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Roy Choudhury D, Maurya A, Singh NK, Singh GP, Singh R. Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces. PLANTS (BASEL, SWITZERLAND) 2024; 13:1707. [PMID: 38931139 PMCID: PMC11207502 DOI: 10.3390/plants13121707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length-width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies.
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Affiliation(s)
- Debjani Roy Choudhury
- Division of Genomic Resources, ICAR—National Bureau of Plant Genetic Resources, New Delhi 110012, India; (D.R.C.); (A.M.)
| | - Avantika Maurya
- Division of Genomic Resources, ICAR—National Bureau of Plant Genetic Resources, New Delhi 110012, India; (D.R.C.); (A.M.)
| | | | | | - Rakesh Singh
- Division of Genomic Resources, ICAR—National Bureau of Plant Genetic Resources, New Delhi 110012, India; (D.R.C.); (A.M.)
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Li G, Zhu W, Tian M, Liu R, Ruan Y, Liu C. Genome-Wide Identification of the SPP/SPPL Gene Family and BnaSPPL4 Regulating Male Fertility in Rapeseed ( Brassica napus L.). Int J Mol Sci 2024; 25:3936. [PMID: 38612746 PMCID: PMC11012144 DOI: 10.3390/ijms25073936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Signal peptide peptidase (SPP) and its homologs, signal peptide peptidase-like (SPPL) proteases, are members of the GxGD-type aspartyl protease family, which is widespread in plants and animals and is a class of transmembrane proteins with significant biological functions. SPP/SPPLs have been identified; however, the functions of SPP/SPPL in rapeseed (Brassica napus L.) have not been reported. In this study, 26 SPP/SPPLs were identified in rapeseed and categorized into three groups: SPP, SPPL2, and SPPL3. These members mainly contained the Peptidase_A22 and PA domains, which were distributed on 17 out of 19 chromosomes. Evolutionary analyses indicated that BnaSPP/SPPLs evolved with a large number of whole-genome duplication (WGD) events and strong purifying selection. Members are widely expressed and play a key role in the growth and development of rapeseed. The regulation of rapeseed pollen fertility by the BnaSPPL4 gene was further validated through experiments based on bioinformatics analysis, concluding that BnaSPPL4 silencing causes male sterility. Cytological observation showed that male infertility caused by loss of BnaSPPL4 gene function occurs late in the mononucleate stage due to microspore dysplasia.
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Affiliation(s)
- Guangze Li
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Wenjun Zhu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Minyu Tian
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Rong Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Ying Ruan
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Yuelushan Laboratory, Hunan Agricultural University, Changsha 410128, China; (G.L.); (W.Z.); (M.T.); (R.L.); (Y.R.)
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, China
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Thulasi Devendrakumar K, Peng TS, Pierdzig L, Jackson E, Lipka V, Li X. Signal Peptide Peptidase and PI4Kβ1/2 play opposite roles in plant ER stress response and immunity. STRESS BIOLOGY 2024; 4:20. [PMID: 38507026 PMCID: PMC10954597 DOI: 10.1007/s44154-024-00155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024]
Abstract
The Arabidopsis pi4kβ1,2 mutant is mutated in the phosphatidylinositol 4-kinase (PI4K) β1 and PI4Kβ2 enzymes which are involved in the biosynthesis of phosphatidylinositol 4-phosphate (PI4P), a minor membrane lipid with important signaling roles. pi4kβ1,2 plants display autoimmunity and shorter roots. Though the pi4kβ1,2 mutant has been extensively characterized, the source of its autoimmunity remains largely unknown. In this study, through a genetic suppressor screen, we identified multiple partial loss-of-function alleles of signal peptide peptidase (spp) that can suppress all the defects of pi4kβ1,2. SPP is an intramembrane cleaving aspartic protease. Interestingly, pi4kβ1,2 plants display enhanced ER stress response and mutations in SPP can suppress such phenotype. Furthermore, reduced ER stress responses were observed in the spp single mutants. Overall, our study reveals a previously unknown function of PI4Kβ and SPP in ER stress and plant immunity.
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Affiliation(s)
- Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tony ShengZhe Peng
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Leon Pierdzig
- Department of Plant Cell Biology, Georg August Universität Göttingen, 37077, Göttingen, Lower Saxony, Germany
| | - Edan Jackson
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Volker Lipka
- Department of Plant Cell Biology, Georg August Universität Göttingen, 37077, Göttingen, Lower Saxony, Germany
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6013-6033. [PMID: 35768189 DOI: 10.1093/jxb/erac290] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Moin M, Saha A, Bakshi A, Madhav MS, Kirti PB. Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants. Gene 2021; 789:145670. [PMID: 33892070 DOI: 10.1016/j.gene.2021.145670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Abstract
We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.
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Affiliation(s)
- Mazahar Moin
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Achala Bakshi
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - M S Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad 500030, India
| | - P B Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India; Agri-Biotech Foundation, PJTS Agricultural University, Hyderabad 500030, India
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Sadder MT, Alshomali I, Ateyyeh A, Musallam A. Physiological and molecular responses for long term salinity stress in common fig ( Ficus carica L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:107-117. [PMID: 33627966 PMCID: PMC7873141 DOI: 10.1007/s12298-020-00921-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/15/2020] [Accepted: 12/28/2020] [Indexed: 05/09/2023]
Abstract
UNLABELLED Salinity stress in increasingly becoming a major challenge in current and expanding agricultural ecosystems. Unlike temporal abiotic stresses, plants are usually exposed to salinity stress for an entire lifespan. Therefore, a long term effect (10 weeks) of continuous salinity exposure was investigated for three common fig landraces (Zraki, Mwazi, and Khdari). Both relative water content and chlorophyll content decreased with elevated salinity stress, while stem length barely changed. The most prominent decline was observed in root biomass. The data would align common fig to moderately tolerant threshold slop with a C50 range of 100 to 150 mM NaCl. A high and significant correlation was evident between root biomass and chlorophyll content (85%). Concurrently, differential expression of putative salinity responsive genes in common fig were determined; signal peptide peptidase-like 2B (FcSPPL2B), dehydration responsive element binding protein (FcDREB), calcineurin B-like protein (CBL)-CBL-interacting serine/threonine-protein kinase 11 (FcCIPK11), sorbitol dehydrogenase (FcSORD) and dehydrin (FcDHN). The data were discussed for each gene in respect of its potential role in salinity stress mitigation. The combined physiological and molecular data would conclude Zraki as the most salinity tolerant genotype. The major implication of the data emphasizes the tremendous genotype by environment (salinity stress) interaction in common fig. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s12298-020-00921-z).
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Affiliation(s)
- Monther T. Sadder
- Department of Horticulture and Crop Science, Faculty of Agriculture, University of Jordan, Amman, 11942 Jordan
| | - Ibrahim Alshomali
- Department of Horticulture and Crop Science, Faculty of Agriculture, University of Jordan, Amman, 11942 Jordan
| | - Ahmad Ateyyeh
- Department of Horticulture and Crop Science, Faculty of Agriculture, University of Jordan, Amman, 11942 Jordan
| | - Anas Musallam
- National Agricultural Research Center, P.O Box: 639, Baq’a, 19381 Jordan
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7
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Kusunoki K, Hoshi M, Tamura T, Maeda T, Abe K, Asakura T. Yeast-based reporter assay system for identifying the requirements of intramembrane proteolysis by signal peptide peptidase of Arabidopsis thaliana. FEBS Open Bio 2020; 10:1833-1842. [PMID: 32686366 PMCID: PMC7459403 DOI: 10.1002/2211-5463.12936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/11/2020] [Accepted: 07/05/2020] [Indexed: 11/09/2022] Open
Abstract
Signal peptide peptidase (SPP) is an aspartic protease with two active sites, YD and GXGD, in the transmembrane domain. SPP cleaves signal peptides, and the released fragments play key roles in the immune system, embryo development and protein turnover in cells. Despite SPP having an important function, a general system to identify the requirements of intramembrane proteolysis by SPP has not been developed because proteolysis occurs in the membrane. In this study, we first established a reporter assay system in yeast to verify the cleavage activity of the Arabidopsis thaliana SPP (AtSPP). Next, we screened candidate substrates of AtSPP from A. thaliana pollen and roots. In the pollen, 13 signal peptides with 'pollen' and 'cell wall' as gene ontology terms were selected. In the roots, mutants overexpressing AtSPP were constructed, and gene expression changes were compared with the wild‐type. Nine signal peptides expressed in the roots were selected. Then we used the candidate substrates in our reporter assay system to determine the requirements for proteolysis by AtSPP. Fifteen of 22 signal peptides were cleaved by AtSPP. The absence of the positively charged amino acids, His and Lys on the C terminus of the signal sequence, was observed in cleaved substrates. Moreover, mutation of a helix breaker‐to‐Leu substitution in the intramembrane region in substrates prevented cleavage by AtSPP. These results indicated that substrates of AtSPP required the helix breaker structure to be cleaved.
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Affiliation(s)
- Kenta Kusunoki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
| | - Masako Hoshi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
| | - Tomoko Tamura
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Keiko Abe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
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Midorikawa K, Kuroda M, Yamashita H, Tamura T, Abe K, Asakura T. Oryza sativa Brittle Culm 1-like 6 modulates β-glucan levels in the endosperm cell wall. PLoS One 2019; 14:e0217212. [PMID: 31120929 PMCID: PMC6532911 DOI: 10.1371/journal.pone.0217212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 05/07/2019] [Indexed: 11/18/2022] Open
Abstract
The endosperm cell wall affects post-harvest grain quality by affecting the mechanical fragility and water absorption of the grain. Therefore, understanding the mechanism underlying endosperm cell wall synthesis is important for determining the growth and quality of cereals. However, the molecular machinery mediating endosperm cell wall biosynthesis is not well understood. In this study, we investigated the role of Oryza sativa Brittle Culm 1-like 6 (OsBC1L6), a member of the COBRA-like protein family, in cellulose synthesis in rice. OsBC1L6 mRNA was expressed in ripening seeds during endosperm enlargement. When OsBC1L6-RFP was expressed in Arabidopsis cell cultures, this fusion protein was transported to the plasma membrane. To investigate the target molecules of OsBC1L6, we analyzed the binding interactions of OsBC1L6 with cellohexaose and the analogs using surface plasmon resonance, determining that cellohexaose bound to OsBC1L6. The β-glucan contents were significantly reduced in OsBC1L6-RNAi calli and OsBC1L6-deficient seeds from a Tos insertion mutant, compared to their wild-type counterparts. These findings suggest that OsBC1L6 modulates β-glucan synthesis during endosperm cell wall formation by interacting with cellulose moieties on the plasma membrane during seed ripening.
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Affiliation(s)
- Keiko Midorikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaharu Kuroda
- Division of Crop Development, Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Niigata, Japan
- * E-mail: (TA); (MK)
| | - Haruyuki Yamashita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoko Tamura
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Keiko Abe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC), Life Science & Environmental Research Center (LiSE), Kanagawa, Japan
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail: (TA); (MK)
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Ahn E, Hu Z, Perumal R, Prom LK, Odvody G, Upadhyaya HD, Magill C. Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut. PLoS One 2019; 14:e0216671. [PMID: 31086384 PMCID: PMC6516728 DOI: 10.1371/journal.pone.0216671] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 02/04/2023] Open
Abstract
In previous studies, a sorghum mini core collection was scored over several years for response to Colletotrichum sublineola, Peronosclerospora sorghi, and Sporisorium reilianum, the causal agents of the disease anthracnose, downy mildew, and head smut, respectively. The screening results were combined with over 290,000 Single nucleotide polymorphic (SNP) loci from an updated version of a publicly available genotype by sequencing (GBS) dataset available for the mini core collection. GAPIT (Genome Association and Prediction Integrated Tool) R package was used to identify chromosomal locations that differ in disease response. When the top scoring SNPs were mapped to the most recent version of the published sorghum genome, in each case, a nearby and most often the closest annotated gene has precedence for a role in host defense.
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Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Ramasamy Perumal
- Kansas State University, Agricultural Research Center, Hays, Kansas, United States of America
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, Texas, United States of America
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, Texas, United States of America
| | - Hari D. Upadhyaya
- ICRISAT, Patancheru, Telangana, India
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Clint Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
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Plastid intramembrane proteolysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:910-4. [PMID: 25528366 DOI: 10.1016/j.bbabio.2014.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 01/25/2023]
Abstract
Progress in the field of regulated intramembrane proteolysis (RIP) in recent years has not surpassed plant biology. Nevertheless, reports on RIP in plants, and especially in chloroplasts, are still scarce. Of the four different families of intramembrane proteases, only two have been linked to chloroplasts so far, rhomboids and site-2 proteases (S2Ps). The lack of chloroplast-located rhomboid proteases was associated with reduced fertility and aberrations in flower morphology, probably due to perturbations in jasmonic acid biosynthesis, which occurs in chloroplasts. Mutations in homologues of S2P resulted in chlorophyll deficiency and impaired chloroplast development, through a yet unknown mechanism. To date, the only known substrate of RIP in chloroplasts is a PHD transcription factor, located in the envelope. Upon proteolytic cleavage by an unknown protease, the soluble N-terminal domain of this protein is released from the membrane and relocates to the nucleus, where it activates the transcription of the ABA response gene ABI4. Continuing studies on these proteases and substrates, as well as identification of the genes responsible for different chloroplast mutant phenotypes, are expected to shed more light on the roles of intramembrane proteases in chloroplast biology.
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Voss M, Schröder B, Fluhrer R. Mechanism, specificity, and physiology of signal peptide peptidase (SPP) and SPP-like proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2828-39. [PMID: 24099004 DOI: 10.1016/j.bbamem.2013.03.033] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/25/2013] [Accepted: 03/29/2013] [Indexed: 01/09/2023]
Abstract
Signal peptide peptidase (SPP) and the homologous SPP-like (SPPL) proteases SPPL2a, SPPL2b, SPPL2c and SPPL3 belong to the family of GxGD intramembrane proteases. SPP/SPPLs selectively cleave transmembrane domains in type II orientation and do not require additional co-factors for proteolytic activity. Orthologues of SPP and SPPLs have been identified in other vertebrates, plants, and eukaryotes. In line with their diverse subcellular localisations ranging from the ER (SPP, SPPL2c), the Golgi (SPPL3), the plasma membrane (SPPL2b) to lysosomes/late endosomes (SPPL2a), the different members of the SPP/SPPL family seem to exhibit distinct functions. Here, we review the substrates of these proteases identified to date as well as the current state of knowledge about the physiological implications of these proteolytic events as deduced from in vivo studies. Furthermore, the present knowledge on the structure of intramembrane proteases of the SPP/SPPL family, their cleavage mechanism and their substrate requirements are summarised. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Matthias Voss
- Adolf Butenandt Institute for Biochemistry, Ludwig-Maximilians University Munich, Schillerstr. 44, 80336 Munich, Germany
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12
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Adam Z. Emerging roles for diverse intramembrane proteases in plant biology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2933-6. [PMID: 24099011 DOI: 10.1016/j.bbamem.2013.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 04/21/2013] [Accepted: 05/11/2013] [Indexed: 11/28/2022]
Abstract
Progress in the field of regulated intramembrane proteolysis (RIP) in recent years has made its impact on plant biology as well. Although this field within plant research is still in its infancy, some interesting observations have started to emerge. Gene encoding orthologs of rhomboid proteases, site-2 proteases (S2P), presenilin/γ-secretases, and signal peptide peptidases are found in plant genomes and some of these gene products were identified in different plant cell membranes. The lack of chloroplast-located rhomboid proteases was associated with reduced fertility and aberrations in flower morphology. Mutations in homologues of S2P resulted in chlorophyll deficiency and impaired chloroplast development. An S2P was also implicated in the response to ER stress through cleavage of ER-membrane bZIP transcription factors, allowing their migration to the nucleus and activation of the transcription of BiP chaperones. Other membrane-bound transcription factors of the NAC and PHD families were also demonstrated to undergo RIP and relocalization to the nucleus. These and other new data are expected to shed more light on the roles of intramembrane proteases in plant biology in the future. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
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Hoshi M, Ohki Y, Ito K, Tomita T, Iwatsubo T, Ishimaru Y, Abe K, Asakura T. Experimental detection of proteolytic activity in a signal peptide peptidase of Arabidopsis thaliana. BMC BIOCHEMISTRY 2013; 14:16. [PMID: 23829174 PMCID: PMC3710259 DOI: 10.1186/1471-2091-14-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/02/2013] [Indexed: 11/23/2022]
Abstract
Background Signal peptide peptidase (SPP) is a multi-transmembrane aspartic protease involved in intramembrane-regulated proteolysis (RIP). RIP proteases mediate various key life events by releasing bioactive peptides from the plane of the membrane region. We have previously isolated Arabidopsis SPP (AtSPP) and found that this protein is expressed in the ER. An AtSPP-knockout plant was found to be lethal because of abnormal pollen formation; however, there is negligible information describing the physiological function of AtSPP. In this study, we have investigated the proteolytic activity of AtSPP to define the function of SPPs in plants. Results We found that an n-dodecyl-ß-maltoside (DDM)-solubilized membrane fraction from Arabidopsis cells digested the myc-Prolactin-PP-Flag peptide, a human SPP substrate, and this activity was inhibited by (Z-LL)2-ketone, an SPP-specific inhibitor. The proteolytic activities from the membrane fractions solubilized by other detergents were not inhibited by (Z-LL)2-ketone. To confirm the proteolytic activity of AtSPP, the protein was expressed as either a GFP fusion protein or solely AtSPP in yeast. SDS-PAGE analysis showed that migration of the fragments that were cleaved by AtSPP were identical in size to the fragments produced by human SPP using the same substrate. These membrane-expressed proteins digested the substrate in a manner similar to that in Arabidopsis cells. Conclusions The data from the in vitro cell-free assay indicated that the membrane fraction of both Arabidopsis cells and AtSPP recombinantly expressed in yeast actually possessed proteolytic activity for a human SPP substrate. We concluded that plant SPP possesses proteolytic activity and may be involved in RIP.
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Affiliation(s)
- Masako Hoshi
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
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Li P, Zang W, Li Y, Xu F, Wang J, Shi T. AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. Nucleic Acids Res 2010; 39:D1130-3. [PMID: 21036873 PMCID: PMC3013798 DOI: 10.1093/nar/gkq959] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research, the overall protein interaction network frameworks of several model organisms have been created through data collection and integration. However, most of the networks processed only show simple relationships without boundary, weight or direction, which do not truly reflect the biological reality. In vivo, different types of protein interactions, such as the assembly of protein complexes or phosphorylation, often have their specific functions and qualifications. Ignorance of these features will bring much bias to the network analysis and application. Therefore, we annotate the Arabidopsis proteins in the AtPID database with further information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. The latest updated AtPID database is available at http://www.megabionet.org/atpid/.
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Affiliation(s)
- Peng Li
- Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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Tamura T, Kuroda M, Oikawa T, Kyozuka J, Terauchi K, Ishimaru Y, Abe K, Asakura T. Signal peptide peptidases are expressed in the shoot apex of rice, localized to the endoplasmic reticulum. PLANT CELL REPORTS 2009; 28:1615-1621. [PMID: 19688213 DOI: 10.1007/s00299-009-0760-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 07/15/2009] [Accepted: 07/29/2009] [Indexed: 05/28/2023]
Abstract
Signal peptide peptidase (SPP) is a multi-transmembrane aspartic proteinase involved in regulated intramembrane proteolysis, which is implicated in fundamental life processes such as immunological response, cell signaling, tissue differentiation, and embryogenesis. In this study, we identified two rice SPPs: OsSPP1 and OsSPP2. Green fluorescent protein-fused OsSPP1 and OsSPP2 were localized to the ER in cultured plant cells. In situ hybridization showed that OsSPPs were strongly expressed in vegetative shoot apex, young panicle, developing panicle, and the early developing florets. Undifferentiated cells, which have the potential to differentiate into all of the aerial parts of the plant are presented in the shoot apex. OsSPPs are located in both the undifferentiated cells, and the early differentiated cells at the shoot apex. These results suggest that rice SPPs have an important function in differentiation and development at the shoot apex. The expression of the shoot apex and ER localization is equal to dicot Arabidopsis thaliana, and will have common crucial roles in plant.
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Affiliation(s)
- Tomoko Tamura
- Department of Applied Biological Chemistry, The University of Tokyo, Japan
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Iwata Y, Fedoroff NV, Koizumi N. Arabidopsis bZIP60 is a proteolysis-activated transcription factor involved in the endoplasmic reticulum stress response. THE PLANT CELL 2008; 4:514-6. [PMID: 19017746 PMCID: PMC2613661 DOI: 10.1105/tpc.108.061002] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Revised: 10/18/2008] [Accepted: 10/31/2008] [Indexed: 05/18/2023]
Abstract
Proteins synthesized in the endoplasmic reticulum (ER) of eukaryotic cells must be folded correctly before translocation out of the ER. Disruption of protein folding results in the induction of genes for ER-resident chaperones, for example, BiP. This phenomenon is known as the ER stress response. We report here that bZIP60, an Arabidopsis thaliana basic leucine zipper (bZIP) transcription factor with a transmembrane domain, is involved in the ER stress response. When compared with wild-type Arabidopsis plants, homozygous bzip60 mutant plants show a markedly weaker induction of many ER stress-responsive genes. The bZIP60 protein resides in the ER membrane under unstressed condition and is cleaved in response to ER stress caused by either tunicamycin or DTT. The N-terminal fragment containing the bZIP domain is then translocated into the nucleus. Cleavage of bZIP60 is independent of the function of Arabidopsis homologs of mammalian S1P and S2P proteases, which mediate the proteolytic cleavage of the mammalian transcription factor ATF6. In Arabidopsis, expression of the bZIP60 gene and cleavage of the bZIP60 protein are observed in anthers in the absence of stress treatment, suggesting that the ER stress response functions in the normal development of active secretory cells.
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Affiliation(s)
- Yuji Iwata
- Huck Institutes of the Life Sciences, Pensylvania State University, University Park, Pensylvania 16802, USA
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