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Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2024; 42:6600-6612. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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2
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Qanmber G, You Q, Yang Z, Fan L, Zhang Z, Chai M, Gao B, Li F, Yang Z. Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton. J Adv Res 2024; 58:13-30. [PMID: 37207930 PMCID: PMC10982868 DOI: 10.1016/j.jare.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION The unavailability of intergenic region annotation in whole genome sequencing and pan-genomics hinders efforts to enhance crop improvement. OBJECTIVES Despite advances in research, the impact of post-transcriptional regulation on fiber development and translatome profiling at different stages of fiber growth in cotton (G. hirsutum) remains unexplored. METHODS We utilized a combination of reference-guided de novo transcriptome assembly and ribosome profiling techniques to uncover the hidden mechanisms of translational control in eight distinct tissues of upland cotton. RESULTS Our study identified P-site distribution at three-nucleotide periodicity and dominant ribosome footprint at 27 nucleotides. Specifically, we have detected 1,589 small open reading frames (sORFs), including 1,376 upstream ORFs (uORFs) and 213 downstream ORFs (dORFs), as well as 552 long non-coding RNAs (lncRNAs) with potential coding functions, which fine-tune the annotation of the cotton genome. Further, we have identified novel genes and lncRNAs with strong translation efficiency (TE), while sORFs were found to affect mRNA transcription levels during fiber elongation. The reliability of these findings was confirmed by the high consistency in correlation and synergetic fold change between RNA-sequencing (RNA-seq) and Ribosome-sequencing (Ribo-seq) analyses. Additionally, integrated omics analysis of the normal fiber ZM24 and short fiber pag1 cotton mutant revealed several differentially expressed genes (DEGs), and fiber-specific expressed (high/low) genes associated with sORFs (uORFs and dORFs). These findings were further supported by the overexpression and knockdown of GhKCS6, a gene associated with sORFs in cotton, and demonstrated the potential regulation of the mechanism governing fiber elongation on both the transcriptional and post-transcriptional levels. CONCLUSION Reference-guided transcriptome assembly and the identification of novel transcripts fine-tune the annotation of the cotton genome and predicted the landscape of fiber development. Our approach provided a high-throughput method, based on multi-omics, for discovering unannotated ORFs, hidden translational control, and complex regulatory mechanisms in crop plants.
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Affiliation(s)
- Ghulam Qanmber
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Liqiang Fan
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhibin Zhang
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Mao Chai
- National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Baibai Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; National Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Feng YZ, Zhu QF, Xue J, Chen P, Yu Y. Shining in the dark: the big world of small peptides in plants. ABIOTECH 2023; 4:238-256. [PMID: 37970469 PMCID: PMC10638237 DOI: 10.1007/s42994-023-00100-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/24/2023] [Indexed: 11/17/2023]
Abstract
Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.
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Affiliation(s)
- Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qing-Feng Zhu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Pei Chen
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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A Proteomics Data Mining Strategy for the Identification of Quinoa Grain Proteins with Potential Immunonutritional Bioactivities. Foods 2023; 12:foods12020390. [PMID: 36673481 PMCID: PMC9858122 DOI: 10.3390/foods12020390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Quinoa proteins are attracting global interest for their wide amino acid profile and as a promising source for the development of biomedical treatments, including those against immune-mediated diseases. However, information about the bioactivity of quinoa proteins is scarce. In this study, a quinoa grain proteome map obtained by label-free mass spectrometry-based shotgun proteomics was investigated for the identification of quinoa grain proteins with potential immunonutritional bioactivities, including those related to cancer. After carefully examining the sequence similarities of the 1211 identified quinoa grain proteins against already described bioactive proteins from other plant organisms, 71, 48, and 3 of them were classified as antimicrobial peptides (AMPs), oxidative stress induced peptides (OSIPs), and serine-type protease inhibitors (STPIs), respectively, suggesting their potential as immunomodulatory, anti-inflammatory, and anticancer agents. In addition, data interpretation using Venn diagrams, heat maps, and scatterplots revealed proteome similarities and differences with respect to the AMPs, OSIPs, and STPIs, and the most relevant bioactive proteins in the predominant commercial quinoa grains (i.e., black, red, white (from Peru), and royal (white from Bolivia)). The presented proteomics data mining strategy allows easy screening for potentially relevant quinoa grain proteins and commercial classes for immunonutrition, as a basis for future bioactivity testing.
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Guo R, Yu X, Gregory BD. The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes. PLANT DIRECT 2023; 7:e479. [PMID: 36643787 PMCID: PMC9831718 DOI: 10.1002/pld3.479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
RNA turnover is essential in maintaining messenger RNA (mRNA) homeostasis during various developmental stages and stress responses. Co-translational mRNA decay (CTRD), a process in which mRNAs are degraded while still associated with translating ribosomes, has recently been discovered to function in yeast and three angiosperm transcriptomes. However, it is still unclear how prevalent CTRD across the plant lineage. Moreover, the sequence features of co-translationally decayed mRNAs have not been well-studied. Here, utilizing a collection of publicly available degradome sequencing datasets for another seven angiosperm transcriptomes, we have confirmed that CTRD is functioning in at least 10 angiosperms and likely throughout the plant lineage. Additionally, we have identified sequence features shared by the co-translationally decayed mRNAs in these species, implying a possible conserved triggering mechanism for this pathway. Given that degradome sequencing datasets can also be used to identify actively translating upstream open reading frames (uORFs), which are quite understudied in plants, we have identified numerous actively translating uORFs in the same 10 angiosperms. These findings reveal that actively translating uORFs are prevalent in plant transcriptomes, some of which are conserved across this lineage. We have also observed conserved sequence features in the regions flanking these uORFs' stop codons that might contribute to ribosome stalling at these sequences. Finally, we discovered that there were very few overlaps between the mRNAs harboring actively translating uORFs and those sorted into the co-translational decay pathway in the majority of the studied angiosperms, suggesting that these two processes might be nearly mutually exclusive in those species. In total, our findings provide the identification of CTRD and actively translating uORFs across a broad collection of plants and provide novel insights into the important sequence features associated with these collections of mRNAs and regulatory elements, respectively.
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Affiliation(s)
- Rong Guo
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Xiang Yu
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Present address:
School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Pei MS, Liu HN, Wei TL, Yu YH, Guo DL. Large-scale discovery of non-conventional peptides in grape ( Vitis vinifera L.) through peptidogenomics. HORTICULTURE RESEARCH 2022; 9:uhac023. [PMID: 35531313 PMCID: PMC9070638 DOI: 10.1093/hr/uhac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.
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Affiliation(s)
- Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
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Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech 2022; 12:76. [PMID: 35251879 PMCID: PMC8873315 DOI: 10.1007/s13205-022-03147-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated rate of ribosome profiling and mass spectrometry development, have made identification of small open reading frames (sORFs) (< 100 codons) in various plant genomes possible. The past 50 years have seen sORFs being isolated from many organisms. However, to date, a comprehensive sORF annotation pipeline is as yet unavailable, hence, addressed in our review. Here, we also provide current information on classification and functions of plant sORFs and their potential applications in crop improvement programs.
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Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int J Mol Sci 2021; 22:13128. [PMID: 34884929 PMCID: PMC8658490 DOI: 10.3390/ijms222313128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
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Affiliation(s)
| | | | - Igor Fesenko
- Department of Functional Genomics and Proteomics of Plants, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (I.L.); (V.I.)
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Aggarwal S, Kumar A, Jain M, Sudan J, Singh K, Kumari S, Mustafiz A. C-terminally encoded peptides (CEPs) are potential mediators of abiotic stress response in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2019-2033. [PMID: 33088046 PMCID: PMC7548271 DOI: 10.1007/s12298-020-00881-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/18/2020] [Accepted: 09/04/2020] [Indexed: 05/13/2023]
Abstract
Intracellular signaling is a critical determinant of the normal growth and development of plants. Signaling peptides, also known as peptide hormones, along with classical phytohormones, are the significant players of plant intracellular signaling. C-terminally encoded peptide (CEP), a 15-amino acid post-translationally peptide identified in Arabidopsis, plays a pivotal role in lateral root formation, nodulation, and act as long-distance root to shoot signaling molecule in N-starvation conditions. Expression of CEP gene members in Arabidopsis is perturbed by nitrogen starvation; however, not much is known regarding their role in other abiotic stress conditions. To gain a comprehensive insight into CEP biology, we identified CEP genes across diverse plant genera (Glycine max, Sorghum bicolor, Brassica rapa, Zea mays, and Oryza sativa) using bioinformatics tools. In silico promoter analysis revealed that CEP gene promoters show an abundance of abiotic stress-responsive elements suggesting a possible role of CEPs in abiotic stress signaling. Spatial and temporal expression patterns of CEP via RNA seq and microarray revealed that various CEP genes are transcriptionally regulated in response to abiotic stresses. Validation of rice CEP genes expression by qRT-PCR showed that OsCEP1, OsCEP8, OsCEP9, and OsCEP10 were highly upregulated in response to different abiotic stress conditions. Our findings suggest these CEP genes might be important mediators of the abiotic stress response and warrant further overexpression/knockout studies to delineate their precise role in abiotic stress response.
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Affiliation(s)
- Sakshi Aggarwal
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Ashish Kumar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Muskan Jain
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Jebi Sudan
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, 180009 India
| | - Kapil Singh
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Sumita Kumari
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, 180009 India
| | - Ananda Mustafiz
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
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10
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Wang S, Tian L, Liu H, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J, Wu L. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. MOLECULAR PLANT 2020; 13:1078-1093. [PMID: 32445888 DOI: 10.1016/j.molp.2020.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3' UTRs, 5' UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.
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Affiliation(s)
- Shunxi Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Lei Tian
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xueyan Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xingmeng Jia
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xu Zheng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shubiao Wu
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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Oshiro KGN, Rodrigues G, Monges BED, Cardoso MH, Franco OL. Bioactive Peptides Against Fungal Biofilms. Front Microbiol 2019; 10:2169. [PMID: 31681179 PMCID: PMC6797862 DOI: 10.3389/fmicb.2019.02169] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
Infections caused by invasive fungal biofilms have been widely associated with high morbidity and mortality rates, mainly due to the advent of antibiotic resistance. Moreover, fungal biofilms impose an additional challenge, leading to multidrug resistance. This fact, along with the contamination of medical devices and the limited number of effective antifungal agents available on the market, demonstrates the importance of finding novel drug candidates targeting pathogenic fungal cells and biofilms. In this context, an alternative strategy is the use of antifungal peptides (AFPs) against fungal biofilms. AFPs are considered a group of bioactive molecules with broad-spectrum activities and multiple mechanisms of action that have been widely used as template molecules for drug design strategies aiming at greater specificity and biological efficacy. Among the AFP classes most studied in the context of fungal biofilms, defensins, cathelicidins and histatins have been described. AFPs can also act by preventing the formation of fungal biofilms and eradicating preformed biofilms through mechanisms associated with cell wall perturbation, inhibition of planktonic fungal cells’ adhesion onto surfaces, gene regulation and generation of reactive oxygen species (ROS). Thus, considering the critical scenario imposed by fungal biofilms and associated infections and the application of AFPs as a possible treatment, this review will focus on the most effective AFPs described to date, with a core focus on antibiofilm peptides, as well as their efficacy in vivo, application on surfaces and proposed mechanisms of action.
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Affiliation(s)
- Karen G N Oshiro
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Gisele Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Bruna Estéfani D Monges
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Marlon Henrique Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
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Shen H, Ming Y, Xu C, Xu Y, Zhao S, Zhang Q. Deregulation of long noncoding RNA (TUG1) contributes to excessive podocytes apoptosis by activating endoplasmic reticulum stress in the development of diabetic nephropathy. J Cell Physiol 2019; 234:15123-15133. [PMID: 30671964 DOI: 10.1002/jcp.28153] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
The objective of this study was to investigate the molecular mechanism of how TUG1 interferes with the expression of C/EBP homologous protein (CHOP), peroxisome-proliferator-activated receptor-γ coactivator-1 alpha (PGC-1α), which contributes to the development of diabetic nephropathy. Real-time polymerase chain reaction and western blot analysis were performed to explore the regulatory relationship among TUG1, CHOP, PGC-1α, and caspase-3. Terminal deoxynucleotidyl transferase dUTP nick-end labeling was performed to confirm TUG1 involved in diabetic nephropathy (DN) through influencing podocytes apoptosis. TUG1 was highly expressed in a cell following treatment with high glucose, and PGC-1α and cleaved caspase-3 levels were much lower, while CHOP level was much higher in high glucose group (HG), furthermore, CHOP inhibited PGC-1α expression. TUG1 negatively regulated CHOP expression, and positively regulated PGC-1α expression. Meanwhile, total caspase-3 level in cell treated with or without HG transfected with CHOP small interfering ribonucleic acid (siRNA), TUG1, and TUG1 siRNA showed no evident difference with their corresponding control, while CHOP siRNA and TUG1 evidently decreased, and TUG1 siRNA remarkably increased cleaved caspase-3 level in HG or normal glucose groups in comparison with corresponding control. TUG1 and PGC-1α levels were much lower, while CHOP level was much higher in participants diagnosed with DN. A higher level of CHOP protein and lower level of PGC-1α were observed in subjects diagnosed with DN. Finally, podocytes apoptosis in the DN group was significantly promoted compared with that in nondiabetic renal disease group. Our current study has suggested for the first time that the long noncoding RNA (lncRNA) TUG1 influenced podocytes apoptosis via mediating endoplasmic reticulum stress (ERS)-CHOP-PGC-1α signaling pathway in HG-induced DN.
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Affiliation(s)
- Hongchun Shen
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yao Ming
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Chuanlan Xu
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yanwen Xu
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Sha Zhao
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Qiong Zhang
- Department of Nephrology, The Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
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13
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Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res 2019; 29:1464-1477. [PMID: 31387879 PMCID: PMC6724668 DOI: 10.1101/gr.253302.119] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Ilya Kirov
- Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation
| | - Andrey Kniazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Regina Khazigaleeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Viktor Zgoda
- Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Georgy Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
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14
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Xie J, Chen S, Xu W, Zhao Y, Zhang D. Origination and Function of Plant Pseudogenes. PLANT SIGNALING & BEHAVIOR 2019; 14:1625698. [PMID: 31161861 PMCID: PMC6619919 DOI: 10.1080/15592324.2019.1625698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pseudogenes, nonfunctional genomic sequences derived from functional protein-coding genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Studies on the evolution and functional aspects of plant pseudogenes are limited, despite their abundance in the plant genome. To date, most researches on pseudogenes focus on mammals. Here, we summarized current knowledge on pseudogenes including the historical and recent progress, analyzes their essential roles in gene regulation in hope of further stimulating researches in plant species for understanding gene regulation and evolution.
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Affiliation(s)
- Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Sisi Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Weijie Xu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Yiyang Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- CONTACT Deqiang Zhang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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15
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Hazarika RR, Sostaric N, Sun Y, van Noort V. Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana. PLoS One 2018; 13:e0205179. [PMID: 30321192 PMCID: PMC6188750 DOI: 10.1371/journal.pone.0205179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/20/2018] [Indexed: 02/07/2023] Open
Abstract
Several recent studies indicate that small Open Reading Frames (sORFs) embedded within multiple eukaryotic non-coding RNAs can be translated into bioactive peptides of up to 100 amino acids in size. However, the functional roles of the 607 Stress Induced Peptides (SIPs) previously identified from 189 Transcriptionally Active Regions (TARs) in Arabidopsis thaliana remain unclear. To provide a starting point for functional annotation of these plant-derived peptides, we performed a large-scale prediction of peptide binding sites on protein surfaces using coarse-grained peptide docking. The docked models were subjected to further atomistic refinement and binding energy calculations. A total of 530 peptide-protein pairs were successfully docked. In cases where a peptide encoded by a TAR is predicted to bind at a known ligand or cofactor-binding site within the protein, it can be assumed that the peptide modulates the ligand or cofactor-binding. Moreover, we predict that several peptides bind at protein-protein interfaces, which could therefore regulate the formation of the respective complexes. Protein-peptide binding analysis further revealed that peptides employ both their backbone and side chain atoms when binding to the protein, forming predominantly hydrophobic interactions and hydrogen bonds. In this study, we have generated novel predictions on the potential protein-peptide interactions in A. thaliana, which will help in further experimental validation.
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Affiliation(s)
- Rashmi R. Hazarika
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Nikolina Sostaric
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Yifeng Sun
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Faculty of Engineering Technology, Campus Group T, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- * E-mail:
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16
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Khazigaleeva RA, Fesenko IA. Biologically active peptides encoded by small open reading frames. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s106816201706005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Ramada MHS, Brand GD, Abrão FY, Oliveira M, Filho JLC, Galbieri R, Gramacho KP, Prates MV, Bloch C. Encrypted Antimicrobial Peptides from Plant Proteins. Sci Rep 2017; 7:13263. [PMID: 29038449 PMCID: PMC5643462 DOI: 10.1038/s41598-017-13685-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022] Open
Abstract
Examples of bioactive peptides derived from internal sequences of proteins are known for decades. The great majority of these findings appear to be fortuitous rather than the result of a deliberate and methodological-based enterprise. In the present work, we describe the identification and the biological activities of novel antimicrobial peptides unveiled as internal fragments of various plant proteins founded on our hypothesis-driven search strategy. All putative encrypted antimicrobial peptides were selected based upon their physicochemical properties that were iteratively selected by an in-house computer program named Kamal. The selected peptides were chemically synthesized and evaluated for their interaction with model membranes. Sixteen of these peptides showed antimicrobial activity against human and/or plant pathogens, some with a wide spectrum of activity presenting similar or superior inhibition efficacy when compared to classical antimicrobial peptides (AMPs). These original and previously unforeseen molecules constitute a broader and undisputable set of evidences produced by our group that illustrate how the intragenic concept is a workable reality and should be carefully explored not only for microbicidal agents but also for many other biological functions.
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Affiliation(s)
- M H S Ramada
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, 70770-917, Brasília, DF, Brazil
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900, Brasília, DF, Brazil
- Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160, Brasília, DF, Brazil
| | - G D Brand
- Laboratório de Síntese e Análise de Biomoléculas, Instituto de Química, Universidade de Brasília, Brasília, DF, Brazil
| | - F Y Abrão
- Faculdade de Farmácia, FacUnicamps, 74535-280, Goiânia, GO, Brazil
| | - M Oliveira
- Faculdade de Farmácia, FacUnicamps, 74535-280, Goiânia, GO, Brazil
| | - J L Cardozo Filho
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, 70770-917, Brasília, DF, Brazil
- Departamento de Fitopatologia, Instituto Mato-Grossense do Algodão, 78850-000, Primavera do Leste, MT, Brazil
| | - R Galbieri
- Departamento de Fitopatologia, Instituto Mato-Grossense do Algodão, 78850-000, Primavera do Leste, MT, Brazil
| | - K P Gramacho
- Laboratório de Fitopatologia Molecular, Centro de Pesquisa do Cacau, 45600-970, Itabuna, BA, Brazil
| | - M V Prates
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, 70770-917, Brasília, DF, Brazil
| | - C Bloch
- Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, 70770-917, Brasília, DF, Brazil.
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18
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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19
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Vie AK, Najafi J, Winge P, Cattan E, Wrzaczek M, Kangasjärvi J, Miller G, Brembu T, Bones AM. The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3557-3571. [PMID: 28586470 PMCID: PMC5853212 DOI: 10.1093/jxb/erx168] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/04/2017] [Indexed: 05/13/2023]
Abstract
Small signalling peptides have emerged as important cell to cell messengers in plant development and stress responses. However, only a few of the predicted peptides have been functionally characterized. Here, we present functional characterization of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. Localization studies suggest that the peptides require a signal peptide and C-terminal processing to be correctly transported out of the cell. Both IDL6 and IDL7 appear to be unstable transcripts under post-transcriptional regulation. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEIN (ZFP) genes, WRKY genes, and genes encoding calcium-dependent proteins. IDL7 expression was rapidly induced by hydrogen peroxide, and idl7 and idl6 idl7 double mutants displayed reduced cell death upon exposure to extracellular reactive oxygen species (ROS). Co-treatment of the bacterial elicitor flg22 with IDL7 peptide attenuated the rapid ROS burst induced by treatment with flg22 alone. Taken together, our results suggest that IDL7, and possibly IDL6, act as negative modulators of stress-induced ROS signalling in Arabidopsis.
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Affiliation(s)
- Ane Kjersti Vie
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Javad Najafi
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ester Cattan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michael Wrzaczek
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Finland
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Finland
- Distinguished Scientist Fellowship Program, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tore Brembu
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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20
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Weiller F, Moore JP, Young P, Driouich A, Vivier MA. The Brassicaceae species Heliophila coronopifolia produces root border-like cells that protect the root tip and secrete defensin peptides. ANNALS OF BOTANY 2017; 119:803-813. [PMID: 27481828 PMCID: PMC5379576 DOI: 10.1093/aob/mcw141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/03/2016] [Accepted: 06/02/2016] [Indexed: 05/16/2023]
Abstract
Background and Aims Root border cells and border-like cells (BLCs), the latter originally described in Arabidopsis thaliana , have been described as cells released at the root tips of the species in which they occur. BLCs are thought to provide protection to root meristems similar to classical root border cells. In addition, four defensin peptides (Hc-AFP1-4) have previously been characterized from Heliophila coronopifolia , a South African semi-desert flower, and found to be strongly antifungal. This provided an opportunity to evaluate if the BLCs of H. coronopifolia indeed produce these defensins, which would provide evidence towards a defence role for BLCs. Methods Fluorescence microscopy, using live-cell-imaging technology, was used to characterize the BLCs of H. coronopifolia . Quantitative real-time PCR (qRT-PCR) analysis and immunofluorescence microscopy was used to characterize these defensin peptides. Key Results BLCs originated at the root apical meristem and formed a protective sheath at the tip and along the sides as the root elongated in solid medium. BLCs have a cellulose-enriched cell wall, intact nuclei and are embedded in a layer of pectin-rich mucilage. Pectinase treatments led to the dissolution of the sheath and dissociation of the root BLCs. Hc-AFP1-4 genes were all expressed in root tissues, but Hc-AFP3 transcripts were the most abundant in these tissues as measured by qRT-PCR. A polyclonal antibody that was cross-reactive with all four defensins, and probably recognizing a general plant defensin epitope, was used in fluorescence microscopy analysis to examine the presence of the peptides in the root tip and BLCs. Data confirmed the peptides present in the root tip tissues, the mucilage sheath and the BLCs. Conclusions This study provides a link between defensin peptides and BLCs, both embedded in a protective pectin mucilage sheath, during normal plant growth and development. The presence of the Hc-AFP3 defensin peptides in the BLCs suggests a role for these cells in root protection.
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Affiliation(s)
- Florent Weiller
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Grand Réseau de Recherche VASI de Haute Normandie, Normandie Université, Université de Rouen, 76821 Mont Saint Aignan cedex, France
| | - John P. Moore
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| | - Philip Young
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
| | - Azeddine Driouich
- Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Grand Réseau de Recherche VASI de Haute Normandie, Normandie Université, Université de Rouen, 76821 Mont Saint Aignan cedex, France
| | - Melané A. Vivier
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
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21
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Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BPA, van Noort V. ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. BMC Bioinformatics 2017; 18:37. [PMID: 28095775 PMCID: PMC5240266 DOI: 10.1186/s12859-016-1458-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/31/2016] [Indexed: 12/24/2022] Open
Abstract
Background Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. Results To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides. Conclusion To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1458-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rashmi R Hazarika
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Barbara De Coninck
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.,Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, B-9052, Belgium
| | - Lidia R Yamamoto
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Laura R Martin
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Bruno P A Cammue
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.,Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, B-9052, Belgium
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium.
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22
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Verbandt S, Henriques ST, Spincemaille P, Harvey PJ, Chandhok G, Sauer V, De Coninck B, Cassiman D, Craik DJ, Cammue BPA, De Cremer K, Thevissen K. Identification of survival-promoting OSIP108 peptide variants and their internalization in human cells. Mech Ageing Dev 2016; 161:247-254. [PMID: 27491841 DOI: 10.1016/j.mad.2016.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/30/2016] [Accepted: 07/30/2016] [Indexed: 11/19/2022]
Abstract
The plant-derived decapeptide OSIP108 increases tolerance of yeast and human cells to apoptosis-inducing agents, such as copper and cisplatin. We performed a whole amino acid scan of OSIP108 and conducted structure-activity relationship studies on the induction of cisplatin tolerance (CT) in yeast. The use of cisplatin as apoptosis-inducing trigger in this study should be considered as a tool to better understand the survival-promoting nature of OSIP108 and not for purposes related to anti-cancer treatment. We found that charged residues (Arg, His, Lys, Glu or Asp) or a Pro on positions 4-7 improved OSIP108 activity by 10% or more. The variant OSIP108[G7P] induced the most pronounced tolerance to toxic concentrations of copper and cisplatin in yeast and/or HepG2 cells. Both OSIP108 and OSIP108[G7P] were shown to internalize equally into HeLa cells, but at a higher rate than the inactive OSIP108[E10A], suggesting that the peptides can internalize into cells and that OSIP108 activity is dependent on subsequent intracellular interactions. In conclusion, our studies demonstrated that tolerance/survival-promoting properties of OSIP108 can be significantly improved by single amino acid substitutions, and that these properties are dependent on (an) intracellular target(s), yet to be determined.
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Affiliation(s)
- Sara Verbandt
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | | | - Pieter Spincemaille
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium; Department of Laboratory Medicine, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Peta J Harvey
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Gursimran Chandhok
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Vanessa Sauer
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - David Cassiman
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - David J Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.
| | - Kaat De Cremer
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, CMPG, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
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Verbandt S, Cammue BPA, Thevissen K. Yeast as a model for the identification of novel survival-promoting compounds applicable to treat degenerative diseases. Mech Ageing Dev 2016; 161:306-316. [PMID: 27287065 DOI: 10.1016/j.mad.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/31/2016] [Accepted: 06/07/2016] [Indexed: 12/18/2022]
Abstract
Programmed cell death (PCD) plays an important role in development and normal metabolic functioning of organisms. Excessive cell death is the cause of many degenerative diseases, like neurodegenerative disorders and Wilson's disease, for which current therapies remain insufficient. Current therapies are mainly focused on decreasing the disease symptoms following cell death, rather than blocking the cell death process itself. The latter can be obtained by either decreasing the presence of the toxic trigger (like protein aggregation in case of many commonly known neurodegenerative diseases) or by blocking death-inducing signaling cascade(s). Given the high conservation in PCD processes between yeast and mammalian cells, in this review, we will focus on yeast as a model organism to study PCD-related diseases as well as on its use for drug discovery purposes. More specifically, we will provide a comprehensive overview of new compounds, which were identified in yeast-based drug screens, that either decrease the amount of toxic trigger or inhibit PCD signaling cascades under PCD-inducing conditions.
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Affiliation(s)
- Sara Verbandt
- Centre of Microbial and Plant Genetics CMPG, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics CMPG, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics CMPG, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
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Maróti G, Downie JA, Kondorosi É. Plant cysteine-rich peptides that inhibit pathogen growth and control rhizobial differentiation in legume nodules. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:57-63. [PMID: 26116977 DOI: 10.1016/j.pbi.2015.05.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/13/2015] [Accepted: 05/31/2015] [Indexed: 05/25/2023]
Abstract
Plants must co-exist with both pathogenic and beneficial microbes. Antimicrobial peptides with broad antimicrobial activities represent one of the first lines of defense against pathogens. Many plant cysteine-rich peptides with potential antimicrobial properties have been predicted. Amongst them, defensins and defensin-like peptides are the most abundant and plants can express several hundreds of them. In some rhizobial-legume symbioses special defensin-like peptides, the nodule-specific cysteine-rich (NCR) peptides have evolved in those legumes whose symbiotic partner terminally differentiates. In Medicago truncatula, >700 NCRs exist and collectively act as plant effectors inducing irreversible differentiation of rhizobia to nitrogen-fixing bacteroids. Cationic NCR peptides have a broad range of potent antimicrobial activities but do not kill the endosymbionts.
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Affiliation(s)
- Gergely Maróti
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62., Szeged 6726, Hungary
| | - J Allan Downie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Éva Kondorosi
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62., Szeged 6726, Hungary.
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25
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Guo H, Jiang C, Sun X. Therapeutical effects and mechanism of salubrinal combined with ulinastatin on treating paraquat poisoning. Cell Biochem Biophys 2015; 70:1559-63. [PMID: 25030410 DOI: 10.1007/s12013-014-0095-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To explore therapeutic effects and underlying mechanism of Salubrinal combined with Ulinastatin (UTI) on acute Paraquat (PQ) poisoning. Four hundred rats were randomly allocated into UTI group, SAL group, SAL + UTI and control group according to random number table with 100 rats in each group. Acute PQ poisoning models were established, and all rats received UTI, Salubrinal, SAL + UTI and normal saline injection, respectively. Afterward, we analyzed the change of lung tissue and explored the mechanism. Acute PQ poisoning caused significantly damage in rat lung tissue structure, and UTI could effectively repair lung tissue damage. Salubrinal suppressed hemorrhage and fibrosis, but promoted inflammatory infiltration. In contrast, UTI + Salubrinal suppressed hemorrhage, fibrosis and inflammatory infiltration, but could not improve lung tissue damage. Expression of LC3 and Bcl-2 showed statistically significant difference among different groups (p < 0.05). LC3 and Bcl-2 levels in UTI group were much higher than in the other groups, and LC3 and Bcl-2 levels in UTI + SAL group was second higher. LC expression in SAL group was lower than in UTI group and UTI + SAL group with Bcl-2 in control group significantly lower than in the other groups (p < 0.05). Expression of Caspase-3 and Bcl-2/Bax in lung tissue in different groups had statistically significant difference (p < 0.05). Caspase-3 in UTI group was lower than in the other groups; however, Bcl-2/Bax in UTI group was higher than in the other groups (p < 0.05). Acute PQ poisoning can cause endoplasmic reticulum stress-autophagy in rat, and UTI can increase Bcl-2 expression, decrease Caspase-3, which can inhibit progress of lung injury by suppressing apoptosis and exert good therapeutic effects. Although salubrinal has marked effects on protecting lung tissue, it can increase Bcl-2 expression, which is not beneficial to lung tissue protection. The underlying mechanism still needs further exploration.
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Affiliation(s)
- Hua Guo
- Department of Emergency, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China,
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26
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McLaughlin JE, Bin-Umer MA, Widiez T, Finn D, McCormick S, Tumer NE. A Lipid Transfer Protein Increases the Glutathione Content and Enhances Arabidopsis Resistance to a Trichothecene Mycotoxin. PLoS One 2015; 10:e0130204. [PMID: 26057253 PMCID: PMC4461264 DOI: 10.1371/journal.pone.0130204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/17/2015] [Indexed: 12/02/2022] Open
Abstract
Fusarium head blight (FHB) or scab is one of the most important plant diseases worldwide, affecting wheat, barley and other small grains. Trichothecene mycotoxins such as deoxynivalenol (DON) accumulate in the grain, presenting a food safety risk and health hazard to humans and animals. Despite considerable breeding efforts, highly resistant wheat or barley cultivars are not available. We screened an activation tagged Arabidopsis thaliana population for resistance to trichothecin (Tcin), a type B trichothecene in the same class as DON. Here we show that one of the resistant lines identified, trichothecene resistant 1 (trr1) contains a T-DNA insertion upstream of two nonspecific lipid transfer protein (nsLTP) genes, AtLTP4.4 and AtLTP4.5. Expression of both nsLTP genes was induced in trr1 over 10-fold relative to wild type. Overexpression of AtLTP4.4 provided greater resistance to Tcin than AtLTP4.5 in Arabidopsis thaliana and in Saccharomyces cerevisiae relative to wild type or vector transformed lines, suggesting a conserved protection mechanism. Tcin treatment increased reactive oxygen species (ROS) production in Arabidopsis and ROS stain was associated with the chloroplast, the cell wall and the apoplast. ROS levels were attenuated in Arabidopsis and in yeast overexpressing AtLTP4.4 relative to the controls. Exogenous addition of glutathione and other antioxidants enhanced resistance of Arabidopsis to Tcin while the addition of buthionine sulfoximine, an inhibitor of glutathione synthesis, increased sensitivity, suggesting that resistance was mediated by glutathione. Total glutathione content was significantly higher in Arabidopsis and in yeast overexpressing AtLTP4.4 relative to the controls, highlighting the importance of AtLTP4.4 in maintaining the redox state. These results demonstrate that trichothecenes cause ROS accumulation and overexpression of AtLTP4.4 protects against trichothecene-induced oxidative stress by increasing the glutathione-based antioxidant defense.
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Affiliation(s)
- John E. McLaughlin
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Mohamed Anwar Bin-Umer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Thomas Widiez
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Daniel Finn
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Susan McCormick
- Bacterial Foodborne Pathogens and Mycology Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois, United States of America
| | - Nilgun E. Tumer
- Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
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Chu Q, Ma J, Saghatelian A. Identification and characterization of sORF-encoded polypeptides. Crit Rev Biochem Mol Biol 2015; 50:134-41. [PMID: 25857697 DOI: 10.3109/10409238.2015.1016215] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular biology, genomics and proteomics methods have been utilized to reveal a non-annotated class of endogenous polypeptides (small proteins and peptides) encoded by short open reading frames (sORFs), or small open reading frames (smORFs). We refer to these polypeptides as s(m)ORF-encoded polypeptides or SEPs. The early SEPs were identified via genetic screens, and many of the RNAs that contain s(m)ORFs were originally considered to be non-coding; however, elegant work in bacteria and flies demonstrated that these s(m)ORFs code for functional polypeptides as small as 11-amino acids in length. The discovery of these initial SEPs led to search for these molecules using methods such as ribosome profiling and proteomics, which have revealed the existence of many SEPs, including novel human SEPs. Unlike screens, omics methods do not necessarily link a SEP to a cellular or biological function, but functional genomic and proteomic strategies have demonstrated that at least some of these newly discovered SEPs have biochemical and cellular functions. Here, we provide an overview of these results and discuss the future directions in this emerging field.
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Affiliation(s)
- Qian Chu
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, Helmsley Center for Genomic Medicine , La Jolla, CA , USA and
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28
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Goyal RK, Mattoo AK. Multitasking antimicrobial peptides in plant development and host defense against biotic/abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:135-49. [PMID: 25438794 DOI: 10.1016/j.plantsci.2014.05.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 05/20/2023]
Abstract
Crop losses due to pathogens are a major threat to global food security. Plants employ a multilayer defense against a pathogen including the use of physical barriers (cell wall), induction of hypersensitive defense response (HR), resistance (R) proteins, and synthesis of antimicrobial peptides (AMPs). Unlike a complex R gene-mediated immunity, AMPs directly target diverse microbial pathogens. Many a times, R-mediated immunity breaks down and plant defense is compromised. Although R-gene dependent pathogen resistance has been well studied, comparatively little is known about the interactions of AMPs with host defense and physiology. AMPs are ubiquitous, low molecular weight peptides that display broad spectrum resistance against bacteria, fungi and viruses. In plants, AMPs are mainly classified into cyclotides, defensins, thionins, lipid transfer proteins, snakins, and hevein-like vicilin-like and knottins. Genetic distance lineages suggest their conservation with minimal effect of speciation events during evolution. AMPs provide durable resistance in plants through a combination of membrane lysis and cellular toxicity of the pathogen. Plant hormones - gibberellins, ethylene, jasmonates, and salicylic acid, are among the physiological regulators that regulate the expression of AMPs. Transgenically produced AMP-plants have become a means showing that AMPs are able to mitigate host defense responses while providing durable resistance against pathogens.
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Affiliation(s)
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, ARS's Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.
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Spincemaille P, Chandhok G, Zibert A, Schmidt H, Verbeek J, Chaltin P, Cammue BP, Cassiman D, Thevissen K. Angiotensin II type 1 receptor blockers increase tolerance of cells to copper and cisplatin. MICROBIAL CELL 2014; 1:352-364. [PMID: 28357214 PMCID: PMC5349125 DOI: 10.15698/mic2014.11.175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The human pathology Wilson disease (WD) is characterized by toxic copper (Cu)
accumulation in brain and liver, resulting in, among other indications,
mitochondrial dysfunction and apoptosis of hepatocytes. In an effort to identify
novel compounds that can alleviate Cu-induced toxicity, we screened the
Pharmakon 1600 repositioning library using a Cu-toxicity yeast screen. We
identified 2 members of the drug class of Angiotensin II Type 1 receptor
blockers (ARBs) that could increase yeast tolerance to Cu, namely Candesartan
and Losartan. Subsequently, we show that specific ARBs can increase yeast
tolerance to Cu and/or the chemotherapeutic agent cisplatin (Cp). The latter
also induces mitochondrial dysfunction and apoptosis in mammalian cells. We
further demonstrate that specific ARBs can prevent the prevalence of Cu-induced
apoptotic markers in yeast, with Candesartan Cilexetil being the ARB which
demonstrated most pronounced reduction of apoptosis-related markers. Next, we
tested the sensitivity of a selection of yeast knockout mutants affected in
detoxification of reactive oxygen species (ROS) and Cu for Candesartan Cilexetil
rescue in presence of Cu. These data indicate that Candesartan Cilexetil
increases yeast tolerance to Cu irrespectively of major ROS-detoxifying
proteins. Finally, we show that specific ARBs can increase mammalian cell
tolerance to Cu, as well as decrease the prevalence of Cu-induced apoptotic
markers. All the above point to the potential of ARBs in preventing Cu-induced
toxicity in yeast and mammalian cells.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Gursimran Chandhok
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Andree Zibert
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Hartmut Schmidt
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Jef Verbeek
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Patrick Chaltin
- CISTIM Leuven vzw, Bio-Incubator 2, Wetenschapspark Arenberg, Gaston Geenslaan 2, 3001 Heverlee, Belgium. ; Centre for Drug Design and Discovery (CD3), KU Leuven R&D, Waaistraat 6, Box 5105, 3000 Leuven
| | - Bruno P Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium. ; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - David Cassiman
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Li YL, Dai XR, Yue X, Gao XQ, Zhang XS. Identification of small secreted peptides (SSPs) in maize and expression analysis of partial SSP genes in reproductive tissues. PLANTA 2014; 240:713-28. [PMID: 25048445 DOI: 10.1007/s00425-014-2123-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/03/2014] [Indexed: 05/14/2023]
Abstract
Maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. Partial SSP gene expressions in reproductive tissues were determined by qRT-PCR. Small secreted peptides (SSPs) are important cell-cell communication messengers in plants. Most information on plant SSPs come from Arabidopsis thaliana and Oryza sativa, while little is known about the SSPs of other grass species such as maize (Zea mays). In this study, we identified 1,491 SSP genes from maize genomic sequences. These putative SSP genes were distributed throughout the ten maize chromosomes. Among them, 611 SSPs were classified into 198 superfamilies according to their conserved domains, and 725 SSPs with four or more cysteines at their C-termini shared similar cysteine arrangements with their counterparts in other plant species. Moreover, the SSPs requiring post-translational modification, as well as defensin-like (DEFL) proteins, were identified. Further, the expression levels of 110 SSP genes were analyzed in reproductive tissues, including male flower, pollen, silk, and ovary. Most of the genes encoding basal-layer antifungal peptide-like, small coat proteins-like, thioredoxin-like proteins, γ-thionins-like, and DEFL proteins showed high expression levels in the ovary and male flower compared with their levels in silk and mature pollen. The rapid alkalinization factor-like genes were highly expressed only in the mature ovary and mature pollen, and pollen Ole e 1-like genes showed low expression in silk. The results of this study provide basic information for further analysis of SSP functions in the reproductive process of maize.
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Affiliation(s)
- Ye Long Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
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31
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Spincemaille P, Pham DH, Chandhok G, Verbeek J, Zibert A, Libbrecht L, Schmidt H, Esguerra CV, de Witte PA, Cammue BP, Cassiman D, Thevissen K. The plant decapeptide OSIP108 prevents copper-induced toxicity in various models for Wilson disease. Toxicol Appl Pharmacol 2014; 280:345-51. [DOI: 10.1016/j.taap.2014.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/30/2014] [Accepted: 08/05/2014] [Indexed: 02/07/2023]
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Spincemaille P, Alborzinia H, Dekervel J, Windmolders P, van Pelt J, Cassiman D, Cheneval O, Craik DJ, Schur J, Ott I, Wölfl S, Cammue BPA, Thevissen K. The plant decapeptide OSIP108 can alleviate mitochondrial dysfunction induced by cisplatin in human cells. Molecules 2014; 19:15088-102. [PMID: 25244288 PMCID: PMC6271462 DOI: 10.3390/molecules190915088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 02/07/2023] Open
Abstract
We investigated the effect of the Arabidopsis thaliana-derived decapeptide OSIP108 on human cell tolerance to the chemotherapeutic agent cisplatin (Cp), which induces apoptosis and mitochondrial dysfunction. We found that OSIP108 increases the tolerance of HepG2 cells to Cp and prevents Cp-induced changes in basic cellular metabolism. More specifically, we demonstrate that OSIP108 reduces Cp-induced inhibition of respiration, decreases glycolysis and prevents Cp-uptake in HepG2 cells. Apart from its protective action against Cp in human cells, OSIP108 also increases the yeast Saccharomyces cerevisiae tolerance to Cp. A limited yeast-based study of OSIP108 analogs showed that cyclization does not severely affect its activity, which was further confirmed in HepG2 cells. Furthermore, the similarity in the activity of the d-stereoisomer (mirror image) form of OSIP108 with the l-stereoisomer suggests that its mode of action does not involve binding to a stereospecific receptor. In addition, as OSIP108 decreases Cp uptake in HepG2 cells and the anti-Cp activity of OSIP108 analogs without free cysteine is reduced, OSIP108 seems to protect against Cp-induced toxicity only partly via complexation. Taken together, our data indicate that OSIP108 and its cyclic derivatives can protect against Cp-induced toxicity and, thus, show potential as treatment options for mitochondrial dysfunction- and apoptosis-related conditions.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium
| | - Hamed Alborzinia
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Jeroen Dekervel
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, Leuven 3000, Belgium
| | - Petra Windmolders
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, Leuven 3000, Belgium
| | - Jos van Pelt
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, Leuven 3000, Belgium
| | - David Cassiman
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, Leuven 3000, Belgium
| | - Olivier Cheneval
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Old 4072, Australia
| | - David J Craik
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Old 4072, Australia
| | - Julia Schur
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität, Braunschweig, Beethovenstrasse 55, Braunschweig 38106, Germany
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität, Braunschweig, Beethovenstrasse 55, Braunschweig 38106, Germany
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium.
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium
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Guefrachi I, Nagymihaly M, Pislariu CI, Van de Velde W, Ratet P, Mars M, Udvardi MK, Kondorosi E, Mergaert P, Alunni B. Extreme specificity of NCR gene expression in Medicago truncatula. BMC Genomics 2014; 15:712. [PMID: 25156206 PMCID: PMC4168050 DOI: 10.1186/1471-2164-15-712] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. The rhizobia are located intracellularly in the symbiotic nodule cells. In the legume Medicago truncatula these cells produce high amounts of Nodule-specific Cysteine-Rich (NCR) peptides which induce differentiation of the rhizobia into enlarged, polyploid and non-cultivable bacterial cells. NCRs are similar to innate immunity antimicrobial peptides. The NCR gene family is extremely large in Medicago with about 600 genes. Results Here we used the Medicago truncatula Gene Expression Atlas (MtGEA) and other published microarray data to analyze the expression of 334 NCR genes in 267 different experimental conditions. We find that all but five of these genes are expressed in nodules but in no other plant organ or in response to any other biotic interaction or abiotic stress tested. During symbiosis, none of the genes are induced by Nod factors. The NCR genes are activated in successive waves during nodule organogenesis, correlated with bacterial infection of the nodule cells and with a specific spatial localization of their transcripts from the apical to the proximal nodule zones. However, NCR expression is not associated with nodule senescence. According to their Shannon entropy, a measure expressing tissue specificity of gene expression, the NCR genes are among the most specifically expressed genes in M. truncatula. Moreover, when activated in nodules, their expression level is among the highest of all genes. Conclusions Together, these data show that the NCR gene expression is subject to an extreme tight regulation and is only activated during nodule organogenesis in the polyploid symbiotic cells. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-712) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter Mergaert
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique UPR2355, 91198 Gif-sur-Yvette, France.
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Missirian V, Conklin PA, Culligan KM, Huefner ND, Britt AB. High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments. FRONTIERS IN PLANT SCIENCE 2014; 5:364. [PMID: 25136344 PMCID: PMC4117989 DOI: 10.3389/fpls.2014.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/08/2014] [Indexed: 05/19/2023]
Abstract
Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants.
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Affiliation(s)
- Victor Missirian
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Phillip A. Conklin
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Kevin M. Culligan
- Department of Molecular, Cellular, and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Neil D. Huefner
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Anne B. Britt
- Department of Plant Biology, University of California DavisDavis, CA, USA
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Aalen RB. Maturing peptides open for communication. JOURNAL OF EXPERIMENTAL BOTANY 2014; 64:5231-5. [PMID: 24259454 DOI: 10.1093/jxb/ert378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Spincemaille P, Cammue BP, Thevissen K. Sphingolipids and mitochondrial function, lessons learned from yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2014; 1:210-224. [PMID: 28357246 PMCID: PMC5349154 DOI: 10.15698/mic2014.07.156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/10/2014] [Indexed: 01/22/2023]
Abstract
Mitochondrial dysfunction is a hallmark of several neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease, but also of cancer, diabetes and rare diseases such as Wilson's disease (WD) and Niemann Pick type C1 (NPC). Mitochondrial dysfunction underlying human pathologies has often been associated with an aberrant cellular sphingolipid metabolism. Sphingolipids (SLs) are important membrane constituents that also act as signaling molecules. The yeast Saccharomyces cerevisiae has been pivotal in unraveling mammalian SL metabolism, mainly due to the high degree of conservation of SL metabolic pathways. In this review we will first provide a brief overview of the major differences in SL metabolism between yeast and mammalian cells and the use of SL biosynthetic inhibitors to elucidate the contribution of specific parts of the SL metabolic pathway in response to for instance stress. Next, we will discuss recent findings in yeast SL research concerning a crucial signaling role for SLs in orchestrating mitochondrial function, and translate these findings to relevant disease settings such as WD and NPC. In summary, recent research shows that S. cerevisiae is an invaluable model to investigate SLs as signaling molecules in modulating mitochondrial function, but can also be used as a tool to further enhance our current knowledge on SLs and mitochondria in mammalian cells.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Bruno P. Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052,
Ghent, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Structure-activity relationship study of the plant-derived decapeptide OSIP108 inhibiting Candida albicans biofilm formation. Antimicrob Agents Chemother 2014; 58:4974-7. [PMID: 24913176 DOI: 10.1128/aac.03336-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed a structure-activity relationship study of the antibiofilm plant-derived decapeptide OSIP108. Introduction of positively charged amino acids R, H, and K resulted in an up-to-5-fold-increased antibiofilm activity against Candida albicans compared to native OSIP108, whereas replacement of R9 resulted in complete abolishment of its antibiofilm activity. By combining the most promising amino acid substitutions, we found that the double-substituted OSIP108 analogue Q6R/G7K had an 8-fold-increased antibiofilm activity.
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38
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Marmiroli N, Maestri E. Plant peptides in defense and signaling. Peptides 2014; 56:30-44. [PMID: 24681437 DOI: 10.1016/j.peptides.2014.03.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/16/2014] [Accepted: 03/17/2014] [Indexed: 12/17/2022]
Abstract
This review focuses on plant peptides involved in defense against pathogen infection and those involved in the regulation of growth and development. Defense peptides, defensins, cyclotides and anti-microbial peptides are compared and contrasted. Signaling peptides are classified according to their major sites of activity. Finally, a network approach to creating an interactomic peptide map is described.
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Affiliation(s)
- Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy.
| | - Elena Maestri
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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Spincemaille P, Chandhok G, Newcomb B, Verbeek J, Vriens K, Zibert A, Schmidt H, Hannun YA, van Pelt J, Cassiman D, Cammue BPA, Thevissen K. The plant decapeptide OSIP108 prevents copper-induced apoptosis in yeast and human cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1207-1215. [PMID: 24632503 DOI: 10.1016/j.bbamcr.2014.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/24/2014] [Accepted: 03/04/2014] [Indexed: 02/07/2023]
Abstract
We previously identified the Arabidopsis thaliana-derived decapeptide OSIP108, which increases tolerance of plants and yeast cells to oxidative stress. As excess copper (Cu) is known to induce oxidative stress and apoptosis, and is characteristic for the human pathology Wilson disease, we investigated the effect of OSIP108 on Cu-induced toxicity in yeast. We found that OSIP108 increased yeast viability in the presence of toxic Cu concentrations, and decreased the prevalence of Cu-induced apoptotic markers. Next, we translated these results to the human hepatoma HepG2 cell line, demonstrating anti-apoptotic activity of OSIP108 in this cell line. In addition, we found that OSIP108 did not affect intracellular Cu levels in HepG2 cells, but preserved HepG2 mitochondrial ultrastructure. As Cu is known to induce acid sphingomyelinase activity of HepG2 cells, we performed a sphingolipidomic analysis of OSIP108-treated HepG2 cells. We demonstrated that OSIP108 decreased the levels of several sphingoid bases and ceramide species. Moreover, exogenous addition of the sphingoid base dihydrosphingosine abolished the protective effect of OSIP108 against Cu-induced cell death in yeast. These findings indicate the potential of OSIP108 to prevent Cu-induced apoptosis, possibly via its effects on sphingolipid homeostasis.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Gursimran Chandhok
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Benjamin Newcomb
- Department of Medicine and the Stony Brook Cancer Center, University of Stony Brook, Stony Brook, New York, 11794, USA
| | - Jef Verbeek
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Kim Vriens
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Andree Zibert
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Hartmut Schmidt
- Clinic for Transplantation Medicine, Münster University Hospital, Albert-Schweitzer-Campus 1, Building A14, D-48149 Münster, Germany
| | - Yusuf A Hannun
- Department of Medicine and the Stony Brook Cancer Center, University of Stony Brook, Stony Brook, New York, 11794, USA
| | - Jos van Pelt
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - David Cassiman
- Department of Hepatology and Metabolic Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium.,Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Slavoff SA, Heo J, Budnik BA, Hanakahi LA, Saghatelian A. A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem 2014; 289:10950-10957. [PMID: 24610814 DOI: 10.1074/jbc.c113.533968] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The recent discovery of numerous human short open reading frame (sORF)-encoded polypeptides (SEPs) has raised important questions about the functional roles of these molecules in cells. Here, we show that a 69-amino acid SEP, MRI-2, physically interacts with the Ku heterodimer to stimulate DNA double-strand break ligation via nonhomologous end joining. The characterization of MRI-2 suggests that this SEP may participate in DNA repair and underscores the potential of SEPs to serve important biological functions in mammalian cells.
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Affiliation(s)
- Sarah A Slavoff
- Department of Chemistry and Chemical Biology and Harvard University, Cambridge, Massachusetts 02138
| | - Jinho Heo
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Rockford, Illinois 60612
| | - Bogdan A Budnik
- Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138 and
| | - Leslyn A Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, Rockford, Illinois 60612.
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology and Harvard University, Cambridge, Massachusetts 02138.
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Plant-derived decapeptide OSIP108 interferes with Candida albicans biofilm formation without affecting cell viability. Antimicrob Agents Chemother 2014; 58:2647-56. [PMID: 24566179 DOI: 10.1128/aac.01274-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously identified a decapeptide from the model plant Arabidopsis thaliana, OSIP108, which is induced upon fungal pathogen infection. In this study, we demonstrated that OSIP108 interferes with biofilm formation of the fungal pathogen Candida albicans without affecting the viability or growth of C. albicans cells. OSIP108 displayed no cytotoxicity against various human cell lines. Furthermore, OSIP108 enhanced the activity of the antifungal agents amphotericin B and caspofungin in vitro and in vivo in a Caenorhabditis elegans-C. albicans biofilm infection model. These data point to the potential use of OSIP108 in combination therapy with conventional antifungal agents. In a first attempt to unravel its mode of action, we screened a library of 137 homozygous C. albicans mutants, affected in genes encoding cell wall proteins or transcription factors important for biofilm formation, for altered OSIP108 sensitivity. We identified 9 OSIP108-tolerant C. albicans mutants that were defective in either components important for cell wall integrity or the yeast-to-hypha transition. In line with these findings, we demonstrated that OSIP108 activates the C. albicans cell wall integrity pathway and that its antibiofilm activity can be blocked by compounds inhibiting the yeast-to-hypha transition. Furthermore, we found that OSIP108 is predominantly localized at the C. albicans cell surface. These data point to interference of OSIP108 with cell wall-related processes of C. albicans, resulting in impaired biofilm formation.
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