1
|
The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. Int J Mol Sci 2020; 21:ijms21165633. [PMID: 32781615 PMCID: PMC7460601 DOI: 10.3390/ijms21165633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 01/15/2023] Open
Abstract
Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.
Collapse
|
2
|
Grimmer J, Helm S, Dobritzsch D, Hause G, Shema G, Zahedi RP, Baginsky S. Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts. Nat Commun 2020; 11:1662. [PMID: 32245955 PMCID: PMC7125294 DOI: 10.1038/s41467-020-15539-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
The proteasome is an essential protein-degradation machinery in eukaryotic cells that controls protein turnover and thereby the biogenesis and function of cell organelles. Chloroplasts import thousands of nuclear-encoded precursor proteins from the cytosol, suggesting that the bulk of plastid proteins is transiently exposed to the cytosolic proteasome complex. Therefore, there is a cytosolic equilibrium between chloroplast precursor protein import and proteasomal degradation. We show here that a shift in this equilibrium, induced by mild genetic proteasome impairment, results in elevated precursor protein abundance in the cytosol and significantly increased accumulation of functional photosynthetic complexes in protein import-deficient chloroplasts. Importantly, a proteasome lid mutant shows improved photosynthetic performance, even in the absence of an import defect, signifying that functional precursors are continuously degraded. Hence, turnover of plastid precursors in the cytosol represents a mechanism to constrain thylakoid membrane assembly and photosynthetic electron transport.
Collapse
Affiliation(s)
- Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Dirk Dobritzsch
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Gerd Hause
- Biocenter of the University, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle, Saale, Germany
| | - Gerta Shema
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany.
- Biochemistry of Plants, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
| |
Collapse
|
3
|
Frank J, Happeck R, Meier B, Hoang MTT, Stribny J, Hause G, Ding H, Morsomme P, Baginsky S, Peiter E. Chloroplast-localized BICAT proteins shape stromal calcium signals and are required for efficient photosynthesis. THE NEW PHYTOLOGIST 2019; 221:866-880. [PMID: 30169890 DOI: 10.1111/nph.15407] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/17/2018] [Indexed: 05/18/2023]
Abstract
The photosynthetic machinery of plants must be regulated to maximize the efficiency of light reactions and CO2 fixation. Changes in free Ca2+ in the stroma of chloroplasts have been observed at the transition between light and darkness, and also in response to stress stimuli. Such Ca2+ dynamics have been proposed to regulate photosynthetic capacity. However, the molecular mechanisms of Ca2+ fluxes in the chloroplasts have been unknown. By employing a Ca2+ reporter-based approach, we identified two chloroplast-localized Ca2+ transporters in Arabidopsis thaliana, BICAT1 and BICAT2, that determine the amplitude of the darkness-induced Ca2+ signal in the chloroplast stroma. BICAT2 mediated Ca2+ uptake across the chloroplast envelope, and its knockout mutation strongly dampened the dark-induced [Ca2+ ]stroma signal. Conversely, this Ca2+ transient was increased in knockout mutants of BICAT1, which transports Ca2+ into the thylakoid lumen. Knockout mutation of BICAT2 caused severe defects in chloroplast morphology, pigmentation and photosynthetic light reactions, rendering bicat2 mutants barely viable under autotrophic growth conditions, while bicat1 mutants were less affected. These results show that BICAT transporters play a role in chloroplast Ca2+ homeostasis. They are also involved in the regulation of photosynthesis and plant productivity. Further work will be required to reveal whether the effect on photosynthesis is a direct result of their role as Ca2+ transporters.
Collapse
Affiliation(s)
- Julia Frank
- Institute for Biochemistry and Biotechnology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Ricardo Happeck
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Bastian Meier
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Minh Thi Thanh Hoang
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Jiri Stribny
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Gerd Hause
- Biocenter, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Haidong Ding
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Sacha Baginsky
- Institute for Biochemistry and Biotechnology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| | - Edgar Peiter
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
| |
Collapse
|
4
|
Köhler D, Helm S, Agne B, Baginsky S. Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly. PLANT PHYSIOLOGY 2016; 172:2429-2444. [PMID: 27733515 PMCID: PMC5129725 DOI: 10.1104/pp.16.01393] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Toc159-containing complexes at the outer chloroplast envelope membrane form stable supercomplexes with a 1-MD translocon at the inner chloroplast envelope membrane of which Tic56 is one essential subunit. While the single mutants tic56-1 and ppi2 (toc159) have an albino phenotype and are able to grow heterotrophically, we find the double mutant to be embryo lethal. Comprehensive quantitative proteome profiling with both single mutants in combination with GeneChip analyses identified a posttranscriptional defect in the accumulation of plastid ribosomal proteins and diminished expression of plastid encoded proteins. In the tic56-1 mutant, the assembly of functional ribosomes is furthermore hampered by a processing defect of the plastid 23S rRNA. Spectinomycin-treatment of wild-type plants phenocopies the molecular phenotype of plastid proteome accumulation in tic56-1 and to a smaller degree also ppi2 plastids, suggesting that a defect in plastid translation is largely responsible for the phenotype of both import mutants. Import experiments with the tic56-3 mutant revealed no significant defect in the import of small ribosomal protein 16 in the absence of full-length Tic56, suggesting that the defect in ribosome assembly in tic56-1 may be independent of a function of Tic56 in protein import. Our data establish a previously unknown link between plastid protein import, the processing of plastid rRNAs, and the assembly of plastid ribosomes and provide further knowledge on the function of the translocon components and the molecular basis for their albino phenotype.
Collapse
Affiliation(s)
- Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, 06120 Halle (Saale), Germany
| |
Collapse
|
5
|
Lee KE, Heo JE, Kim JM, Hwang CS. N-Terminal Acetylation-Targeted N-End Rule Proteolytic System: The Ac/N-End Rule Pathway. Mol Cells 2016; 39:169-78. [PMID: 26883906 PMCID: PMC4794598 DOI: 10.14348/molcells.2016.2329] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Although Nα-terminal acetylation (Nt-acetylation) is a pervasive protein modification in eukaryotes, its general functions in a majority of proteins are poorly understood. In 2010, it was discovered that Nt-acetylation creates a specific protein degradation signal that is targeted by a new class of the N-end rule proteolytic system, called the Ac/N-end rule pathway. Here, we review recent advances in our understanding of the mechanism and biological functions of the Ac/N-end rule pathway, and its crosstalk with the Arg/N-end rule pathway (the classical N-end rule pathway).
Collapse
Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Ji-Eun Heo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| |
Collapse
|
6
|
Lee DW, Woo S, Geem KR, Hwang I. Sequence Motifs in Transit Peptides Act as Independent Functional Units and Can Be Transferred to New Sequence Contexts. PLANT PHYSIOLOGY 2015; 169:471-84. [PMID: 26149569 PMCID: PMC4577419 DOI: 10.1104/pp.15.00842] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/02/2015] [Indexed: 05/04/2023]
Abstract
A large number of nuclear-encoded proteins are imported into chloroplasts after they are translated in the cytosol. Import is mediated by transit peptides (TPs) at the N termini of these proteins. TPs contain many small motifs, each of which is critical for a specific step in the process of chloroplast protein import; however, it remains unknown how these motifs are organized to give rise to TPs with diverse sequences. In this study, we generated various hybrid TPs by swapping domains between Rubisco small subunit (RbcS) and chlorophyll a/b-binding protein, which have highly divergent sequences, and examined the abilities of the resultant TPs to deliver proteins into chloroplasts. Subsequently, we compared the functionality of sequence motifs in the hybrid TPs with those of wild-type TPs. The sequence motifs in the hybrid TPs exhibited three different modes of functionality, depending on their domain composition, as follows: active in both wild-type and hybrid TPs, active in wild-type TPs but inactive in hybrid TPs, and inactive in wild-type TPs but active in hybrid TPs. Moreover, synthetic TPs, in which only three critical motifs from RbcS or chlorophyll a/b-binding protein TPs were incorporated into an unrelated sequence, were able to deliver clients to chloroplasts with a comparable efficiency to RbcS TP. Based on these results, we propose that diverse sequence motifs in TPs are independent functional units that interact with specific translocon components at various steps during protein import and can be transferred to new sequence contexts.
Collapse
Affiliation(s)
- Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Seungjin Woo
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kyoung Rok Geem
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| |
Collapse
|
7
|
Inoue K. Emerging knowledge of the organelle outer membranes - research snapshots and an updated list of the chloroplast outer envelope proteins. FRONTIERS IN PLANT SCIENCE 2015; 6:278. [PMID: 25983735 PMCID: PMC4415399 DOI: 10.3389/fpls.2015.00278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 05/14/2023]
|
8
|
Lung SC, Smith MD, Weston JK, Gwynne W, Secord N, Chuong SDX. The C-terminus of Bienertia sinuspersici Toc159 contains essential elements for its targeting and anchorage to the chloroplast outer membrane. FRONTIERS IN PLANT SCIENCE 2014; 5:722. [PMID: 25566294 PMCID: PMC4274882 DOI: 10.3389/fpls.2014.00722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/30/2014] [Indexed: 05/11/2023]
Abstract
Most nucleus-encoded chloroplast proteins rely on an N-terminal transit peptide (TP) as a post-translational sorting signal for directing them to the organelle. Although Toc159 is known to be a receptor for specific preprotein TPs at the chloroplast surface, the mechanism for its own targeting and integration into the chloroplast outer membrane is not completely understood. In a previous study, we identified a novel TP-like sorting signal at the C-terminus (CT) of a Toc159 homolog from the single-cell C4 species, Bienertia sinuspersici. In the current study, we have extended our understanding of the sorting signal using transient expression of fluorescently-tagged fusion proteins of variable-length, and with truncated and swapped versions of the CT. As was shown in the earlier study, the 56 residues of the CT contain crucial sorting information for reversible interaction of the receptor with the chloroplast envelope. Extension of this region to 100 residues in the current study stabilized the interaction via membrane integration, as demonstrated by more prominent plastid-associated signals and resistance of the fusion protein to alkaline extraction. Despite a high degree of sequence similarity, the plastid localization signals of the equivalent CT regions of Arabidopsis thaliana Toc159 homologs were not as strong as that of the B. sinuspersici counterparts. Together with computational and circular dichroism analyses of the CT domain structures, our data provide insights into the critical elements of the CT for the efficient targeting and anchorage of Toc159 receptors to the dimorphic chloroplasts in the single-cell C4 species.
Collapse
Affiliation(s)
- Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong KongHong Kong SAR, China
| | - Matthew D. Smith
- Department of Biology, Wilfrid Laurier UniversityWaterloo, ON, Canada
| | - J. Kyle Weston
- Department of Biology, Wilfrid Laurier UniversityWaterloo, ON, Canada
| | - William Gwynne
- Department of Biology, University of WaterlooWaterloo, ON, Canada
| | - Nathan Secord
- Department of Biology, University of WaterlooWaterloo, ON, Canada
| | | |
Collapse
|
9
|
Sheng JD, Lei L, Wang AP. Role of Lin28A/B subtypes in apoptosis of hepatocellular carcinoma cells. Shijie Huaren Xiaohua Zazhi 2014; 22:3891-3897. [DOI: 10.11569/wcjd.v22.i26.3891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To explore the role of Lin28A/B subtypes in apoptosis of hepatocellular carcinoma (HCC) cells, and to analyze the mechanism of action of Lin28A/B in tumorigenesis of HCC.
METHODS: The mRNA and protein expression of Lin28A/B in HCC cells was detected by real-time PCR and Western blot. After siRNAs targeting Lin28A/B were transfected into HCC cells, the expression of Lin28A/B was detected by real-time PCR and Western blot, cell proliferation was assessed by MTT assay, and cell apoptosis was analyzed by FACS.
RESULTS: Real-time PCR showed that the expression of Lin28A/B mRNAs was up-regulated in HCC cells (P < 0.05; P < 0.01), and the up-regulation of Lin28B was more significant than that of Lin28A. Transfection of Lin28A/B siRNAs decreased the expression of Lin28A/B in HCC cells (P < 0.05). MTT assay revealed that Lin28A and Lin28B siRNAs significantly inhibited HCC cell proliferation (P < 0.05; P < 0.01) and promoted cell apoptosis (P < 0.05; P < 0.01). The effect of Lin28B siRNA on cell proliferation and apoptosis was stronger than that of Lin28A siRNA (P < 0.05).
CONCLUSION: Both Lin28A/B take part in the tumorigenesis of HCC. Lin28B may play a major role in HCC tumorigenesis, while Lin28A may play a subordinate role.
Collapse
|