scholarly journals Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9772
Author(s):  
Ryan W. Christian ◽  
Seanna L. Hewitt ◽  
Grant Nelson ◽  
Eric H. Roalson ◽  
Amit Dhingra
Keyword(s):  
Transit Peptide ◽  
Shotgun Proteomics ◽  
Proteomics Data ◽  
Subcellular Targeting ◽  
Chloroplast Transit Peptide ◽  
Transit Peptides ◽  
Alternative Transcription ◽  
Plastid Targeting ◽  
Comparative Genomics Analysis ◽  
Strict Requirement

Subcellular relocalization of proteins determines an organism’s metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.

scholarly journals A novel pathway linking plasma membrane and chloroplasts is co-opted by pathogens to suppress salicylic acid-dependent defences

2019 ◽  
Author(s):  
Laura Medina-Puche ◽  
Huang Tan ◽  
Vivek Dogra ◽  
Mengshi Wu ◽  
Tabata Rosas-Diaz ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Plasma Membrane ◽  
Plant Pathogens ◽  
Plant Defence ◽  
Transit Peptide ◽  
Plant Proteins ◽  
Subcellular Targeting ◽  
Chloroplast Transit Peptide ◽  
Hormonal Responses ◽  
Plant Pathogen Interactions

SUMMARYChloroplasts are crucial players in the activation of defensive hormonal responses during plant-pathogen interactions. Here, we show that a plant virus-encoded protein re-localizes from the plasma membrane to chloroplasts upon triggering plant defence, interfering with the chloroplast-dependent activation of anti-viral salicylic acid (SA) biosynthesis. Strikingly, we have found that plant pathogens from different kingdoms seem to have convergently evolved to target chloroplasts and impair SA-dependent defences following an association with membranes, which is based on the co-existence of two subcellular targeting signals, an N-myristoylation site and a chloroplast transit peptide. This pattern is also present in plant proteins, at least one of which conversely activates SA defences from the chloroplast. Taken together, our results suggest that a pathway linking plasma membrane to chloroplasts and activating defence exists in plants, and that such pathway has been co-opted by plant pathogens during host-pathogen co-evolution to promote virulence through suppression of SA responses.

scholarly journals Programmed chloroplast destruction during leaf senescence involves 13-lipoxygenase (13-LOX)

2016 ◽  
Vol 113 (12) ◽  
pp. 3383-3388 ◽  
Author(s):  
Armin Springer ◽  
ChulHee Kang ◽  
Sachin Rustgi ◽  
Diter von Wettstein ◽  
Christiane Reinbothe ◽  
...  
Keyword(s):  
Leaf Senescence ◽  
Critical Role ◽  
Transit Peptide ◽  
Physiological Changes ◽  
Pathogen Defense ◽  
Chloroplast Transit Peptide ◽  
Selective Destruction ◽  
Plastid Envelope ◽  
Volatile Aldehydes

Leaf senescence is the terminal stage in the development of perennial plants. Massive physiological changes occur that lead to the shut down of photosynthesis and a cessation of growth. Leaf senescence involves the selective destruction of the chloroplast as the site of photosynthesis. Here, we show that 13-lipoxygenase (13-LOX) accomplishes a key role in the destruction of chloroplasts in senescing plants and propose a critical role of its NH2-terminal chloroplast transit peptide. The 13-LOX enzyme identified here accumulated in the plastid envelope and catalyzed the dioxygenation of unsaturated membrane fatty acids, leading to a selective destruction of the chloroplast and the release of stromal constituents. Because 13-LOX pathway products comprise compounds involved in insect deterrence and pathogen defense (volatile aldehydes and oxylipins), a mechanism of unmolested nitrogen and carbon relocation is suggested that occurs from leaves to seeds and roots during fall.

scholarly journals Deep Semi-Supervised Learning Improves Universal Peptide Identification of Shotgun Proteomics Data

2020 ◽  
Author(s):  
John T. Halloran ◽  
Gregor Urban ◽  
David Rocke ◽  
Pierre Baldi
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Peptide Identification ◽  
Shotgun Proteomics ◽  
Database Search ◽  
Supervised Machine Learning ◽  
Superior Performance ◽  
Support Vector ◽  
Proteomics Data ◽  
Learning Classifier

AbstractSemi-supervised machine learning post-processors critically improve peptide identification of shot-gun proteomics data. Such post-processors accept the peptide-spectrum matches (PSMs) and feature vectors resulting from a database search, train a machine learning classifier, and recalibrate PSMs using the trained parameters, often yielding significantly more identified peptides across q-value thresholds. However, current state-of-the-art post-processors rely on shallow machine learning methods, such as support vector machines. In contrast, the powerful training capabilities of deep learning models have displayed superior performance to shallow models in an ever-growing number of other fields. In this work, we show that deep models significantly improve the recalibration of PSMs compared to the most accurate and widely-used post-processors, such as Percolator and PeptideProphet. Furthermore, we show that deep learning is able to adaptively analyze complex datasets and features for more accurate universal post-processing, leading to both improved Prosit analysis and markedly better recalibration of recently developed database-search functions.

scholarly journals atToc159 is a selective transit peptide receptor for the import of nucleus-encoded chloroplast proteins

2004 ◽  
Vol 165 (3) ◽  
pp. 323-334 ◽  
Author(s):  
Matthew D. Smith ◽  
Caleb M. Rounds ◽  
Fei Wang ◽  
Kunhua Chen ◽  
Meshack Afitlhile ◽  
...  
Keyword(s):  
Plant Cell ◽  
Chloroplast Development ◽  
Transit Peptide ◽  
Chloroplast Biogenesis ◽  
Cross Link ◽  
Peptide Receptor ◽  
Chloroplast Proteins ◽  
Transit Peptides ◽  
Import Receptor

The members of the Toc159 family of GTPases act as the primary receptors for the import of nucleus-encoded preproteins into plastids. Toc159, the most abundant member of this family in chloroplasts, is required for chloroplast biogenesis (Bauer, J., K. Chen, A. Hiltbunner, E. Wehrli, M. Eugster, D. Schnell, and F. Kessler. 2000. Nature. 403:203–207) and has been shown to covalently cross-link to bound preproteins at the chloroplast surface (Ma, Y., A. Kouranov, S. LaSala, and D.J. Schnell. 1996. J. Cell Biol. 134:1–13; Perry, S.E., and K. Keegstra. 1994. Plant Cell. 6:93–105). These reports led to the hypothesis that Toc159 functions as a selective import receptor for preproteins that are required for chloroplast development. In this report, we provide evidence that Toc159 is required for the import of several highly expressed photosynthetic preproteins in vivo. Furthermore, we demonstrate that the cytoplasmic and recombinant forms of soluble Toc159 bind directly and selectively to the transit peptides of these representative photosynthetic preproteins, but not representative constitutively expressed plastid preproteins. These data support the function of Toc159 as a selective import receptor for the targeting of a set of preproteins required for chloroplast biogenesis.

Construction of Two Vectors for a Bypass of Monocotyledon Plants Photorespiration

2011 ◽  
Vol 340 ◽  
pp. 351-356
Author(s):  
Xue Liang Bai ◽  
Dan Wang ◽  
Ning Ning Liu ◽  
Li Jing Wei ◽  
Ye Rong Zhu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transgenic Plants ◽  
Binary Vector ◽  
Transit Peptide ◽  
Expression Vectors ◽  
Chloroplast Transit Peptide ◽  
E Coli ◽  
Plant Expression ◽  
Glycolate Dehydrogenase ◽  
Save Energy

In order to modify the photorespiration of monocotyledonous crops, we aimed to construct vectors that will be used to introduce a bypass to the native photorespiration pathway. Firstly, we cloned the encoding sequences of glyoxylate carboligase (GCL) and tartronic semialdehyde reductase (TSR) fromE. coli, glycolate dehydrogenase (GDH) fromArabidopsis thalianaand chloroplast transit peptide (cTP) from rice. Then we constructed a universal vector pEXP harboring the encoding sequence of cTP for targeting a protein into chloroplast. By insertion of these three encoding sequences into the universal vector pEXP, we obtained the expression cassettes for GCL, TSR and GDH, respectively. Finally, we inserted the cassettes for GCL and TSR in tandem into the binary vector pCAMBIA 1301, and for GDH into another binary vector, pPGN, to obtain our plant expression vectors pCAMBIA 1301-TG and pPGN-GDH, respectively. These two expression vectors possess different selection resistance and can be used to transform monocots together, to introduce the bypass pathway of photorespiration. By this way, the transgenic plants can recycle glycolate, the by-product of photosynthesis in C3plants, within the chloroplast, simultaneously, save energy and avoid the loss of ammonia, which will contribute to improved growth.

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