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Ascorbate-Glutathione Cycle Genes Families in Euphorbiaceae: Characterization and Evolutionary Analysis. BIOLOGY 2022; 12:biology12010019. [PMID: 36671712 PMCID: PMC9855080 DOI: 10.3390/biology12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related to development and response to environmental stresses, the pathway has not yet been comprehensively characterized in many crop plants. Among different eudicotyledons, the Euphorbiaceae family is particularly diverse with some species highly tolerant to drought. Here the APX, MDAR, DHAR, and GR genes in Ricinus communis, Jatropha curcas, Manihot esculenta, and Hevea brasiliensis were identified and characterized. The comprehensive phylogenetic and genomic analyses allowed the classification of the genes into different classes, equivalent to cytosolic, peroxisomal, chloroplastic, and mitochondrial enzymes, and revealed the duplication events that contribute to the expansion of these families within plant genomes. Due to the high drought stress tolerance of Ricinus communis, the expression patterns of ascorbate-glutathione cycle genes in response to drought were also analyzed in leaves and roots, indicating a differential expression during the stress. Altogether, these data contributed to the characterization of the expression pattern and evolutionary analysis of these genes, filling the gap in the proposed functions of core components of the antioxidant mechanism during stress response in an economically relevant group of plants.
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Transcriptome Analyses in a Selected Gene Set Indicate Alternative Oxidase (AOX) and Early Enhanced Fermentation as Critical for Salinity Tolerance in Rice. PLANTS 2022; 11:plants11162145. [PMID: 36015448 PMCID: PMC9415304 DOI: 10.3390/plants11162145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/30/2022] [Accepted: 08/16/2022] [Indexed: 12/31/2022]
Abstract
Plants subjected to stress need to respond rapidly and efficiently to acclimatize and survive. In this paper, we investigated a selected gene set potentially involved in early cell reprogramming in two rice genotypes with contrasting salinity tolerance (Pokkali tolerant and IR29 susceptible) in order to advance knowledge of early molecular mechanisms of rice in dealing with salt stress. Selected genes were evaluated in available transcriptomic data over a short period of 24 h and involved enzymes that avoid ROS formation (AOX, UCP and PTOX), impact ATP production (PFK, ADH and COX) or relate to the antioxidant system. Higher transcript accumulation of AOX (ROS balancing), PFK and ADH (alcohol fermentation) was detected in the tolerant genotype, while the sensitive genotype revealed higher UCP and PTOX transcript levels, indicating a predominant role for early transcription of AOX and fermentation in conferring salt stress tolerance to rice. Antioxidant gene analyses supported higher oxidative stress in IR29, with transcript increases of cytosolic CAT and SOD from all cell compartments (cytoplasm, peroxisome, chloroplast and mitochondria). In contrast, Pokkali increased mRNA levels from the AsA-GSH cycle as cytosolic/mitochondrial DHAR was involved in ascorbate recovery. In addition, these responses occurred from 2 h in IR29 and 10 h in Pokkali, indicating early but ineffective antioxidant activity in the susceptible genotype. Overall, our data suggest that AOX and ADH can play a critical role during early cell reprogramming for improving salt stress tolerance by efficiently controlling ROS formation in mitochondria. We discuss our results in relation to gene engineering and editing approaches to develop salinity-tolerant crops.
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Wallace MD, Debowski AW, Sukhoverkov KV, Mylne JS, Stubbs KA. Herbicidal activity of fluoroquinolone derivatives. PLANT DIRECT 2021; 5:e348. [PMID: 34541445 PMCID: PMC8438536 DOI: 10.1002/pld3.348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Development of herbicides with novel modes of action is crucial for weed control and to hinder herbicide resistance. An attractive novel herbicidal target is plant DNA gyrase, which has been demonstrated to be effectively inhibited by the known antimicrobial ciprofloxacin. Despite this good herbicidal activity, ciprofloxacin is not suitable as a herbicide due to its antimicrobial activity; therefore, a diverse library of analogues was analyzed to gain insight into the aspects required for herbicidal activity. This analysis revealed that significant structural modifications were tolerated and that the fluoride at C-6 and a cyclic amino group at C-7 were not crucial for herbicidal activity. The analysis also revealed that these modifications also affected the antibacterial activity with one compound demonstrating good herbicidal activity and weak antibacterial activity, against both Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Michael D. Wallace
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Aleksandra W. Debowski
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Biomedical SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Kirill V. Sukhoverkov
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyWAAustralia
| | - Joshua S. Mylne
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyWAAustralia
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWAAustralia
| | - Keith A. Stubbs
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
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4
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Wallace MD, Waraich NF, Debowski AW, Corral MG, Maxwell A, Mylne JS, Stubbs KA. Developing ciprofloxacin analogues against plant DNA gyrase: a novel herbicide mode of action. Chem Commun (Camb) 2018; 54:1869-1872. [DOI: 10.1039/c7cc09518j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development of ciprofloxacin analogues against plant DNA gyrase, a novel herbicidal target, with increased herbicidal activity and diminished antibacterial activity is described.
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Affiliation(s)
- Michael D. Wallace
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
| | - Nidda F. Waraich
- Department of Biological Chemistry
- John Innes Centre
- Norwich Research Park
- Norwich
- UK
| | - Aleksandra W. Debowski
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- School of Biomedical Sciences
| | - Maxime G. Corral
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- ARC Centre of Excellence in Plant Energy Biology
| | - Anthony Maxwell
- Department of Biological Chemistry
- John Innes Centre
- Norwich Research Park
- Norwich
- UK
| | - Joshua S. Mylne
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
- ARC Centre of Excellence in Plant Energy Biology
| | - Keith A. Stubbs
- School of Molecular Sciences
- University of Western Australia
- Crawley
- Australia
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5
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Qin C, Cheng L, Zhang H, He M, Shen J, Zhang Y, Wu P. OsGatB, the Subunit of tRNA-Dependent Amidotransferase, Is Required for Primary Root Development in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:599. [PMID: 27200067 PMCID: PMC4852291 DOI: 10.3389/fpls.2016.00599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/18/2016] [Indexed: 05/29/2023]
Abstract
A short-root rice mutant was isolated from an ethyl methane sulfonate-mutagenized library. From map-based cloning strategy, a point mutation, resulting in an amino acid change from proline to leucine, was identified in the fourth exon of a glutamyl-tRNA (Gln) amidotransferase B subunit family protein (OsGatB, LOC_Os11g34210). This gene is an ortholog of Arabidopsis GatB and yeast PET112. GatB is a subunit of tRNA-dependent amidotransferase (AdT), an essential enzyme involved in Gln-tRNA(Gln) synthesis in mitochondria. Although previous studies have described that cessation in mitochondrial translation is lethal at very early developmental stages in plants, this point mutation resulted in a non-lethal phenotype of smaller root meristem and shorter root cell length. In the root, OsGatB was predominantly expressed in the root tip and played an important role in cell division and elongation there. OsGatB was localized in the mitochondria, and mitochondrial structure and function were all affected in Osgatb root tip cells.
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Affiliation(s)
- Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Linming Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Huanhuan Zhang
- The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang UniversityHangzhou, China
| | - Meiling He
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Jingqin Shen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Yunhong Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, China
| | - Ping Wu
- The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang UniversityHangzhou, China
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Maira N, Torres TM, de Oliveira AL, de Medeiros SRB, Agnez-Lima LF, Lima JPMS, Scortecci KC. Identification, characterisation and molecular modelling of two AP endonucleases from base excision repair pathway in sugarcane provide insights on the early evolution of green plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:622-31. [PMID: 23957429 DOI: 10.1111/plb.12083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/01/2013] [Indexed: 05/21/2023]
Abstract
Unlike bacteria and mammals, plant DNA repair pathways are not well characterised, especially in monocots. The understanding of these processes in the plant cell is of major importance, since they may be directly involved in plant acclimation and adaptation to stressful environments. Hence, two sugarcane ESTs were identified as homologues of AP endonuclease from the base-excision repair pathway: ScARP1 and ScARP3. In order to understand their probable function and evolutionary origin, structural and phylogenetic studies were performed using bioinformatics approaches. The two predicted proteins present a considerable amino acid sequence similarity, and molecular modelling procedures indicate that both are functional, since the main structural motifs remain conserved. However, inspection of the sort signal regions on the full-length cDNAs indicated that these proteins have a distinct organelle target. Furthermore, variances in their promoter cis-element motifs were also found. Although the mRNA expression pattern was similar, there were significant differences in their expression levels. Taken together, these data raise the hypothesis that the ScARP is an example of a probable gene duplication event that occurred before monocotyledon/dicotyledon segregation, followed by a sub-functionalisation event in the Poaceae, leading to new intracellular targeting and different expression levels.
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Affiliation(s)
- N Maira
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys. Biochem J 2014; 458:513-23. [PMID: 24428730 DOI: 10.1042/bj20131451] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plasmodium parasites possess two endosymbiotic organelles: a mitochondrion and a relict plastid called the apicoplast. To accommodate the translational requirements of these organelles in addition to its cytosolic translation apparatus, the parasite must maintain a supply of charged tRNA molecules in each of these compartments. In the present study we investigate how the parasite manages these translational requirements for charged tRNACys with only a single gene for CysRS (cysteinyl-tRNA synthetase). We demonstrate that the single PfCysRS (Plasmodium falciparum CysRS) transcript is alternatively spliced, and, using a combination of endogenous and heterologous tagging experiments in both P. falciparum and Toxoplasma gondii, we show that CysRS isoforms traffic to the cytosol and apicoplast. PfCysRS can recognize and charge the eukaryotic tRNACys encoded by the Plasmodium nucleus as well as the bacterial-type tRNA encoded by the apicoplast genome, albeit with a preference for the eukaryotic type cytosolic tRNA. The results of the present study indicate that apicomplexan parasites have lost their original plastidic cysteinyl-tRNA synthetase, and have replaced it with a dual-targeted eukaryotic type CysRS that recognizes plastid and nuclear tRNACys. Inhibitors of the Plasmodium dual-targeted CysRS would potentially offer a therapy capable of the desirable immediate effects on parasite growth as well as the irreversibility of inhibitors that disrupt apicoplast inheritance.
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8
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Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
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Baudisch B, Langner U, Garz I, Klösgen RB. The exception proves the rule? Dual targeting of nuclear-encoded proteins into endosymbiotic organelles. THE NEW PHYTOLOGIST 2014; 201:80-90. [PMID: 24024706 DOI: 10.1111/nph.12482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 08/05/2013] [Indexed: 05/17/2023]
Abstract
Plant cells harbor two types of endosymbiotic organelle: mitochondria and chloroplasts. As a consequence of endosymbiotic gene transfer, the majority of their proteins are encoded in the nucleus and post-translationally 're'-imported into the respective target organelle. The corresponding transport signals are usually selective for a single organelle, but several proteins are transported into both the mitochondria and chloroplasts. To estimate the number of proteins with such dual targeting properties in Arabidopsis, we classified the proteins encoded by nuclear genes of endosymbiotic origin according to the respective targeting specificity of their N-terminal transport signals as predicted by the TargetP software package. Selected examples of the resulting protein classes were subsequently analyzed by transient transformation assays as well as by in organello protein transport experiments. It was found that most proteins with high prediction values for both organelles show dual targeting with both experimental approaches. Unexpectedly, however, dual targeting was even found among those proteins that are predicted to be localized solely in one of the two endosymbiotic organelles. In total, among the 16 candidate proteins analyzed, we identified 10 proteins with dual targeting properties. This unexpectedly high proportion suggests that such transport properties are much more abundant than anticipated.
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Affiliation(s)
- Bianca Baudisch
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Uwe Langner
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Ingo Garz
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - Ralf Bernd Klösgen
- Institute of Biology - Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
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10
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Langner U, Baudisch B, Klösgen RB. Organelle import of proteins with dual targeting properties into mitochondria and chloroplasts takes place by the general import pathways. PLANT SIGNALING & BEHAVIOR 2014; 9:e29301. [PMID: 25763617 PMCID: PMC4203536 DOI: 10.4161/psb.29301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
As a consequence of the endosymbiotic gene transfer, most mitochondrial and chloroplastic proteins are nuclear encoded and synthesized in the cytosol as precursor proteins with transit peptides mediating transport to their subcellular destination. It is often assumed that these transit peptides are strictly monospecific for a single organelle. But in recent years more and more proteins have been identified which carry transit peptides that are capable of mediating transport into both mitochondria and chloroplasts. In a recent study we showed with a combination of in silico, in organello, and in vivo approaches that the frequency of such proteins is apparently much higher than usually anticipated.(1) Here we demonstrate with in organello competition experiments that the import of 2 of these dually targeted proteins (GrpE and EF-Tu) takes place by the same import pathways that are used by organelle proteins with "typical" monospecific targeting properties.
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11
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Xu L, Carrie C, Law SR, Murcha MW, Whelan J. Acquisition, conservation, and loss of dual-targeted proteins in land plants. PLANT PHYSIOLOGY 2013; 161:644-62. [PMID: 23257241 PMCID: PMC3561010 DOI: 10.1104/pp.112.210997] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The dual-targeting ability of a variety of proteins from Physcomitrella patens, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. Overall, the targeting ability of over 80 different proteins from rice and P. patens, representing 42 dual-targeted proteins in Arabidopsis, was tested. We found that dual targeting arose early in land plant evolution, as it was evident in many cases with P. patens proteins that were conserved in rice and Arabidopsis. Furthermore, we found that the acquisition of dual-targeting ability is still occurring, evident in P. patens as well as rice and Arabidopsis. The loss of dual-targeting ability appears to be rare, but does occur. Ascorbate peroxidase represents such an example. After gene duplication in rice, individual genes encode proteins that are targeted to a single organelle. Although we found that dual targeting was generally conserved, the ability to detect dual-targeted proteins differed depending on the cell types used. Furthermore, it appears that small changes in the targeting signal can result in a loss (or gain) of dual-targeting ability. Overall, examination of the targeting signals within this study did not reveal any clear patterns that would predict dual-targeting ability. The acquisition of dual-targeting ability also appears to be coordinated between proteins. Mitochondrial intermembrane space import and assembly protein40, a protein involved in oxidative folding in mitochondria and peroxisomes, provides an example where acquisition of dual targeting is accompanied by the dual targeting of substrate proteins.
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12
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Jiang L, Wang S, Li H, Zhang G, Li H. EMBRYONIC FACTOR 31 encodes a tyrosyl-tRNA synthetase that is essential for seed development. Mol Biol Rep 2012; 39:8297-305. [DOI: 10.1007/s11033-012-1678-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:253-9. [PMID: 22683762 DOI: 10.1016/j.bbamcr.2012.05.029] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/26/2012] [Accepted: 05/28/2012] [Indexed: 01/08/2023]
Abstract
Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Baudisch B, Klösgen RB. Dual targeting of a processing peptidase into both endosymbiotic organelles mediated by a transport signal of unusual architecture. MOLECULAR PLANT 2012; 5:494-503. [PMID: 22131051 DOI: 10.1093/mp/ssr092] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
As a result of the endosymbiotic gene transfer, the majority of proteins of mitochondria and chloroplasts are encoded in the nucleus and synthesized in the cytosol as precursor proteins carrying N-terminal transport signals for the 're-import' into the respective target organelle. Most of these transport signals are monospecific, although some of them have dual targeting properties, that is, they are recognized both by mitochondria and by chloroplasts as target organelles. We have identified alpha-MPP2, one of the two isoforms of the substrate binding subunit of mitochondrial processing peptidase of Arabidopsis thaliana, as a novel member of this class of nuclear-encoded organelle proteins. As demonstrated by in organello transport experiments with isolated organelles and by in vivo localization studies employing fluorescent chimeric reporter proteins, the N-terminal region of the alpha-MPP2 precursor comprises transport signals for the import into mitochondria as well as into chloroplasts. Both signals are found within the N-terminal 79 residues of the precursor protein, where they occupy partly separated and partly overlapping regions. Deletion mapping combined with in organello and in vivo protein transport studies demonstrate an unusual architecture of this transport signal, suggesting a composition of three functionally separated domains.
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Affiliation(s)
- Bianca Baudisch
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany
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15
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Hirakawa Y, Burki F, Keeling PJ. Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastid in chlorarachniophytes. J Cell Sci 2012; 125:6176-84. [DOI: 10.1242/jcs.116533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In plants, many nucleus-encoded proteins are targeted to both mitochondria and plastids, and this process is generally mediated by ambiguous N-terminal targeting sequences that are recognized by receptors on both organelles. In many algae, however, plastids were acquired by secondarily engulfing green or red algae, which were retained within the endomembrane system. Protein targeting to these secondary plastids is more complex, and because they do not reside directly in the cytoplasm, dual targeting could not function as it does in plant cells. Here we investigate dual targeting of aminoacyl-tRNA synthetases (aaRSs) in chlorarachniophytes, complex algae that possess secondary plastids and a relict nucleus derived from a green algal endosymbiont. Chlorarachniophytes have four genome-containing compartments, but almost all the aaRSs are nucleus-encoded and present in fewer than four copies (some as few as two), suggesting multiple targeting. We characterized the subcellular localization of two classes, HisRS (three copies) and GlyRS (two copies), using GFP fusion proteins. In both cases, one copy was dually targeted to mitochondria and plastids, but unlike plants this was mediated by translation initiation variants. We also found the periplastidal compartment (the relict green algal cytoplasm) lacks both GlyRS and a cognate tRNA, suggesting pre-charged host tRNAs are imported into this compartment. Leader analysis of other aaRSs suggests alternative translation is a common strategy for dual targeting in these complex cells. Overall, dual targeting to mitochondria and plastids is a shared feature of plastid-bearing organisms, but the increased complexity of trafficking into secondary plastids requires a different strategy.
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Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B. SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. FRONTIERS IN PLANT SCIENCE 2011; 2:43. [PMID: 22639594 PMCID: PMC3355584 DOI: 10.3389/fpls.2011.00043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 08/12/2011] [Indexed: 05/08/2023]
Abstract
Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mitochondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.
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Affiliation(s)
| | - Liam Childs
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Marc Lohse
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | | | - Anja Lude
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
| | - Joachim Selbig
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
| | - Björn Usadel
- Max Planck Institute of Molecular Plant PhysiologyPotsdam, Germany
- *Correspondence: Björn Usadel, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Golm, 14476 Potsdam, Germany. e-mail:
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In silico methods for identifying organellar and suborganellar targeting peptides in Arabidopsis chloroplast proteins and for predicting the topology of membrane proteins. Methods Mol Biol 2011; 774:243-80. [PMID: 21822844 DOI: 10.1007/978-1-61779-234-2_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Numerous experimental and in silico approaches have been developed for attempting to identify the -subcellular localisation of proteins. Approximately 2,000-4,000 proteins are thought to be targeted to plastids in plants, but a complete and unambiguous catalogue has yet to be drawn up. This article reviews the various prediction methods that identify plastid targeting sequences, and those that can help estimate location and topology within the plastid or plastid membranes. The most successful approaches are described in detail, with detailed notes to help avoid common pitfalls and advice on interpreting conflicting or ambiguous results. In most cases, it is best to try multiple approaches, and we also cover the powerful new integrated databases that provide a selected blend of experimental data and predictions.
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Brandão MM, Silva-Filho MC. Evolutionary history of Arabidopsis thaliana aminoacyl-tRNA synthetase dual-targeted proteins. Mol Biol Evol 2010; 28:79-85. [PMID: 20624849 DOI: 10.1093/molbev/msq176] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacyl-transfer RNA (tRNA) synthetases (aaRS) are key players in translation and act early in protein synthesis by mediating the attachment of amino acids to their cognate tRNA molecules. In plants, protein synthesis may occur in three subcellular compartments (cytosol, mitochondria, and chloroplasts), which requires multiple versions of the protein to be correctly delivered to its proper destination. The organellar aaRS are nuclear encoded and equipped with targeting information at the N-terminal sequence, which enables them to be specifically translocated to their final location. Most of the aaRS families present organellar proteins that are dual targeted to mitochondria and chloroplasts. Here, we examine the dual targeting behavior of aaRS from an evolutionary perspective. Our results show that Arabidopsis thaliana aaRS sequences are a result of a horizontal gene transfer event from bacteria. However, there is no evident bias indicating one single ancestor (Cyanobacteria or Proteobacteria). The dual-targeted aaRS phylogenetic relationship was characterized into two different categories (paralogs and homologs) depending on the state recovered for both dual-targeted and cytosolic proteins. Taken together, our results suggest that the dual-targeted condition is a gain-of-function derived from gene duplication. Selection may have maintained the original function in at least one of the copies as the additional copies diverged.
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Affiliation(s)
- Marcelo M Brandão
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
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Evans-Roberts KM, Breuer C, Wall MK, Sugimoto-Shirasu K, Maxwell A. Arabidopsis thaliana GYRB3 does not encode a DNA gyrase subunit. PLoS One 2010; 5:e9899. [PMID: 20360860 PMCID: PMC2845627 DOI: 10.1371/journal.pone.0009899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 03/05/2010] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA topoisomerases are enzymes that control the topology of DNA in all cells. DNA gyrase is unique among the topoisomerases in that it is the only enzyme that can actively supercoil DNA using the free energy of ATP hydrolysis. Until recently gyrase was thought to be unique to bacteria, but has now been discovered in plants. The genome of the model plant, Arabidopsis thaliana, is predicted to encode four gyrase subunits: AtGyrA, AtGyrB1, AtGyrB2 and AtGyrB3. METHODOLOGY/PRINCIPAL FINDINGS We found, contrary to previous data, that AtGyrB3 is not essential to the survival of A. thaliana. Bioinformatic analysis suggests AtGyrB3 is considerably shorter than other gyrase B subunits, lacking part of the ATPase domain and other key motifs found in all type II topoisomerases; but it does contain a putative DNA-binding domain. Partially purified AtGyrB3 cannot bind E. coli GyrA or support supercoiling. AtGyrB3 cannot complement an E. coli gyrB temperature-sensitive strain, whereas AtGyrB2 can. Yeast two-hybrid analysis suggests that AtGyrB3 cannot bind to AtGyrA or form a dimer. CONCLUSIONS/SIGNIFICANCE These data strongly suggest that AtGyrB3 is not a gyrase subunit but has another unknown function. One possibility is that it is a nuclear protein with a role in meiosis in pollen.
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Affiliation(s)
| | - Christian Breuer
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
- RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
| | - Melisa K. Wall
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
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Martin W. Evolutionary origins of metabolic compartmentalization in eukaryotes. Philos Trans R Soc Lond B Biol Sci 2010; 365:847-55. [PMID: 20124349 PMCID: PMC2817231 DOI: 10.1098/rstb.2009.0252] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary 'homing device' that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a 'minor mistargeting' mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.
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Affiliation(s)
- William Martin
- Institute of Botany III, University of Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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