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Horn A, Lu Y, Astorga Ríos FJ, Toft Simonsen H, Becker JD. Transcriptional and functional characterization in the terpenoid precursor pathway of the early land plant Physcomitrium patens. PLANT BIOLOGY (STUTTGART, GERMANY) 2025; 27:29-39. [PMID: 39601615 DOI: 10.1111/plb.13741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 10/14/2024] [Indexed: 11/29/2024]
Abstract
Isoprenoids comprise the largest group of plant specialized metabolites. 1-deoxy-D-xylulose-5-phosphate synthase (DXS) is one of the major rate-limiting enzymes in their biosynthesis. The DXS family expanded structurally and functionally during evolution and is believed to have significantly contributed to metabolic complexity and diversity in plants. This family has not yet been studied in Physcomitrium patens or other bryophytes. Here, we assessed the degree of evolutionary expansion in the DXS family in bryophytes and, more specifically, in P. patens using phylogenetic analysis. Transcriptome profiling was applied to investigate tissue-specific, developmental, and environmental responses, such as salt stress, in the DXS family. Moreover, the effect of salt stress on terpenoid biosynthesis was monitored through metabolomics. The phylogenetic analysis of DXS revealed that a structural expansion occurred in bryophytes, but not in P. patens. Functional complementation assay revealed functional activity in all four copies. Comparative transcriptomics showed tissue- and condition-specific divergence in the expression profiles of DXS copies and demonstrated specific stress responses for PpDXS1D, particularly to salt stress. These findings coincide with increased flux in the pathway towards downstream metabolites under salt stress. Additionally, co-expression network analysis revealed significant differences between the co-expressed genes of the DXS copies and illustrated enrichment of stress-responsive genes in the PpDXS1D network. These results suggest that the DXS family in P. patens is conserved but undergoes differential transcriptional regulation, which might allow P. patens to fine-tune DXS levels under different conditions, such as abiotic stress.
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Affiliation(s)
- A Horn
- ITQB NOVA-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Y Lu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - F J Astorga Ríos
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Université Jean Monnet Saint-Etienne, CNRS, LBVpam, Saint-Etienne, France
| | - H Toft Simonsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Université Jean Monnet Saint-Etienne, CNRS, LBVpam, Saint-Etienne, France
| | - J D Becker
- ITQB NOVA-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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2
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Afkar S. Assessment of chemical compositions and antibacterial activity of the essential oil of Mentha piperita in response to salicylic acid. Nat Prod Res 2024; 38:3562-3573. [PMID: 37700677 DOI: 10.1080/14786419.2023.2256020] [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: 06/06/2023] [Revised: 08/22/2023] [Accepted: 09/02/2023] [Indexed: 09/14/2023]
Abstract
Mentha piperita, as a species of the mint family, is used in various medical, cosmetic, industrial and culinary products. The effect of different concentrations of salicylic acid (SA) (0. 0.5, 1 mM) on phytochemical activity and antimicrobial potential of Mentha piperita essential oil against six human pathogenic bacteria (Streptococcus agalactiae, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Listeria monocytogenes) were investigated. According to the results to prevent the growth of L. monocytogenes and S. agalactiae, Gram-positive bacteria, peppermint, essential oil treatment with 1 mM salicylic acid is suggested. But to prevent the growth of Gram-negative bacteria P. aeruginosa and E. coli, peppermint essential oil of control plants is proposed. These results showed that salicylic acid elicitor changed the type and amount of peppermint essential oil compounds. Probably, salicylic acid elicitor improved antimicrobial properties of peppermint essential oil with a change in essential oil components. The inhibitory activity of essential oil depends on the type of microorganism, the concentration of essential oil and the concentration and time of salicylic acid treatment.
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Affiliation(s)
- Soheila Afkar
- Agriculture Department, Payame Noor University, Tehran, Iran
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3
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Fang P, Yu S, Ma X, Hou L, Li T, Gao K, Wang Y, Sun Q, Shang L, Liu Q, Nie M, Yang J. Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications. Heliyon 2024; 10:e28484. [PMID: 38601527 PMCID: PMC11004759 DOI: 10.1016/j.heliyon.2024.e28484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
Antimicrobial peptides (AMPs) constitute a group of small molecular peptides that exhibit a wide range of antimicrobial activity. These peptides are abundantly present in the innate immune system of various organisms. Given the rise of multidrug-resistant bacteria, microbiological studies have identified AMPs as potential natural antibiotics. In the context of antimicrobial resistance across various human pathogens, AMPs hold considerable promise for clinical applications. However, numerous challenges exist in the detection of AMPs, particularly by immunological and molecular biological methods, especially when studying of newly discovered AMPs in proteomics. This review outlines the current status of AMPs research and the strategies employed in their development, considering resent discoveries and methodologies. Subsequently, we focus on the advanced techniques of mass spectrometry for the quantification of AMPs in diverse samples, and analyzes their application, advantages, and limitations. Additionally, we propose suggestions for the future development of tandem mass spectrometry for the detection of AMPs.
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Affiliation(s)
- Panpan Fang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Songlin Yu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Xiaoli Ma
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Lian Hou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Tiewei Li
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Kaijie Gao
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Yingyuan Wang
- Department of Neonatal Intensive Care Unit, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Qianqian Sun
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Lujun Shang
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550004, PR China
| | - Qianqian Liu
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Manjie Nie
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Junmei Yang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
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4
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Satchanska G, Davidova S, Gergova A. Diversity and Mechanisms of Action of Plant, Animal, and Human Antimicrobial Peptides. Antibiotics (Basel) 2024; 13:202. [PMID: 38534637 DOI: 10.3390/antibiotics13030202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial peptides (AMPs) are usually made up of fewer than 100 amino acid residues. They are found in many living organisms and are an important factor in those organisms' innate immune systems. AMPs can be extracted from various living sources, including bacteria, plants, animals, and even humans. They are usually cationic peptides with an amphiphilic structure, which allows them to easily bind and interact with the cellular membranes of viruses, bacteria, fungi, and other pathogens. They can act against both Gram-negative and Gram-positive pathogens and have various modes of action against them. Some attack the pathogens' membranes, while others target their intracellular organelles, as well as their nucleic acids, proteins, and metabolic pathways. A crucial area of AMP use is related to their ability to help with emerging antibiotic resistance: some AMPs are active against resistant strains and are susceptible to peptide engineering. This review considers AMPs from three key sources-plants, animals, and humans-as well as their modes of action and some AMP sequences.
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Affiliation(s)
- Galina Satchanska
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
| | - Slavena Davidova
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
| | - Alexandra Gergova
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
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5
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Palit S, Bhide AJ, Mohanasundaram B, Pala M, Banerjee AK. Peptides from conserved tandem direct repeats of SHORT-LEAF regulate gametophore development in moss P. patens. PLANT PHYSIOLOGY 2023; 194:434-455. [PMID: 37770073 DOI: 10.1093/plphys/kiad515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023]
Abstract
Tandem direct repeat (TDR)-containing proteins, present across all domains of life, play crucial roles in plant development and defense mechanisms. Previously, we identified that disruption of a bryophyte-specific protein family, SHORT-LEAF (SHLF), possessing the longest reported TDRs, is the cause of the shlf mutant phenotype in Physcomitrium patens. shlf exhibits reduced apical dominance, altered auxin distribution, and 2-fold shorter leaves. However, the molecular role of SHLF was unclear due to the absence of known conserved domains. Through a series of protein domain deletion analyses, here, we demonstrate the importance of the signal peptide and the conserved TDRs and report a minimal functional protein (miniSHLF) containing the N-terminal signal peptide and first two TDRs (N-TDR1-2). We also demonstrate that SHLF behaves as a secretory protein and that the TDRs contribute to a pool of secreted peptides essential for SHLF function. Further, we identified that the mutant secretome lacks SHLF peptides, which are abundant in WT and miniSHLF secretomes. Interestingly, shlf mutants supplemented with the secretome or peptidome from WT or miniSHLF showed complete or partial phenotypic recovery. Transcriptomic and metabolomic analyses revealed that shlf displays an elevated stress response, including high ROS activity and differential accumulation of genes and metabolites involved in the phenylpropanoid pathway, which may affect auxin distribution. The TDR-specific synthetic peptide SHLFpep3 (INIINAPLQGFKIA) also rescued the mutant phenotypes, including the altered auxin distribution, in a dosage-dependent manner and restored the mutant's stress levels. Our study shows that secretory SHLF peptides derived from conserved TDRs regulate moss gametophore development.
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Affiliation(s)
- Shirsa Palit
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Amey J Bhide
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | | | - Madhusmita Pala
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Anjan K Banerjee
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
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Ansari MA, Chauhan W, Shoaib S, Alyahya SA, Ali M, Ashraf H, Alomary MN, Al-Suhaimi EA. Emerging therapeutic options in the management of diabetes: recent trends, challenges and future directions. Int J Obes (Lond) 2023; 47:1179-1199. [PMID: 37696926 DOI: 10.1038/s41366-023-01369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 07/04/2023] [Accepted: 08/17/2023] [Indexed: 09/13/2023]
Abstract
Diabetes is a serious health issue that causes a progressive dysregulation of carbohydrate metabolism due to insufficient insulin hormone, leading to consistently high blood glucose levels. According to the epidemiological data, the prevalence of diabetes has been increasing globally, affecting millions of individuals. It is a long-term condition that increases the risk of various diseases caused by damage to small and large blood vessels. There are two main subtypes of diabetes: type 1 and type 2, with type 2 being the most prevalent. Genetic and molecular studies have identified several genetic variants and metabolic pathways that contribute to the development and progression of diabetes. Current treatments include gene therapy, stem cell therapy, statin therapy, and other drugs. Moreover, recent advancements in therapeutics have also focused on developing novel drugs targeting these pathways, including incretin mimetics, SGLT2 inhibitors, and GLP-1 receptor agonists, which have shown promising results in improving glycemic control and reducing the risk of complications. However, these treatments are often expensive, inaccessible to patients in underdeveloped countries, and can have severe side effects. Peptides, such as glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1), are being explored as a potential therapy for diabetes. These peptides are postprandial glucose-dependent pancreatic beta-cell insulin secretagogues and have received much attention as a possible treatment option. Despite these advances, diabetes remains a major health challenge, and further research is needed to develop effective treatments and prevent its complications. This review covers various aspects of diabetes, including epidemiology, genetic and molecular basis, and recent advancements in therapeutics including herbal and synthetic peptides.
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Affiliation(s)
- Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Waseem Chauhan
- Department of Hematology, Duke University, Durham, NC, 27710, USA
| | - Shoaib Shoaib
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sami A Alyahya
- Wellness and Preventive Medicine Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Mubashshir Ali
- USF Health Byrd Alzheimer's Center and Neuroscience Institute, Department of Molecular Medicine, Tampa, FL, USA
| | - Hamid Ashraf
- Rajiv Gandhi Center for Diabetes and Endocrinology, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad N Alomary
- Advanced Diagnostic and Therapeutic Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia.
| | - Ebtesam A Al-Suhaimi
- King Abdulaziz & his Companions Foundation for Giftedness & Creativity, Riyadh, Saudi Arabia.
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7
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Maasch JRMA, Torres MDT, Melo MCR, de la Fuente-Nunez C. Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning. Cell Host Microbe 2023; 31:1260-1274.e6. [PMID: 37516110 PMCID: PMC11625410 DOI: 10.1016/j.chom.2023.07.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023]
Abstract
Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.
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Affiliation(s)
- Jacqueline R M A Maasch
- Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo C R Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Pankaew C, Supdensong K, Tothong C, Roytrakul S, Phaonakrop N, Kongbangkerd A, Limmongkon A. Combining elicitor treatment of chitosan, methyl jasmonate, and cyclodextrin to induce the generation of immune response bioactive peptides in peanut hairy root culture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111670. [PMID: 36914116 DOI: 10.1016/j.plantsci.2023.111670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/15/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
The endogenous peptides from peanut hairy root culture were induced upon elicitor treatment with chitosan (CHT), methyl jasmonate (MeJA), and cyclodextrin (CD): CHT+MeJA+CD. The peptides secreted into the liquid culture medium play an important role in plant signaling and stress responses. By performing gene ontology (GO) analysis, a number of plant proteins involved in biotic and abiotic defense responses were identified, such as endochitinase, defensin, antifungal protein, cationic peroxidase and Bowman-Birk type protease inhibitor A-II. The bioactivity of 14 peptides synthesized from secretome analysis was determined. Peptide BBP1-4, derived from the diverse region of Bowman-Birk type protease inhibitor, displayed high antioxidant activity and mimicked the property of chitinase and β-1,3-glucanase enzymes. The antimicrobial activity against S. aureus, S. typhimurium, and E. coli was evidenced with different peptide concentrations. Additionally, peptide BBP1-4 has the potential to be a useful candidate for an immune response property, as it was found to increase the expression of some pathogenesis-related (PR) proteins and stilbene biosynthesis genes in peanut hairy root tissues. The findings indicate that secreted peptides may play a role in plant responses to both abiotic and biotic stresses. These peptides, which possess bioactive properties, could be considered as potential candidates for use in the pharmaceutical, agricultural, and food industries.
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Affiliation(s)
- Chanyanut Pankaew
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kanitha Supdensong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chonnikan Tothong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Sittiruk Roytrakul
- Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Narumon Phaonakrop
- Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Anupan Kongbangkerd
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Apinun Limmongkon
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
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9
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Dague AL, Valeeva LR, McCann NM, Sharipova MR, Valentovic MA, Bogomolnaya LM, Shakirov EV. Identification and Analysis of Antimicrobial Activities from a Model Moss Ceratodon purpureus. Metabolites 2023; 13:350. [PMID: 36984790 PMCID: PMC10057591 DOI: 10.3390/metabo13030350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
The emergence of bacterial drug resistance is often viewed as the next great health crisis of our time. While more antimicrobial agents are urgently needed, very few new antibiotics are currently in the production pipeline. Here, we aim to identify and characterize novel antimicrobial natural products from a model dioicous moss, Ceratodon purpureus. We collected secreted moss exudate fractions from two C. purpureus strains, male R40 and female GG1. Exudates from the female C. purpureus strain GG1 did not exhibit inhibitory activity against any tested bacteria. However, exudates from the male moss strain R40 exhibited strong inhibitory properties against several species of Gram-positive bacteria, including Staphylococcus aureus and Enterococcus faecium, though they did not inhibit the growth of Gram-negative bacteria. Antibacterial activity levels in C. purpureus R40 exudates significantly increased over four weeks of moss cultivation in liquid culture. Size fractionation experiments indicated that the secreted bioactive compounds have a relatively low molecular weight of less than 1 kDa. Additionally, the R40 exudate compounds are thermostable and not sensitive to proteinase K treatment. Overall, our results suggest that the bioactive compounds present in C. purpureus R40 exudates can potentially add new options for treating infections caused by antibiotic-resistant Gram-positive bacteria.
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Affiliation(s)
- Ashley L. Dague
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Lia R. Valeeva
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Natalie M. McCann
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
| | - Monica A. Valentovic
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Lydia M. Bogomolnaya
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
| | - Eugene V. Shakirov
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
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10
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Aguilera A, Distéfano A, Jauzein C, Correa-Aragunde N, Martinez D, Martin MV, Sueldo DJ. Do photosynthetic cells communicate with each other during cell death? From cyanobacteria to vascular plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7219-7242. [PMID: 36179088 DOI: 10.1093/jxb/erac363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
As in metazoans, life in oxygenic photosynthetic organisms relies on the accurate regulation of cell death. During development and in response to the environment, photosynthetic cells activate and execute cell death pathways that culminate in the death of a specific group of cells, a process known as regulated cell death (RCD). RCD control is instrumental, as its misregulation can lead to growth penalties and even the death of the entire organism. Intracellular molecules released during cell demise may act as 'survival' or 'death' signals and control the propagation of cell death to surrounding cells, even in unicellular organisms. This review explores different signals involved in cell-cell communication and systemic signalling in photosynthetic organisms, in particular Ca2+, reactive oxygen species, lipid derivates, nitric oxide, and eATP. We discuss their possible mode-of-action as either 'survival' or 'death' molecules and their potential role in determining cell fate in neighbouring cells. By comparing the knowledge available across the taxonomic spectrum of this coherent phylogenetic group, from cyanobacteria to vascular plants, we aim at contributing to the identification of conserved mechanisms that control cell death propagation in oxygenic photosynthetic organisms.
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Affiliation(s)
- Anabella Aguilera
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 39231 Kalmar, Sweden
| | - Ayelén Distéfano
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Cécile Jauzein
- Ifremer, Centre de Brest, DYNECO-Pelagos, F-29280 Plouzané, France
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Dana Martinez
- Instituto de Fisiología Vegetal (INFIVE-CONICET), Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (FIBA), Universidad Nacional de Mar del Plata,7600 Mar del Plata, Argentina
| | - Daniela J Sueldo
- Norwegian University of Science and Technology, 7491 Trondheim, Norway
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11
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Valeeva LR, Dague AL, Hall MH, Tikhonova AE, Sharipova MR, Valentovic MA, Bogomolnaya LM, Shakirov EV. Antimicrobial Activities of Secondary Metabolites from Model Mosses. Antibiotics (Basel) 2022; 11:1004. [PMID: 35892395 PMCID: PMC9331938 DOI: 10.3390/antibiotics11081004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/06/2023] Open
Abstract
Plants synthetize a large spectrum of secondary metabolites with substantial structural and functional diversity, making them a rich reservoir of new biologically active compounds. Among different plant lineages, the evolutionarily ancient branch of non-vascular plants (Bryophytes) is of particular interest as these organisms produce many unique biologically active compounds with highly promising antibacterial properties. Here, we characterized antibacterial activity of metabolites produced by different ecotypes (strains) of the model mosses Physcomitrium patens and Sphagnum fallax. Ethanol and hexane moss extracts harbor moderate but unstable antibacterial activity, representing polar and non-polar intracellular moss metabolites, respectively. In contrast, high antibacterial activity that was relatively stable was detected in soluble exudate fractions of P. patens moss. Antibacterial activity levels in P. patens exudates significantly increased over four weeks of moss cultivation in liquid culture. Interestingly, secreted moss metabolites are only active against a number of Gram-positive, but not Gram-negative, bacteria. Size fractionation, thermostability and sensitivity to proteinase K assays indicated that the secreted bioactive compounds are relatively small (less than <10 kDa). Further analysis and molecular identification of antibacterial exudate components, combined with bioinformatic analysis of model moss genomes, will be instrumental in the identification of specific genes involved in the bioactive metabolite biosynthesis.
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Affiliation(s)
- Lia R. Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (L.R.V.); (A.E.T.); (M.R.S.)
| | - Ashley L. Dague
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA; (A.L.D.); (M.H.H.)
| | - Mitchell H. Hall
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA; (A.L.D.); (M.H.H.)
| | - Anastasia E. Tikhonova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (L.R.V.); (A.E.T.); (M.R.S.)
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (L.R.V.); (A.E.T.); (M.R.S.)
| | - Monica A. Valentovic
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA;
| | - Lydia M. Bogomolnaya
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA;
| | - Eugene V. Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA; (A.L.D.); (M.H.H.)
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA;
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12
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Effect of FKBP12-Derived Intracellular Peptides on Rapamycin-Induced FKBP-FRB Interaction and Autophagy. Cells 2022; 11:cells11030385. [PMID: 35159195 PMCID: PMC8834644 DOI: 10.3390/cells11030385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Intracellular peptides (InPeps) generated by proteasomes were previously suggested as putative natural regulators of protein-protein interactions (PPI). Here, the main aim was to investigate the intracellular effects of intracellular peptide VFDVELL (VFD7) and related peptides on PPI. The internalization of the peptides was achieved using a C-terminus covalently bound cell-penetrating peptide (cpp; YGRKKRRQRRR). The possible inhibition of PPI was investigated using a NanoBiT® luciferase structural complementation reporter system, with a pair of plasmids vectors each encoding, simultaneously, either FK506-binding protein (FKBP) or FKBP-binding domain (FRB) of mechanistic target of rapamycin complex 1 (mTORC1). The interaction of FKBP-FRB within cells occurs under rapamycin induction. Results shown that rapamycin-induced interaction between FKBP-FRB within human embryonic kidney 293 (HEK293) cells was inhibited by VFD7-cpp (10-500 nM) and FDVELLYGRKKRRQRRR (VFD6-cpp; 1-500 nM); additional VFD7-cpp derivatives were either less or not effective in inhibiting FKBP-FRB interaction induced by rapamycin. Molecular dynamics simulations suggested that selected peptides, such as VFD7-cpp, VFD6-cpp, VFAVELLYGRKKKRRQRRR (VFA7-cpp), and VFEVELLYGRKKKRRQRRR (VFA7-cpp), bind to FKBP and to FRB protein surfaces. However, only VFD7-cpp and VFD6-cpp induced changes on FKBP structure, which could help with understanding their mechanism of PPI inhibition. InPeps extracted from HEK293 cells were found mainly associated with macromolecular components (i.e., proteins and/or nucleic acids), contributing to understanding InPeps' intracellular proteolytic stability and mechanism of action-inhibiting PPI within cells. In a model of cell death induced by hypoxia-reoxygenation, VFD6-cpp (1 µM) increased the viability of mouse embryonic fibroblasts cells (MEF) expressing mTORC1-regulated autophagy-related gene 5 (Atg5), but not in autophagy-deficient MEF cells lacking the expression of Atg5. These data suggest that VFD6-cpp could have therapeutic applications reducing undesired side effects of rapamycin long-term treatments. In summary, the present report provides further evidence that InPeps have biological significance and could be valuable tools for the rational design of therapeutic molecules targeting intracellular PPI.
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13
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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: 10] [Impact Index Per Article: 2.5] [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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14
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Guillory A, Bonhomme S. Phytohormone biosynthesis and signaling pathways of mosses. PLANT MOLECULAR BIOLOGY 2021; 107:245-277. [PMID: 34245404 DOI: 10.1007/s11103-021-01172-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.
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Affiliation(s)
- Ambre Guillory
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Sandrine Bonhomme
- INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, 78000, Versailles, France.
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15
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Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res 2021; 49:10328-10346. [PMID: 34570232 DOI: 10.1093/nar/gkab816] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Andrey Knyazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Anna Glushkevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Daria Kharlampieva
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation
| | - Vassili Lazarev
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region, 141701, Russian Federation
| | - Michael Taliansky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation.,The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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16
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Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1. Biochim Biophys Acta Gen Subj 2021; 1865:129989. [PMID: 34389467 DOI: 10.1016/j.bbagen.2021.129989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we describe a new class of cryptides (peptides encrypted within a larger protein) with antimicrobial properties, named schistocins, derived from SmKI-1, a key protein in Shistosoma mansoni survival. This is a multi-functional protein with biotechnological potential usage as a therapeutic molecule in inflammatory diseases and to control schistosomiasis. METHODS We used our algorithm enCrypted, to perform an in silico proteolysis of SmKI-1 and a screening for potential antimicrobial activity. The selected peptides were chemically synthesized, tested in vitro and evaluated by both structural (CD, NMR) and biophysical (ITC) studies to access their structure-function relationship. RESULTS EnCrypted was capable of predicting AMPs in SmKI-1. Our biophysical analyses described a membrane-induced conformational change from random coil-to-α-helix and a peptide-membrane equilibrium for all schistocins. Our structural data allowed us to suggest a well-known mode of peptide-membrane interaction in which electrostatic attraction between the cationic peptides and anionic membranes results in the bilayer disordering. Moreover, the NMR exchange H/D data with the higher entropic contribution observed for the peptide-membrane interaction showed that shistocins have different orientations upon the membrane. CONCLUSIONS This work demonstrate the robustness for using the physicochemical features of predicted peptides in the identification of new bioactive cryptides besides the relevance of combining these analyses with biophysical methods to understand the peptide-membrane affinity and improve further algorithms. GENERAL SIGNIFICANCE Bioprospecting cryptides can be conducted through data mining of protein databases demonstrating the success of our strategy. The peptides-based agents derived from SmKI-1 might have high impact for system-biology and biotechnology.
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17
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Lyapina I, Filippova A, Kovalchuk S, Ziganshin R, Mamaeva A, Lazarev V, Latsis I, Mikhalchik E, Panasenko O, Ivanov O, Ivanov V, Fesenko I. Possible role of small secreted peptides (SSPs) in immune signaling in bryophytes. PLANT MOLECULAR BIOLOGY 2021; 106:123-143. [PMID: 33713297 DOI: 10.1007/s11103-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Plants utilize a plethora of peptide signals to regulate their immune response. Peptide ligands and their cognate receptors involved in immune signaling share common motifs among many species of vascular plants. However, the origin and evolution of immune peptides is still poorly understood. Here, we searched for genes encoding small secreted peptides in the genomes of three bryophyte lineages-mosses, liverworts and hornworts-that occupy a critical position in the study of land plant evolution. We found that bryophytes shared common predicted small secreted peptides (SSPs) with vascular plants. The number of SSPs is higher in the genomes of mosses than in both the liverwort Marchantia polymorpha and the hornwort Anthoceros sp. The synthetic peptide elicitors-AtPEP and StPEP-specific for vascular plants, triggered ROS production in the protonema of the moss Physcomitrella patens, suggesting the possibility of recognizing peptide ligands from angiosperms by moss receptors. Mass spectrometry analysis of the moss Physcomitrella patens, both the wild type and the Δcerk mutant secretomes, revealed peptides that specifically responded to chitosan treatment, suggesting their role in immune signaling.
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Affiliation(s)
- Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Filippova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Ivan Latsis
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Elena Mikhalchik
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Oleg Panasenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Oleg Ivanov
- V.F. Kuprevich Institute of Experimental Botany of the National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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18
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Bosso A, Di Maro A, Cafaro V, Di Donato A, Notomista E, Pizzo E. Enzymes as a Reservoir of Host Defence Peptides. Curr Top Med Chem 2021; 20:1310-1323. [PMID: 32223733 DOI: 10.2174/1568026620666200327173815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/21/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022]
Abstract
Host defence peptides (HDPs) are powerful modulators of cellular responses to various types of insults caused by pathogen agents. To date, a wide range of HDPs, from species of different kingdoms including bacteria, plant and animal with extreme diversity in structure and biological activity, have been described. Apart from a limited number of peptides ribosomally synthesized, a large number of promising and multifunctional HDPs have been identified within protein precursors, with properties not necessarily related to innate immunity, consolidating the fascinating hypothesis that proteins have a second or even multiple biological mission in the form of one or more bio-active peptides. Among these precursors, enzymes constitute certainly an interesting group, because most of them are mainly globular and characterized by a fine specific internal structure closely related to their catalytic properties and also because they are yet little considered as potential HDP releasing proteins. In this regard, the main aim of the present review is to describe a panel of HDPs, identified in all canonical classes of enzymes, and to provide a detailed description on hydrolases and their corresponding HDPs, as there seems to exist a striking link between these structurally sophisticated catalysts and their high content in cationic and amphipathic cryptic peptides.
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Affiliation(s)
- Andrea Bosso
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Alberto Di Donato
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples 'Federico II', Naples, Italy
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19
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Pan YH, Gao LJ, Liang YT, Zhao Y, Liang HF, Chen WW, Yang XH, Qing DJ, Gao J, Wu H, Huang J, Zhou WY, Huang CC, Dai GX, Deng GF. OrMKK3 Influences Morphology and Grain Size in Rice. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2021; 66:269-282. [PMID: 33424241 PMCID: PMC7780602 DOI: 10.1007/s12374-020-09290-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 05/28/2023]
Abstract
Although morphology and grain size are important to rice growth and yield, the identity of abundant natural allelic variations that determine agronomically important differences in crops is unknown. Here, we characterized the function of mitogen-activated protein kinase 3 from Oryza officinalis Wall. ex Watt encoded by OrMKK3. Different alternative splicing variants occurred in OrMKK3. Green fluorescent protein (GFP)-OrMKK3 fusion proteins localized to the cell membrane and nuclei of rice protoplasts. Overexpression of OrMKK3 influenced the expression levels of the grain size-related genes SMG1, GW8, GL3, GW2, and DEP3. Phylogenetic analysis showed that OrMKK3 is well conserved in plants while showing large amounts of variation between indica, japonica, and wild rice. In addition, OrMKK3 slightly influenced brassinosteroid (BR) responses and the expression levels of BR-related genes. Our findings thus identify a new gene, OrMKK3, influencing morphology and grain size and that represents a possible link between mitogen-activated protein kinase and BR response pathways in grain growth. Supplementary Information The online version contains supplementary material available at 10.1007/s12374-020-09290-2.
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Affiliation(s)
- Ying Hua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Li Jun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Yun Tao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Hai Fu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Wei Wei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Xing Hai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Dong Jin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Ju Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Hao Wu
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Wei Yong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
| | - Cheng Cui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Gao Xing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007 China
| | - Guo Fu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007 China
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20
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Gunjegaonkar SM, Wankhede SB, Shanmugarajan TS, Shinde SD. Bioactive role of plant stress hormone methyl jasmonate against lipopolysaccharide induced arthritis. Heliyon 2020; 6:e05432. [PMID: 33225090 PMCID: PMC7666351 DOI: 10.1016/j.heliyon.2020.e05432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/28/2020] [Accepted: 11/02/2020] [Indexed: 10/26/2022] Open
Abstract
The current investigation was carried out to screen antiarthritic potential of Methyl Jasmonate (MJ) against lipopolysaccharide (LPS) induced arthritis. Cartilage damage was induced in experimental animals by intraplantar administration of LPS (1 mg/kg) and antiarthritic effect of MJ was screened in two doses of MJ-1 (20 mg/kg), MJ-2 (40 mg/kg) by intraperitoneally administration. Indomethacin (30 mg/kg p.o.) was used as standard drug. The severity of arthritis was evaluated by assessing arthritis score, secondary lesions, motility test, stair climbing ability, and dorsal flexion pain score method. The estimation of blood cytokine tumor necrosis factor- aplha (TNF-α),interleukine (IL-2 and IL-6) and thymus/spleen index was carried out to access the severity of inflammation. Estimation of hepaticenzymatic antioxidant activity superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), glutathione peroxidase (GPx)and radiological examination was carried out on 28th day. Results indicated that MJ showed significant reduction in severity of arthritis by decreasing arthritis score, secondary lesions where as significant increase in motility, climbing ability and flexion pain score was observed. Significant decreased in blood cytokine viz. TNF-α, IL-2, IL-6 andthymus/spleen index was observed in MJ treated animals in dose dependent manner. MJ treated animals showed significant increased and restoration of hepatic antioxidant enzymatic activityof SOD, CAT, GSH, GPx where asradiological examination indicates protective effect on joint structure as compared to LPS treated rats. These current studies conclude that MJ has protective role in arthritis.
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Affiliation(s)
- S M Gunjegaonkar
- JSPM's Charak College of Pharmacy and Research, Department of Pharmacology, Gate No. 720/1&2, Pune-Nagar Road, Wagholi, 412207, Pune, Maharashtra, India
| | - S B Wankhede
- JSPM's Charak College of Pharmacy and Research, Department of Pharmaceutical Chemistry, Gate No. 720/1&2, Pune-Nagar Road, Wagholi, 412207, Pune, Maharashtra, India
| | - T S Shanmugarajan
- Vels Institute of Science, Technology and Advanced Studies, School of Pharmaceutical Sciences, Department of Pharmaceutics, Velan Nagar, P. V. Vaithiyalingam Road, Pallavaram, Chennai, 600 117, Tamil Nadu, India
| | - S D Shinde
- Shri. R. D. Bhakt College of Pharmacy, Department of Pharmacology, Jalna 431203, Maharashtra, India
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21
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Mamaeva A, Taliansky M, Filippova A, Love AJ, Golub N, Fesenko I. The role of chloroplast protein remodeling in stress responses and shaping of the plant peptidome. THE NEW PHYTOLOGIST 2020; 227:1326-1334. [PMID: 32320487 DOI: 10.1111/nph.16620] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
In addition to photosynthesis, chloroplasts perform a variety of important cellular functions in the plant cell, which can, for example, regulate plant responses to abiotic and biotic stress conditions. Under stress, intensive chloroplast protein remodeling and degradation can occur, releasing large numbers of endogenous peptides. These protein-derived peptides can be found intracellularly, but also in the plant secretome. Although the pathways of chloroplast protein degradation and the types of chloroplast proteases implicated in this process have received much attention, the role of the resulting peptides is less well understood. In this review we summarize the data on peptide generation processes during the remodeling of the chloroplast proteome under stress conditions and discuss the mechanisms leading to these changes. We also review the experimental evidence which supports the concept that peptides derived from chloroplast proteins can function as regulators of plant responses to (a)biotic stresses.
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Affiliation(s)
- Anna Mamaeva
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Michael Taliansky
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Anna Filippova
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Andrew J Love
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Nina Golub
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Igor Fesenko
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
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22
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Ali A, Alzeyoudi SAR, Almutawa SA, Alnajjar AN, Vijayan R. Molecular basis of the therapeutic properties of hemorphins. Pharmacol Res 2020; 158:104855. [PMID: 32438036 DOI: 10.1016/j.phrs.2020.104855] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022]
Abstract
Hemorphins are endogenous peptides, 4-10 amino acids long, belonging to the family of atypical opioid peptides released during the sequential cleavage of hemoglobin protein. Hemorphins have been shown to exhibit diverse therapeutic effects in both human and animal models. However, the precise cellular and molecular mechanisms involved in such effects remain elusive. In this review, we summarize and propose potential mechanisms based on studies that investigated the biological activity of hemorphins of different lengths on multiple therapeutic targets. Special emphasis is given to molecular events related to renin-angiotensin system (RAS), opioid receptors and insulin-regulated aminopeptidase receptor (IRAP). This review provides a comprehensive coverage of the molecular mechanisms that underpin the therapeutic potential of hemorphins. Furthermore, it highlights the role of various hemorphin residues in pathological conditions, which could be explored further for therapeutic purposes.
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Affiliation(s)
- Amanat Ali
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | | | - Shamma Abdulla Almutawa
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Alya Nasir Alnajjar
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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23
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The Role of Peptide Signals Hidden in the Structure of Functional Proteins in Plant Immune Responses. Int J Mol Sci 2019; 20:ijms20184343. [PMID: 31491850 PMCID: PMC6770897 DOI: 10.3390/ijms20184343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 02/04/2023] Open
Abstract
Plants have evolved a sophisticated innate immune system to cope with a diverse range of phytopathogens and insect herbivores. Plasma-membrane-localized pattern recognition receptors (PRRs), such as receptor-like kinases (RLK), recognize special signals, pathogen- or damage-associated molecular patterns (PAMPs or DAMPs), and trigger immune responses. A growing body of evidence shows that many peptides hidden in both plant and pathogen functional protein sequences belong to the group of such immune signals. However, the origin, evolution, and release mechanisms of peptide sequences from functional and nonfunctional protein precursors, known as cryptic peptides, are largely unknown. Various special proteases, such as metacaspase or subtilisin-like proteases, are involved in the release of such peptides upon activation during defense responses. In this review, we discuss the roles of cryptic peptide sequences hidden in the structure of functional proteins in plant defense and plant-pathogen interactions.
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24
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Zakirova EY, Chastukhina IB, Valeeva LR, Vorobev VV, Rizvanov AA, Palotás A, Shakirov EV. Stable Co-Cultivation of the Moss Physcomitrella patens with Human Cells in vitro as a New Approach to Support Metabolism of Diseased Alzheimer Cells. J Alzheimers Dis 2019; 70:75-89. [PMID: 31177231 DOI: 10.3233/jad-190333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is a devastating slowly progressive neurodegenerative disorder with no cure. While there are many hypotheses, the exact mechanism causing this pathology is still unknown. Among many other features, AD is characterized by brain hypometabolism and decreased sugar availability, to which neurons eventually succumb. In light of this aspect of the disease, we hypothesized that boosting fuel supply to neurons may help them survive or at least alleviate some of the symptoms. Here we demonstrate that live moss Physcomitrella patens cells can be safely co-cultured with human fibroblasts in vitro and thus have a potential for providing human cells with energy and other vital biomolecules. These data may form the foundation for the development of novel approaches to metabolic bioengineering and treatment of diseased cells based on live plants. In addition, by providing alternative energy sources to human tissues, the biotechnological potential of this interkingdom setup could also serve as a springboard to foster innovative dietary processes addressing current challenges of mankind such as famine or supporting long-haul space flight.
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Affiliation(s)
| | | | | | | | | | - András Palotás
- Kazan Federal University, Kazan, Russia.,Asklepios-Med (Private Medical Practice and Research Center), Szeged, Hungary
| | - Eugene V Shakirov
- Kazan Federal University, Kazan, Russia.,University of Texas at Austin, Austin, TX, USA
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