for the tobacco chloroplast atpI gene on translation in vivo. Two reporter constructs, differing only in their 5'-untranslated regions (5'UTRs) were stably incorporated into tobacco chloroplast genomes and their expression analyzed. One 5'UTR was derived from the wild-type (WT) atpI gene. The second, Holo-substitution (Holo-sub), had nonchloroplast sequence replacing all wild-type nucleotides, except for the putative RBS. The abundance of reporter RNA was the same for both 5'UTRs. However, translation controlled by Holo-sub was less than 4% that controlled by WT. These in vivo experiments support the idea that translation initiation in land plant chloroplasts depends on 5'UTR elements outside the putative RBS.
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Affiliation(s)
- Joshua J Baecker
- Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York 14260 USA
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20
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Ross CLN, Patel RR, Mendelson TC, Ware VC. Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function. Nucleic Acids Res 2007; 35:4503-14. [PMID: 17584789 PMCID: PMC1934995 DOI: 10.1093/nar/gkm428] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 05/11/2007] [Accepted: 05/11/2007] [Indexed: 11/16/2022] Open
Abstract
The proposed Drosophila melanogaster L23a ribosomal protein features a conserved C-terminal amino acid signature characteristic of other L23a family members and a unique N-terminal extension [Koyama et al. (Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions. Gene 1999; 226: 339-345)], absent from Saccharomyces cerevisiae L25 that nearly doubles the size of fly L23a. The ability of fly L23a to replace the role of yeast L25 in ribosome biogenesis was determined by creating a yeast strain carrying an L25 chromosomal gene disruption and a plasmid-encoded FLAG-tagged L23a gene. Though affected by a reduced growth rate, the strain is dependent on fly L23a-FLAG function for survival and growth, demonstrating functional compatibility between the fly and yeast proteins. Pulse-chase experiments reveal a delay in rRNA processing kinetics, most notably at a late cleavage step that converts precursor 27S rRNA into mature 25S rRNA, likely contributing to the strain's slower growth pattern. Yet, given the essential requirement for L23(a)/L25 in ribosome biogenesis, there is a remarkable tolerance for accommodating the fly L23a N-terminal extension within the structure of the yeast ribosome. A search of available databases shows that the unique N-terminal extension is shared by multiple insect lineages. An evolutionary perspective on L23a structure and function within insect lineages is discussed.
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Affiliation(s)
| | | | | | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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21
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Nilsson J, Sengupta J, Gursky R, Nissen P, Frank J. Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments. J Mol Biol 2007; 369:429-38. [PMID: 17434183 PMCID: PMC1976601 DOI: 10.1016/j.jmb.2007.03.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 02/28/2007] [Accepted: 03/10/2007] [Indexed: 10/23/2022]
Abstract
Compared to the prokaryotic 70 S ribosome, the eukaryotic 80 S ribosome contains additional ribosomal proteins and extra segments of rRNA, referred to as rRNA expansion segments (ES). These eukaryotic-specific rRNA ES are mainly on the periphery of the 80 S ribosome, as revealed by cryo-electron microscopy (cryo-EM) studies, but their precise function is not known. To address the question of whether the rRNA ES are structurally conserved among 80 S ribosomes of different fungi we performed cryo-electron microscopy on 80 S ribosomes from the thermophilic fungus Thermomyces lanuginosus and compared it to the Saccharomyces cerevisiae 80 S ribosome. Our analysis reveals general structural conservation of the rRNA expansion segments but also changes in ES27 and ES7/39, as well as the absence of a tertiary interaction between ES3 and ES6 in T. lanuginosus. The differences provide a hint on the role of rRNA ES in regulating translation. Furthermore, we show that the stalk region and interactions with elongation factor 2 (eEF2) are different in T. lanuginosus, exhibiting a more extensive contact with domain I of eEF2.
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Affiliation(s)
- Jakob Nilsson
- Department of Molecular Biology, University of Aarhus, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
| | - Jayati Sengupta
- Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
| | - Richard Gursky
- Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
| | - Poul Nissen
- Department of Molecular Biology, University of Aarhus, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
- ¶For correspondence: P.N. (), J.F. ()
| | - Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
- Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, New York 12201-0509, USA
- ¶For correspondence: P.N. (), J.F. ()
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22
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Chang IF. Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes. Proteomics 2007; 6:6158-66. [PMID: 17072909 DOI: 10.1002/pmic.200600225] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In recent years, MS has been widely used to study protein complex in eukaryotes. The identification of interacting proteins of a particular target protein may help defining protein-protein interaction and proteins of unknown functions. To isolate protein complexes, high-speed ultracentrifugation, sucrose density-gradient centrifugation, and coimmunoprecipitation have been widely used. However, the probability of getting nonspecific binding is comparatively high. Alternatively, by use of one- or two-step (tandem affinity purification) epitope-tag affinity purification, protein complexes can be isolated by affinity or immunoaffinity columns. These epitope-tags include protein A, hexahistidine (His), c-Myc, hemaglutinin (HA), calmodulin-binding protein, FLAG, maltose-binding protein, Strep, etc. The isolated protein complex can then be subjected to protease (i.e., trypsin) digestion followed by an MS analysis for protein identification. An example, the epitope-tag purification of the Arabidopsis cytosolic ribosomes, is addressed in this article to show the success of the application. Several representative protein complexes in eukaryotes been isolated and characterized by use of this approach are listed. In this review, the comparison among different tag systems, validation of interacting relationship, and choices of MS analysis method are addressed. The successful rate, advantages, limitations, and challenges of the epitope-tag purification are also discussed.
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Affiliation(s)
- Ing-Feng Chang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
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23
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LeBarron J, Mitra K, Frank J. Displaying 3D data on RNA secondary structures: coloRNA. J Struct Biol 2006; 157:262-70. [PMID: 17070699 DOI: 10.1016/j.jsb.2006.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 08/23/2006] [Accepted: 08/25/2006] [Indexed: 12/20/2022]
Abstract
RNA performs a variety of diverse functions and therefore must adopt many different three-dimensional conformations. The number and complexity of RNA structures that are currently available are steadily increasing, necessitating the generation of versatile structure visualization tools. Here, we describe a new RNA secondary and tertiary structure visualization tool, the display program coloRNA. This program colors each nucleotide in a secondary structure schematic according to the value of an assigned property of the corresponding backbone phosphate group, such as the distance between corresponding residues in two atomic models of the same RNA molecule. To assist in analyzing tertiary structure, coloRNA also colors nucleotides based on the three-dimensional distances between a user-selected nucleotide and all others. Minimum and maximum thresholds can be used to focus in on, or eliminate, a particular value range. coloRNA can display a user-specified group of nucleotides by outlining the structure in an automatically assigned, but user-changeable color. As an example, we have used coloRNA to analyze a pair of recently published structures of the Escherichia coli 70S ribosome. When coloRNA is used to display the conformational difference between the two structures, the large movement of the small subunit head stands visually out from the background changes in the remaining domains of the small subunit.
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Affiliation(s)
- Jamie LeBarron
- Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA
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Rothberg KG, Burdette DL, Pfannstiel J, Jetton N, Singh R, Ruben L. The RACK1 homologue from Trypanosoma brucei is required for the onset and progression of cytokinesis. J Biol Chem 2006; 281:9781-90. [PMID: 16469736 PMCID: PMC1997280 DOI: 10.1074/jbc.m600133200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The receptor for activated C kinase 1 (RACK1) is a conserved scaffold protein that helps regulate a range of cell activities including cell growth, shape, and protein translation. We report that a homologue of RACK1 is required for cytokinesis in pathogenic Trypanosoma brucei. The protein, referred to as TRACK, is comprised of WD repeat elements and can complement cpc2 null mutants of Schizosaccharomyces pombe. TRACK is expressed throughout the trypanosome life cycle and is distributed predominantly in a perinuclear region and the cytoplasm but not along the endoplasmic reticulum, mitochondrion, or cleavage furrow of dividing cells. When tetracycline-inducible RNA interference (RNAi) is used to deplete the cellular content of TRACK, the cells remain metabolically active, but growth is inhibited. In bloodstream forms, growth arrest is due to a delay in the onset of cytokinesis. By contrast, procyclic forms are able to initiate cytokinesis in the absence of TRACK but arrest midway through cell cleavage. The RNAi cells undergo multiple rounds of partial cytokinesis and accumulate nuclei and cytoplasmic extensions with attached flagella. The TRACK RNAi construct is also inducible within infected mice. Under these conditions parasites are eliminated from peripheral blood within 3 days post-infection. Taken as a whole, these data indicate that trypanosomes utilize a RACK1 homologue to regulate the final stages of mitosis. Moreover, disrupting the interaction between TRACK and its partners might be targeted in the design of novel therapies.
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Affiliation(s)
- Karen G Rothberg
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275, USA
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25
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Göttler T, Holler E. Screening for beta-poly(L-malate) binding proteins by affinity chromatography. Biochem Biophys Res Commun 2006; 341:1119-27. [PMID: 16476581 DOI: 10.1016/j.bbrc.2006.01.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 01/17/2006] [Indexed: 10/25/2022]
Abstract
Poly(beta-L-malic acid) is a cell type-specific polymer of myxomycetes (true slime molds) with the physiological role to organize mobility of certain proteins over the giant multinucleated plasmodia. We have developed an affinity chromatography employing 1,6-diamino-n-hexane-Sepharose-coupled poly(malic acid) to identify such proteins in cellular extracts of Physarum polycephalum. Molecular masses were measured by SDS-PAGE and non-denaturing PAGE after silver staining and/or Western blotting. Protein complexes/subunits were detected by 2-dimensional non-denaturing PAGE/SDS-PAGE. A simplified gel shift experiment displayed binding to fragmented calf thymus DNA. Nuclei were richest in poly(malate) binding proteins followed by cytoplasm and membranes. A protein of 370 kDa dissociated into 11 subunits of 11-29 kDa, indicative of a highly complex protein. This and other proteins displayed binding to nucleic acid in gel shift experiments. Poly(malate) is considered a structural and functional equivalent of long contiguous aspartate repeats in proteins of eukaryotes.
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Affiliation(s)
- Thomas Göttler
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
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