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Canas JJ, Arregui SW, Zhang S, Knox T, Calvert C, Saxena V, Schwaderer AL, Hains DS. DEFA1A3 DNA gene-dosage regulates the kidney innate immune response during upper urinary tract infection. Life Sci Alliance 2024; 7:e202302462. [PMID: 38580392 PMCID: PMC10997819 DOI: 10.26508/lsa.202302462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
Antimicrobial peptides (AMPs) are host defense effectors with potent neutralizing and immunomodulatory functions against invasive pathogens. The AMPs α-Defensin 1-3/DEFA1A3 participate in innate immune responses and influence patient outcomes in various diseases. DNA copy-number variations in DEFA1A3 have been associated with severity and outcomes in infectious diseases including urinary tract infections (UTIs). Specifically, children with lower DNA copy numbers were more susceptible to UTIs. The mechanism of action by which α-Defensin 1-3/DEFA1A3 copy-number variations lead to UTI susceptibility remains to be explored. In this study, we use a previously characterized transgenic knock-in of the human DEFA1A3 gene mouse to dissect α-Defensin 1-3 gene dose-dependent antimicrobial and immunomodulatory roles during uropathogenic Escherichia coli (UPEC) UTI. We elucidate the relationship between kidney neutrophil- and collecting duct intercalated cell-derived α-Defensin 1-3/DEFA1A3 expression and UTI. We further describe cooperative effects between α-Defensin 1-3 and other AMPs that potentiate the neutralizing activity against UPEC. Cumulatively, we demonstrate that DEFA1A3 directly protects against UPEC meanwhile impacting pro-inflammatory innate immune responses in a gene dosage-dependent manner.
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Affiliation(s)
- Jorge J Canas
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Samuel W Arregui
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shaobo Zhang
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Taylor Knox
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christi Calvert
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vijay Saxena
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew L Schwaderer
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Hospital for Children, Indiana University Health, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David S Hains
- Division of Pediatric Nephrology, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Hospital for Children, Indiana University Health, Indianapolis, IN, USA
- Kidney and Urology Translational Research Center, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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2
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She M, Zhou H, Dong W, Xu Y, Gao L, Gao J, Yang Y, Yang Z, Cai D, Chen S. Modular metabolic engineering of Bacillus amyloliquefaciens for high-level production of green biosurfactant iturin A. Appl Microbiol Biotechnol 2024; 108:311. [PMID: 38676716 DOI: 10.1007/s00253-024-13083-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 04/29/2024]
Abstract
As a kind of biosurfactants, iturin A has attracted people's wide attentions due to their features of biodegradability, environmentally friendly, etc.; however, high production cost limited its extensive application, and the aim of this research wants to improve iturin A production in Bacillus amyloliquefaciens. Firstly, dual promoter was applied to strengthen iturin A synthetase expression, and its yield was increased to 1.25 g/L. Subsequently, original 5'-UTRs of downstream genes (ituA, ituB, and ituC) in iturin A synthetase cluster were optimized, which significantly increased mRNA secondary stability, and iturin A yield produced by resultant strain HZ-T3 reached 2.32 g/L. Secondly, synthetic pathway of α-glucosidase inhibitor 1-deoxynojirimycin was blocked to improve substrate corn starch utilization, and iturin A yield was increased by 34.91% to 3.13 g/L. Thirdly, efficient precursor (fatty acids, Ser, and Pro) supplies were proven as the critical role in iturin A synthesis, and 5.52 g/L iturin A was attained by resultant strain, through overexpressing yngH, serC, and introducing ocD. Meanwhile, genes responsible for poly-γ-glutamic acid, extracellular polysaccharide, and surfactin syntheses were deleted, which led to a 30.98% increase of iturin A yield. Finally, lipopeptide transporters were screened, and iturin A yield was increased by 17.98% in SwrC overexpression strain, reached 8.53 g/L, which is the highest yield of iturin A ever reported. This study laid a foundation for industrial production and application development of iturin A, and provided the guidance of metabolic engineering breeding for efficient production of other metabolites synthesized by non-ribosomal peptide synthetase. KEY POINTS: • Optimizing 5'-UTR is an effective tactics to regulate synthetase cluster expression. • Blocking 1-DNJ synthesis benefited corn starch utilization and iturin A production. • The iturin A yield attained in this work was the highest yield reported so far.
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Affiliation(s)
- Menglin She
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Huijuan Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Wanrong Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Yuxiang Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Lin Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Jiaming Gao
- Hubei Corporation of China National Tobacco Corporation, Wuhan, 430000, People's Republic of China
| | - Yong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Zhifan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China.
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Lin Z, Agarwal V, Cong Y, Pomponi SA, Schmidt EW. Short macrocyclic peptides in sponge genomes. Proc Natl Acad Sci U S A 2024; 121:e2314383121. [PMID: 38442178 PMCID: PMC10945851 DOI: 10.1073/pnas.2314383121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL34946
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
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Zhang W, Forester NT, Chettri P, Heilijgers M, Mace WJ, Maes E, Morozova Y, Applegate ER, Johnson RD, Johnson LJ. Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins in Epichloë festucae. J Agric Food Chem 2023; 71:13965-13978. [PMID: 37704203 PMCID: PMC10540207 DOI: 10.1021/acs.jafc.3c03073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
The various grass-induced epichloëcyclins of the Epichloë spp. are ribosomally synthesized and post-translationally modified peptides (RiPPs), produced as small, secreted cyclopeptides from a single gene, gigA. Here, four clustered and coregulated genes (gigA, gigB, gigC, and kexB) with predicted roles in epichloëcyclin production in Epichloë festucae were evaluated through gene disruption. Subsequent chemical analysis indicates that GigB is a DUF3328 domain-containing protein associated with cyclization of epichloëcyclins; GigC is a methyltransferase enzyme responsible for N-methylation of desmethylepichloëcyclins; and KexB is a subtilisin-like enzyme, partly responsible for the propeptide cleavage of epichloëcyclin intermediates. Symbiotic effects on the host phenotype were not observed for gigA, gigC, or kexB mutants, although ΔgigB infection correlated with increased host tiller height and biomass, while only ΔkexB exhibited an effect on endophyte morphology. Disrupting epichloëcyclin biosynthesis showed negligible influence on the biosynthesis of E. festucae-associated alkaloids. Epichloëcyclins may perform other secondary metabolism functions in Epichloë and other fungi.
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Affiliation(s)
- Wei Zhang
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Natasha T. Forester
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Pranav Chettri
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Maurice Heilijgers
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Wade J. Mace
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Evelyne Maes
- Lincoln
Research Centre, AgResearch Limited, Lincoln 7608, New Zealand
| | - Yulia Morozova
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Emma R. Applegate
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Richard D. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Linda J. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
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Williams P, Hill P, Bonev B, Chan WC. Quorum-sensing, intra- and inter-species competition in the staphylococci. Microbiology (Reading) 2023; 169:001381. [PMID: 37578829 PMCID: PMC10482373 DOI: 10.1099/mic.0.001381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
In Gram-positive bacteria such as Staphylococcus aureus and the coagulase-negative staphylococci (CoNS), the accessory gene regulator (agr) is a highly conserved but polymorphic quorum-sensing system involved in colonization, virulence and biofilm development. Signalling via agr depends on the interaction of an autoinducing peptide (AIP) with AgrC, a transmembrane sensor kinase that, once phosphorylated activates the response regulator AgrA. This in turn autoinduces AIP biosynthesis and drives target gene expression directly via AgrA or via the post-transcriptional regulator, RNAIII. In this review we describe the molecular mechanisms underlying the agr-mediated generation of, and response to, AIPs and the molecular basis of AIP-dependent activation and inhibition of AgrC. How the environment impacts on agr functionality is considered and the consequences of agr dysfunction for infection explored. We also discuss the concept of AIP-driven competitive interference between S. aureus and the CoNS and its anti-infective potential.
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Affiliation(s)
- Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Phil Hill
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Boyan Bonev
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C. Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Xu Y, Wu JY, Liu QJ, Xue JY. Genome-Wide Identification and Evolutionary Analyses of SrfA Operon Genes in Bacillus. Genes (Basel) 2023; 14:422. [PMID: 36833349 PMCID: PMC9956979 DOI: 10.3390/genes14020422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/21/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
A variety of secondary metabolites contributing to plant growth are synthesized by bacterial nonribosomal peptide synthases (NRPSs). Among them, the NRPS biosynthesis of surfactin is regulated by the SrfA operon. To explore the molecular mechanism for the diversity of surfactins produced by bacteria within the genus Bacillus, we performed a genome-wide identification study focused on three critical genes of the SrfA operon-SrfAA, SrfAB and SrfAC-from 999 Bacillus genomes (belonging to 47 species). Gene family clustering indicated the three genes can be divided into 66 orthologous groups (gene families), of which a majority comprised members of multiple genes (e.g., OG0000009 had members of all three SrfAA, SrfAB and SrfAC genes), indicating high sequence similarity among the three genes. Phylogenetic analyses also found that none of the three genes formed monophyletic groups, but were usually arranged in a mixed manner, suggesting the close evolutionary relationship among the three genes. Considering the module structure of the three genes, we propose that self-duplication, especially tandem duplications, might have contributed to the initial establishment of the entire SrfA operon, and further gene fusion and recombination as well as accumulated mutations might have continuously shaped the different functional roles of SrfAA, SrfAB and SrfAC. Overall, this study provides novel insight into metabolic gene clusters and operon evolution in bacteria.
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Affiliation(s)
- Ying Xu
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
| | - Jia-Yi Wu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing-Jie Liu
- State Key Laboratory of Enhanced Oil Recovery, PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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de Lima Ferreira JK, de Mello Varani A, Tótola MR, Fernandes Almeida M, de Sousa Melo D, Ferreira Silva E Batista C, Chalfun-Junior A, Pimenta de Oliveira KK, Wurdig Roesch LF, Satler Pylro V. Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914. Braz J Microbiol 2022; 53:2051-2063. [PMID: 36083529 PMCID: PMC9679098 DOI: 10.1007/s42770-022-00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023] Open
Abstract
Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.
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Affiliation(s)
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias E Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Sao Paulo, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Michelle Fernandes Almeida
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Dirceu de Sousa Melo
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | - Antonio Chalfun-Junior
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | | | - Victor Satler Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil.
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Roudier J, Balandraud N, Auger I. How RA Associated HLA-DR Molecules Contribute to the Development of Antibodies to Citrullinated Proteins: The Hapten Carrier Model. Front Immunol 2022; 13:930112. [PMID: 35774784 PMCID: PMC9238433 DOI: 10.3389/fimmu.2022.930112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
The risk to develop ACPA positive rheumatoid arthritis (RA), the most destructive type of autoimmune arthritis, is carried by HLA-DRB1 alleles containing a 5 amino acid motif: the shared epitope (SE). RA is preceded by the emergence of disease specific anti citrullinated protein antibodies (ACPA). SE positive HLA-DRB1 alleles are associated with ACPA and ACPA positive RA, not with ACPA negative RA, suggesting that ACPA contribute to the pathogenesis of RA. Understanding how HLA-DRB1 genotypes influence ACPA could lead to a curative or preventive treatment of RA. The “Shared epitope binds citrullinated peptides “ hypothesis suggests that RA associated HLA-DR alleles present citrullinated peptides to T cells that help ACPA producing B cells. The “Hapten carrier model” suggests that PAD4 is the target of the T cells which help ACPA specific B cells through a hapten carrier mechanism in which PAD4 is the carrier and citrullinated peptides are the haptens. Direct binding assay of citrullinated peptides to purified HLA-DR molecules does not support the “shared epitope binds citrullinated peptides” hypothesis. The Odds Ratios to develop ACPA positive RA associated with each of 12 common HLA-DRB1 genotypes match the probability that the two HLA-DR molecules they encode can bind at least one peptide from PAD4, not from citrullinated fibrinogen. Thus, PAD4 tolerization might stop the carrier effect and switch off production of ACPA.
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Affiliation(s)
- Jean Roudier
- Faculté de Médecine, Aix Marseille Université, Marseille, France
- Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM U1097 Immunogénétique de la Polyarthrite Rhumatoïde, Marseille, France
- *Correspondence: Jean Roudier,
| | - Nathalie Balandraud
- Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM U1097 Immunogénétique de la Polyarthrite Rhumatoïde, Marseille, France
| | - Isabelle Auger
- INSERM U1097 Immunogénétique de la Polyarthrite Rhumatoïde, Marseille, France
- Faculté des Sciences, Aix Marseille Université, Marseille, France
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Marinović I, Čečuk-Jeličić E, Perković D, Marasović Krstulović D, Aljinović J, Šošo D, Škorić E, Martinović Kaliterna D. Association of HLA-DRB1 alleles with rheumatoid arthritis in Split-Dalmatia County in southern Croatia. Wien Klin Wochenschr 2022; 134:463-470. [PMID: 35238988 DOI: 10.1007/s00508-022-02010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the distribution of HLA-DRB1 alleles in patients with rheumatoid arthritis (RA) in the Sinj Region (SR) and the rest of the Split-Dalmatia County (SDC) in Croatia and to determine their relationship with disease severity. METHODS A total of 74 RA patients and 80 healthy controls from the SR, and 74 RA patients and 80 healthy controls from the rest of the SDC were genotyped using sequence-specific oligonucleotide primed PCR. High-resolution typing of HLA-DRB1*04 alleles was performed using the single specific primed polymerase chain reaction (PCR-SSP) method. Serum anti-CCP, rheumatoid factor, C‑reactive protein, and erythrocyte sedimentation rate were measured in all RA patients, whereas disease activity was assessed by DAS-28 and functional status by the Health Assessment Questionnaire Disability Index. RESULTS The HLA-DRB1*04 allele was more frequent in patients with RA from the SR than that in patients from the rest of the SDC (18.2% vs. 9.5%; P = 0.014), whereas the HLA-DRB1*15 allele was more frequent in patients with RA from the rest of the SDC than in patients from the SR (16.2% vs. 7.4%; P = 0.010). Shared epitope (SE) positive patients from the SR had significantly higher serum anti-CCP and RF antibody levels (P = 0.014 and P = 0.004, respectively), higher disease activity (P = 0.043), and worse functional status (P < 0.001), than SE-positive patients from the rest of the SDC. CONCLUSION The observed higher incidence of more severe forms of RA in the SR in comparison to the rest of the SDC might be associated with the higher incidence of HLA-DRB1*04 allele in the SR.
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Affiliation(s)
- Ivanka Marinović
- Department of Physical Medicine and Rehabilitation with Rheumatology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia.
- Department of Health Studies, University of Split, Ruđera Boškovića 35, 21000, Split, Croatia.
| | - Esma Čečuk-Jeličić
- Department of Blood Transfusion Tissue Typing Laboratory, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
- Department of Health Studies, University of Split, Ruđera Boškovića 35, 21000, Split, Croatia
| | - Dijana Perković
- Department of Rheumatology and Clinical Immunology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
- University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Daniela Marasović Krstulović
- Department of Rheumatology and Clinical Immunology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
- University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
| | - Jure Aljinović
- Department of Physical Medicine and Rehabilitation with Rheumatology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
- Department of Health Studies, University of Split, Ruđera Boškovića 35, 21000, Split, Croatia
| | - Daniela Šošo
- Department of Physical Medicine and Rehabilitation with Rheumatology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
| | - Ela Škorić
- Department of Physical Medicine and Rehabilitation with Rheumatology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
| | - Dušanka Martinović Kaliterna
- Department of Rheumatology and Clinical Immunology, University Hospital of Split, Spinčićeva 1, 21000, Split, Croatia
- University of Split School of Medicine, Šoltanska 2, 21000, Split, Croatia
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Abstract
Macrocyclic peptides represent promising scaffolds for targeting biomolecules with high affinity and selectivity, making methods for the diversification and functional selection of these macrocycles highly valuable for drug discovery purposes. We recently reported a novel phage display platform (called MOrPH-PhD) for the creation and functional exploration of combinatorial libraries of genetically encoded cyclic peptides. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive non-canonical amino acid is integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. Using this system, it is possible to rapidly generate and screen large libraries of phage-displayed macrocyclic peptides (up to 108 to 1010 members) in order to identify high-affinity binders of a target protein of interest. Herein, we describe step-by-step protocols for the production of MOrPH-PhD libraries, the screening of these libraries against an immobilized protein target, and the isolation and characterization of functional macrocyclic peptides from these genetically encoded libraries.
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Affiliation(s)
- Yu Gu
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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11
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Liew HT, To J, Zhang X, Hemu X, Chan NY, Serra A, Sze SK, Liu CF, Tam JP. The legumain McPAL1 from Momordica cochinchinensis is a highly stable Asx-specific splicing enzyme. J Biol Chem 2021; 297:101325. [PMID: 34710371 PMCID: PMC8600085 DOI: 10.1016/j.jbc.2021.101325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
Legumains, also known as asparaginyl endopeptidases (AEPs), cleave peptide bonds after Asn/Asp (Asx) residues. In plants, certain legumains also have ligase activity that catalyzes biosynthesis of Asx-containing cyclic peptides. An example is the biosynthesis of MCoTI-I/II, a squash family-derived cyclic trypsin inhibitor, which involves splicing to remove the N-terminal prodomain and then N-to-C-terminal cyclization of the mature domain. To identify plant legumains responsible for the maturation of these cyclic peptides, we have isolated and characterized a legumain involved in splicing, McPAL1, from Momordica cochinchinensis (Cucurbitaceae) seeds. Functional studies show that recombinantly expressed McPAL1 displays a pH-dependent, trimodal enzymatic profile. At pH 4 to 6, McPAL1 selectively catalyzed Asp-ligation and Asn-cleavage, but at pH 6.5 to 8, Asn-ligation predominated. With peptide substrates containing N-terminal Asn and C-terminal Asp, such as is found in precursors of MCoTI-I/II, McPAL1 mediates proteolysis at the Asn site and then ligation at the Asp site at pH 5 to 6. Also, McPAL1 is an unusually stable legumain that is tolerant of heat and high pH. Together, our results support that McPAL1 is a splicing legumain at acidic pH that can mediate biosynthesis of MCoTI-I/II. We purport that the high thermal and pH stability of McPAL1 could have applications for protein engineering.
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Affiliation(s)
- Heng Tai Liew
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aida Serra
- IMDEA Food Research Institute, +Pec Proteomics, Campus of International Excellence UAM+CSIC, Old Cantoblanco Hospital, Cantoblanco, Madrid, Spain; Proteored - Instituto de Salud Carlos III (ISCIII), Campus UAM, Cantoblanco, Madrid, Spain
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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12
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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13
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Martínez-Cárdenas A, Cruz-Zamora Y, Fajardo-Hernández CA, Villanueva-Silva R, Cruz-García F, Raja HA, Figueroa M. Genome Mining and Molecular Networking-Based Metabolomics of the Marine Facultative Aspergillus sp. MEXU 27854. Molecules 2021; 26:molecules26175362. [PMID: 34500798 PMCID: PMC8433890 DOI: 10.3390/molecules26175362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
The marine-facultative Aspergillus sp. MEXU 27854, isolated from the Caleta Bay in Acapulco, Guerrero, Mexico, has provided an interesting diversity of secondary metabolites, including a series of rare dioxomorpholines, peptides, and butyrolactones. Here, we report on the genomic data, which consists of 11 contigs (N50~3.95 Mb) with a ~30.75 Mb total length of assembly. Genome annotation resulted in the prediction of 10,822 putative genes. Functional annotation was accomplished by BLAST searching protein sequences with different public databases. Of the predicted genes, 75% were assigned gene ontology terms. From the 67 BGCs identified, ~60% belong to the NRPS and NRPS-like classes. Putative BGCs for the dioxomorpholines and other metabolites were predicted by extensive genome mining. In addition, metabolomic molecular networking analysis allowed the annotation of all isolated compounds and revealed the biosynthetic potential of this fungus. This work represents the first report of whole-genome sequencing and annotation from a marine-facultative fungal strain isolated from Mexico.
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Affiliation(s)
- Anahí Martínez-Cárdenas
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
| | - Yuridia Cruz-Zamora
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
| | - Carlos A. Fajardo-Hernández
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
| | - Rodrigo Villanueva-Silva
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
| | - Felipe Cruz-García
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA;
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (A.M.-C.); (Y.C.-Z.); (C.A.F.-H.); (R.V.-S.); (F.C.-G.)
- Correspondence: ; Tel.: +52-55-5622-5290
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14
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Uzunov B, Stefanova K, Radkova M, Descy JP, Gärtner G, Stoyneva-Gärtner M. First Report on Microcystis as a Potential Microviridin Producer in Bulgarian Waterbodies. Toxins (Basel) 2021; 13:toxins13070448. [PMID: 34203459 PMCID: PMC8310014 DOI: 10.3390/toxins13070448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/30/2022] Open
Abstract
Bulgaria, situated on the Balkan Peninsula, is rich in small and shallow, natural and man-made non-lotic waterbodies, which are threatened by blooms of Cyanoprokaryota/Cyanobacteria. Although cyanotoxins in Bulgarian surface waters are receiving increased attention, there is no information on microviridins and their producers. This paper presents results from a phytoplankton study, conducted in August 2019 in three lakes (Durankulak, Vaya, Uzungeren) and five reservoirs (Duvanli, Mandra, Poroy, Sinyata Reka, Zhrebchevo) in which a molecular-genetic analysis (PCR based on the precursor mdnA gene and subsequent translation to amino acid alignments), combined with conventional light microscopy and an HPLC analysis of marker pigments, were applied for the identification of potential microviridin producers. The results provide evidence that ten strains of the genus Microcystis, and of its most widespread species M. aeruginosa in particular, are potentially toxigenic in respect to microviridins. The mdnA sequences were obtained from all studied waterbodies and their translation to amino-acid alignments revealed the presence of five microviridin variants (types B/C, Izancya, CBJ55500.1 (Microcystis 199), and MC19, as well as a variant, which was very close to type A). This study adds to the general understanding of the microviridin occurrence, producers, and sequence diversity.
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Affiliation(s)
- Blagoy Uzunov
- Department of Botany, Faculty of Biology, Sofia University, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria
- Correspondence: (B.U.); (M.S.-G.)
| | - Katerina Stefanova
- AgroBioInstitute, Bulgarian Agricultural Academy, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria; (K.S.); (M.R.)
| | - Mariana Radkova
- AgroBioInstitute, Bulgarian Agricultural Academy, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria; (K.S.); (M.R.)
| | - Jean-Pierre Descy
- Unité d’Océanographie Chimique, Université de Liège, Sart Tilman, 4000 Liège, Belgium;
| | - Georg Gärtner
- Institut für Botanik der Universität Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria;
| | - Maya Stoyneva-Gärtner
- Department of Botany, Faculty of Biology, Sofia University, 8 blvd. Dragan Zankov, 1164 Sofia, Bulgaria
- Correspondence: (B.U.); (M.S.-G.)
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15
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Zimecki M, Kaczmarek K. Effects of Modifications on the Immunosuppressive Properties of Cyclolinopeptide A and Its Analogs in Animal Experimental Models. Molecules 2021; 26:molecules26092538. [PMID: 33925288 PMCID: PMC8123640 DOI: 10.3390/molecules26092538] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/24/2021] [Indexed: 11/16/2022] Open
Abstract
The consequences of manipulations in structure and amino acid composition of native cyclolinopeptide A (CLA) from linen seeds, and its linear precursor on their biological activities and mechanisms of action, are reviewed. The modifications included truncation of the peptide chain, replacement of amino acid residues with proteinogenic or non-proteinogenic ones, modifications of peptide bond, and others. The studies revealed changes in the immunosuppressive potency of these analogs investigated in a number of in vitro and in vivo experimental models, predominantly in rodents, as well as differences in their postulated mechanism of action. The modified peptides were compared with cyclosporine A and parent CLA. Some of the synthesized and investigated peptides show potential therapeutic usefulness.
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Affiliation(s)
- Michał Zimecki
- Laboratory of Immunobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla Str. 12, 53-114 Wrocław, Poland
- Correspondence: (M.Z.); (K.K.); Tel.: +48-713-709-953 (M.Z.); +48-426-313-156 (K.K.)
| | - Krzysztof Kaczmarek
- Institute of Organic Chemistry, Lodz University of Technology, S. Żeromskiego Str. 116, 90-924 Łódź, Poland
- Correspondence: (M.Z.); (K.K.); Tel.: +48-713-709-953 (M.Z.); +48-426-313-156 (K.K.)
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16
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Ho ST, Ho YN, Lin C, Hsu WC, Lee HJ, Peng CC, Cheng HT, Yang YL. Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway. Mar Drugs 2021; 19:md19040209. [PMID: 33918939 PMCID: PMC8069584 DOI: 10.3390/md19040209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/25/2021] [Accepted: 04/07/2021] [Indexed: 12/26/2022] Open
Abstract
Empedopeptins—eight amino acid cyclic lipopeptides—are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.
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Affiliation(s)
- Shang-Tse Ho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
- Department of Wood Based Materials and Design, College of Agriculture, National Chiayi University, Chiayi 60004, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology, College of Life Science, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chih Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
| | - Wei-Chen Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
| | - Han-Jung Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
| | - Chia-Chi Peng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
| | - Han-Tan Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan; (S.-T.H.); (C.L.); (W.-C.H.); (H.-J.L.); (C.-C.P.); (H.-T.C.)
- Correspondence: ; Tel.: +886-2-2787-2089
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Kanmura S, Morinaga Y, Tanaka A, Komaki Y, Iwaya H, Kumagai K, Mawatari S, Sasaki F, Tanoue S, Hashimoto S, Sameshima Y, Ono Y, Ohi H, Ido A. Increased Gene Copy Number of DEFA1A3 Is Associated With the Severity of Ulcerative Colitis. Clin Transl Gastroenterol 2021; 12:e00331. [PMID: 33825720 PMCID: PMC8032364 DOI: 10.14309/ctg.0000000000000331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION DEFA1A3 encodes human neutrophil peptides (HNPs) 1-3 and has multiple copy number variations (CNVs). HNPs are associated with innate immunity. Ulcerative colitis (UC), a chronic inflammatory gastrointestinal disorder, is a life-threatening condition, and predictive markers of UC severity are needed. This study investigated the relationship between DEFA1A3 CNV and UC severity. METHODS This study enrolled 165 patients with UC. The relationship between DEFA1A3 CNV and disease severity was analyzed based on Mayo score, patient characteristics, and treatment methods. In addition, serum and stimulated neutrophil-derived HNP concentrations were also measured in patients with high and low DEFA1A3 CNV. RESULTS DEFA1A3 CNV was significantly correlated with Mayo score and white blood cell count (R = 0.46, P < 0.0001; R = 0.29, P = 0.003, respectively), and only high copy numbers of DEFA1A3 were independent factors for severe UC (P < 0.001, odds ratio: 1.88, 95% confidence interval, 1.34-2.61). The number of severe UC patients with high DEFA1A3 CNV was significantly greater than those with low CNV. We confirmed the associations between DEFA1A3 and UC severity using a validation cohort. In addition, the HNP concentration in high-copy number patients was significantly higher after neutrophil stimulation than that in low-copy number patients. DISCUSSION This study demonstrated that there is a correlation between DEFA1A3 copy number and severity in patients with UC. In addition, neutrophils from UC patients with higher DEFA1A3 CNV had high reactivity of secretion of HNPs after stimulation. DEFA1A3 CNV may be a novel severity marker and a potential therapeutic target for UC.
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Affiliation(s)
- Shuji Kanmura
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuko Morinaga
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihito Tanaka
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuga Komaki
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiromichi Iwaya
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kotaro Kumagai
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Seiichi Mawatari
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Fumisato Sasaki
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shiroh Tanoue
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shinichi Hashimoto
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yoichi Sameshima
- Department of Gastroenterology, Imamura General Hospital, Kagoshima, Japan
| | - Yohei Ono
- Department of Gastroenterology, Idzuro Imamura Hospital, Kagoshima, Japan
| | - Hidehisa Ohi
- Department of Gastroenterology, Idzuro Imamura Hospital, Kagoshima, Japan
| | - Akio Ido
- Digestive and Lifestyle Diseases, Department of Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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18
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Harken L, Li SM. Modifications of diketopiperazines assembled by cyclodipeptide synthases with cytochrome P 450 enzymes. Appl Microbiol Biotechnol 2021; 105:2277-2285. [PMID: 33625545 PMCID: PMC7954767 DOI: 10.1007/s00253-021-11178-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/22/2022]
Abstract
2,5-Diketopiperazines are the smallest cyclic peptides comprising two amino acids connected via two peptide bonds. They can be biosynthesized in nature by two different enzyme families, either by nonribosomal peptide synthetases or by cyclodipeptide synthases. Due to the stable scaffold of the diketopiperazine ring, they can serve as precursors for further modifications by different tailoring enzymes, such as methyltransferases, prenyltransferases, oxidoreductases like cyclodipeptide oxidases, 2-oxoglutarate-dependent monooxygenases and cytochrome P450 enzymes, leading to the formation of intriguing secondary metabolites. Among them, cyclodipeptide synthase-associated P450s attracted recently significant attention, since they are able to catalyse a broader variety of astonishing reactions than just oxidation by insertion of an oxygen. The P450-catalysed reactions include hydroxylation at a tertiary carbon, aromatisation of the diketopiperazine ring, intramolecular and intermolecular carbon-carbon and carbon-nitrogen bond formation of cyclodipeptides and nucleobase transfer reactions. Elucidation of the crystal structures of three P450s as cyclodipeptide dimerases provides a structural basis for understanding the reaction mechanism and generating new enzymes by protein engineering. This review summarises recent publications on cyclodipeptide modifications by P450s.Key Points• Intriguing reactions catalysed by cyclodipeptide synthase-associated cytochrome P450s• Homo- and heterodimerisation of diketopiperazines• Coupling of guanine and hypoxanthine with diketopiperazines.
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Affiliation(s)
- Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany.
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Abstract
Small synthetic peptides capable of crossing biological membranes represent valuable tools in cell biology and drug delivery. While several cell-penetrating peptides (CPPs) of natural or synthetic origin have been reported, no peptide is currently known to cross both cytoplasmic and outer embryonic membranes. Here, we describe a method to engineer membrane-permeating cyclic peptides (MPPs) with broad permeation activity by screening mRNA display libraries of cyclic peptides against embryos at different developmental stages. The proposed method was demonstrated by identifying peptides capable of permeating Drosophila melanogaster (fruit fly) embryos and mammalian cells. The selected peptide cyclo[Glut-MRKRHASRRE-K*] showed a strong permeation activity of embryos exposed to minimal permeabilization pretreatment, as well as human embryonic stem cells and a murine fibroblast cell line. Notably, in both embryos and mammalian cells, the cyclic peptide outperformed its linear counterpart and the control MPPs. Confocal microscopy and single cell flow cytometry analysis were utilized to assess the degree of permeation both qualitatively and quantitatively. These MPPs have potential application in studying and nondisruptively controlling intracellular or intraembryonic processes.
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Affiliation(s)
- John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
| | - Allison E Schloop
- Genetics Program, North Carolina State University, 112 Derieux Place, Raleigh, North Carolina 27695, United States
| | - Gregory T Reeves
- Department of Chemical Engineering, Texas A&M University, 200 Jack E. Brown Engineering Building, College Station, Texas 77843, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, North Carolina 27606, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
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20
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Fisher MF, Payne CD, Chetty T, Crayn D, Berkowitz O, Whelan J, Rosengren KJ, Mylne JS. The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides. J Biol Chem 2020; 295:14510-14521. [PMID: 32817170 PMCID: PMC7573267 DOI: 10.1074/jbc.ra120.014781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/11/2020] [Indexed: 01/03/2023] Open
Abstract
Cyclic peptides are reported to have antibacterial, antifungal, and other bioactivities. Orbitides are a class of cyclic peptides that are small, head-to-tail cyclized, composed of proteinogenic amino acids and lack disulfide bonds; they are also known in several genera of the plant family Rutaceae. Melicope xanthoxyloides is the Australian rain forest tree of the Rutaceae family in which evolidine, the first plant cyclic peptide, was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, so to redress this we used tandem MS and de novo transcriptomics to rediscover evolidine and decipher its biosynthetic origin from a short precursor just 48 residues in length. We also identified another six M. xanthoxyloides orbitides using the same techniques. These peptides have atypically diverse C termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides, suggesting new cyclizing enzymes await discovery. We examined the structure of two of the novel orbitides by NMR, finding one had a definable structure, whereas the other did not. Mining RNA-seq and whole genome sequencing data from other species of the Rutaceae family revealed that a large and diverse family of peptides is encoded by similar sequences across the family and demonstrates how powerful de novo transcriptomics can be at accelerating the discovery of new peptide families.
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Affiliation(s)
- Mark F Fisher
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Colton D Payne
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Thaveshini Chetty
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - K Johan Rosengren
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
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21
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Fidor A, Grabski M, Gawor J, Gromadka R, Węgrzyn G, Mazur-Marzec H. Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides. Mar Drugs 2020; 18:E442. [PMID: 32858999 PMCID: PMC7551626 DOI: 10.3390/md18090442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Jan Gawor
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
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22
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Konkel R, Toruńska-Sitarz A, Cegłowska M, Ežerinskis Ž, Šapolaitė J, Mažeika J, Mazur-Marzec H. Blooms of Toxic Cyanobacterium Nodularia spumigena in Norwegian Fjords During Holocene Warm Periods. Toxins (Basel) 2020; 12:toxins12040257. [PMID: 32326551 PMCID: PMC7232221 DOI: 10.3390/toxins12040257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/03/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023] Open
Abstract
In paleoecological studies, molecular markers are being used increasingly often to reconstruct community structures, environmental conditions and ecosystem changes. In this work, nodularin, anabaenopeptins and selected DNA sequences were applied as Nodularia spumigena markers to reconstruct the history of the cyanobacterium in the Norwegian fjords. For the purpose of this study, three sediment cores collected in Oslofjorden, Trondheimsfjorden and Balsfjorden were analyzed. The lack of nodularin in most recent sediments is consistent with the fact that only one report on the sporadic occurrence and low amounts of the cyanobacterium in Norwegian Fjords in 1976 has been published. However, analyses of species-specific chemical markers in deep sediments showed that thousands of years ago, N. spumigena constituted an important component of the phytoplankton community. The content of the markers in the cores indicated that the biomass of the cyanobacterium increased during the warmer Holocene periods. The analyses of genetic markers were less conclusive; they showed the occurrence of microcystin/nodularin producing cyanobacteria of Nostocales order, but they did not allow for the identification of the organisms at a species level.
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Affiliation(s)
- Robert Konkel
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
| | - Anna Toruńska-Sitarz
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Science, Powstańców Warszawy 55, PL-81-712 Sopot, Poland;
| | - Žilvinas Ežerinskis
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania; (Ž.E.); (J.Š.)
| | - Justina Šapolaitė
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania; (Ž.E.); (J.Š.)
| | - Jonas Mažeika
- Laboratory of nuclear geophysics and radioecology, Nature research Centre Akademijos Str. 2, LT-08412 Vilnius, Lithuania;
| | - Hanna Mazur-Marzec
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
- Correspondence: ; Tel.: +48-585-236-621
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23
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Abstract
Two genomes of the closest algal sisters to land plants were sequenced, providing potential evidence that bacterial genes were key in adapting to terrestrial stresses.
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Affiliation(s)
- Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.
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24
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Fan X, Xia H, Liu X, Li B, Fang J. Rational design of type-IA receptor-derived cyclic peptides to target human bone morphogenic protein 2. J Biosci 2019; 44:130. [PMID: 31894111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human bone morphogenetic protein 2 (BMP2) is a bone-growth regulatory factor involved in the formation of bone and cartilage, and has been recogn ized as an attractive therapeutic target for a variety of bone diseases and defects. Here, we report successful design of a head-to-tail cyclic peptide based on crystal structure to target BMP2. Computational alanine scanning identifies two hotspot regions at the crystal complex interface of BMP2 with its type-IA receptor; promising one is stripped from the interface to derive a linear self-inhibitory peptide RPS2[r78-94] that covers residues 78-94 of the receptor protein. Dynamics simulation and energetics analysis reveal that the peptide is highly flexible in isolated state and cannot spontaneously bind to BMP2. The RPS2[r78-94] peptide is further extended from its N- and C-termini until reaching two spatially vicinal residues 74 and 98 in the crystal structure of intact BMP2-receptor complex system, consequently resulting in a longer peptide RPS2[r74-98], which is then cyclized in a head-to-tail manner to obtain its cyclic counterpart cycRPS2[r74-98]. Computational analysis suggests that the cyclic peptide can well maintain in a conformation similar with its active conformation in complex crystal structure, exhibiting a smaller disorder and a larger potency than its linear counterpart. Further assays confirm that the two linear peptides RPS2[r78-94] and RPS2[r74-98]are nonbinders of BMP2, whereas, as designed, the cyclic peptide cycRPS2[r74-98] can bind to BMP2 with a moderate affinity. The cyclic peptide is expected as a lead molecular entity to develop new and potent peptide-based drugs for BMP2-targeted therapy.
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Affiliation(s)
- Xiaohua Fan
- Department of Joint and Trauma Surgery, Yidu Central Hospital, Weifang Medical University, Qingzhou 262500, China
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25
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Abstract
The family of regulatory proline-containing peptides (PCPs), also known as glyprolines, exhibit significant biological activity. The group of glyprolines includes Gly-Pro (GP), Pro-Gly-Pro (PGP), cyclic Gly-Pro (cGP), as well as PGP derivatives, for example, N-acetylated PGP (N-a-PGP) and N-methylated PGP (N-m-PGP). PCPs are engaged in various biological processes including the proinflammatory neutrophil chemoattraction in lung diseases, inflammatory bowel diseases or ischemic stroke. Glyprolines have been also postulated to play an important role as atheroprotective and anticoagulant agents, exhibit neuroprotective effects in Parkinson's disease, as well as regulate insulin-like growth factor (IGF) homeostasis. It was also noticed that PCPs inhibit proliferation and migration of keratinocytes in wound healing, protection of the gastric mucosa and stimulation of its regeneration. The regulatory glyprolines are derived from endogenous and exogenous sources. Most PCPs are derived from collagen or diet protein degradation. Recently, great interest is concentrated on short proline-rich oligopeptides derived from IGF-1 degradation. The mechanism of PCPs biological activity is not fully explained. It involves receptor-mediated mechanisms, for example, N-a-PGP acts as CXCR1/2 receptor ligand, whereas cGP regulates IGF-1 bioavailability by modifying the IGF-1 binding to the IGF-1 binding protein-3. PGP has been observed to interact with collagen-specific receptors. The data suggest a promising role of PGP as a target of various diseases therapy. This review is focused on the effect of PCPs on metabolic processes in different tissues and the molecular mechanism of their action as an approach to pharmacotherapy of PCPs-dependent diseases.
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Affiliation(s)
- Magdalena Misiura
- Department of Pharmaceutical Analysis and Bioanalysis, Medical University of Bialystok, Białystok, Poland
| | - Wojciech Miltyk
- Department of Pharmaceutical Analysis and Bioanalysis, Medical University of Bialystok, Białystok, Poland
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26
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Wang XS, Chen PHC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl 2019; 58:15904-15909. [PMID: 31398275 PMCID: PMC6803038 DOI: 10.1002/anie.201908713] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 11/10/2022]
Abstract
Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.
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Affiliation(s)
- Xiaoshan Shayna Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Peng-Hsun Chase Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - J Trae Hampton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Catrina A Reed
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Sukant K Das
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3218, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
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27
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Ntushelo K, Ledwaba LK, Rauwane ME, Adebo OA, Njobeh PB. The Mode of Action of Bacillus Species against Fusarium graminearum, Tools for Investigation, and Future Prospects. Toxins (Basel) 2019; 11:toxins11100606. [PMID: 31635255 PMCID: PMC6832908 DOI: 10.3390/toxins11100606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023] Open
Abstract
Fusarium graminearum is a pervasive plant pathogenic fungal species. Biological control agents employ various strategies to weaken their targets, as shown by Bacillus species, which adopt various mechanisms, including the production of bioactive compounds, to inhibit the growth of F. graminearum. Various efforts to uncover the antagonistic mechanisms of Bacillus against F. graminearum have been undertaken and have yielded a plethora of data available in the current literature. This perspective article attempts to provide a unified record of these interesting findings. The authors provide background knowledge on the use of Bacillus as a biocontrol agent as well as details on techniques and tools for studying the antagonistic mechanism of Bacillus against F. graminearum. Emphasizing its potential as a future biological control agent with extensive use, the authors encourage future studies on Bacillus as a useful antagonist of F. graminearum and other plant pathogens. It is also recommended to take advantage of the newly invented analytical platforms for studying biochemical processes to understand the mechanism of action of Bacillus against plant pathogens in general.
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Affiliation(s)
- Khayalethu Ntushelo
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1709, Guateng, South Africa.
| | - Lesiba Klaas Ledwaba
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1709, Guateng, South Africa.
- Agricultural Research Council-Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, Tshwane, South Africa.
| | - Molemi Evelyn Rauwane
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1709, Guateng, South Africa.
| | - Oluwafemi Ayodeji Adebo
- Department of Biotechnology and Food Technology, University of Johannesburg, Corner Siemert and Louisa Street, Doornfontein 2028, Gauteng, South Africa.
| | - Patrick Berka Njobeh
- Department of Biotechnology and Food Technology, University of Johannesburg, Corner Siemert and Louisa Street, Doornfontein 2028, Gauteng, South Africa.
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28
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Pouvreau B, Fenske R, Ivanova A, Murcha MW, Mylne JS. An interstitial peptide is readily processed from within seed proteins. Plant Sci 2019; 285:175-183. [PMID: 31203882 DOI: 10.1016/j.plantsci.2019.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
The importance of de novo protein evolution is apparent, but most examples are de novo coding transcripts evolving from silent or non-coding DNA. The peptide macrocycle SunFlower Trypsin Inhibitor 1 (SFTI-1) evolved over 45 million years from genetic expansion within the N-terminal 'discarded' region of an ancestral seed albumin precursor. SFTI-1 and its adjacent albumin are both processed into separate, mature forms by asparaginyl endopeptidase (AEP). Here to determine whether the evolution of SFTI-1 in a latent region of its precursor was critical, we used a transgene approach in A. thaliana analysed by peptide mass spectrometry and RT-qPCR. SFTI could emerge from alternative locations within preproalbumin as well as emerge with precision from unrelated seed proteins via AEP-processing. SFTI production was possible with the adjacent albumin, but peptide levels dropped greatly without the albumin. The ability for SFTI to be processed from multiple sequence contexts and different proteins suggests that to make peptide, it was not crucial for the genetic expansion that gave rise to SFTI and its family to be within a latent protein region. Interstitial peptides, evolving like SFTI within existing proteins, might be more widespread and as a mechanism, SFTI exemplifies a stable, new, functional peptide that did not need a new gene to evolve de novo.
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Affiliation(s)
- Benjamin Pouvreau
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Ricarda Fenske
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
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29
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Hahn L, Silva PC, Malabarba MC, Malabarba LR, Câmara LFD, Nunes LD, Machado LS, Martins EG, Barthem RB. Genetics and telemetry indicate unexpected movements among structured populations for Brachyplatystoma platynemum in the Amazon. J Fish Biol 2019; 95:633-637. [PMID: 30963582 DOI: 10.1111/jfb.13978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
The genetic analysis of Brachyplatystoma platynemum individuals sampled from the lower Madeira River reinforces the existence of two structured populations in the Amazon Basin (Madeira and Amazon populations). However, the recapture of an individual from the Amazon population in the Solimões River, which was telemetry-tagged in the Madeira River after the damming, indicates that fish from the Amazon population move between the two river systems. This has not yet been observed, however, in the Madeira River population, which is currently divided and isolated in the lower and upper Madeira River by the construction of two dams.
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Affiliation(s)
- Lisiane Hahn
- Divisão de Pesquisas, Neotropical Consultoria Ambiental, Rua Cesário Rosseto, Passo Fundo, Brazil
| | - Priscilla C Silva
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Programa de Pós-Graduação em Biologia Animal, Viçosa, Brazil
| | - Maria C Malabarba
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
| | - Luiz R Malabarba
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Biologia Animal, Porto Alegre, Brazil
| | - Luís F Da Câmara
- Divisão de Pesquisas, Neotropical Consultoria Ambiental, Rua Cesário Rosseto, Passo Fundo, Brazil
| | - Leonardo D Nunes
- Divisão de Pesquisas, Neotropical Consultoria Ambiental, Rua Cesário Rosseto, Passo Fundo, Brazil
| | - Leonardo S Machado
- Divisão de Pesquisas, Neotropical Consultoria Ambiental, Rua Cesário Rosseto, Passo Fundo, Brazil
| | - Eduardo G Martins
- Ecosystem Science and Management Program, University of Northern British Columbia (UNBC), Prince George, Canada
| | - Ronaldo B Barthem
- Departamento de Zoologia/Ictiologia, Museu Paraense Emilio Goeldi, Belém, Brazil
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30
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Hegemann JD, Bobeica SC, Walker MC, Bothwell IR, van der Donk WA. Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications. ACS Synth Biol 2019; 8:1204-1214. [PMID: 31042373 PMCID: PMC6525029 DOI: 10.1021/acssynbio.9b00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclization is a common strategy to confer proteolytic resistance to peptide scaffolds. Thus, cyclic peptides have been the focus of extensive bioengineering efforts. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a superfamily of peptidic natural products that often contain macrocycles. In the RiPP family of lanthipeptides, macrocyclization is accomplished through formation of thioether cross-links between cysteines and dehydrated serines/threonines. The recent production of lanthipeptide libraries and development of methods to display lanthipeptides on yeast or phage highlights their potential for bioengineering and synthetic biology. In this regard, the prochlorosins are especially promising as the corresponding class II lanthipeptide synthetase ProcM matures numerous precursor peptides with diverse core peptide sequences. To facilitate future bioengineering projects, one of its native substrates, ProcA2.8, was subjected in this study to in-depth mutational analysis to test the limitations of ProcM-mediated cyclization. Alanine scan mutagenesis was performed on all residues within the two rings, and multiple prolines were introduced at various positions. Moreover, mutation, deletion, and insertion of residues in the region linking the two lanthionine rings was tested. Additional residues were also introduced or deleted from either ring, and inversion of ring forming residues was attempted to generate diastereomers. The findings were used for epitope grafting of the RGD integrin binding epitope within prochlorosin 2.8, resulting in a low nanomolar affinity binder of the αvβ3 integrin that was more stable toward proteolysis and displayed higher affinity than the linear counterpart.
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Affiliation(s)
- Julian D. Hegemann
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Silvia C. Bobeica
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Mark C. Walker
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Ian R. Bothwell
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
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Luo C, Chen Y, Liu X, Wang X, Wang X, Li X, Zhao Y, Wei L. Engineered biosynthesis of cyclic lipopeptide locillomycins in surrogate host Bacillus velezensis FZB42 and derivative strains enhance antibacterial activity. Appl Microbiol Biotechnol 2019; 103:4467-4481. [PMID: 30989253 DOI: 10.1007/s00253-019-09784-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 01/03/2023]
Abstract
Locillomycins are cyclic lipononapeptides assembled by a nonlinear hexamodular NRPS and have strong antibacterial activity. In this study, we genetically engineered Bacillus velezensis FZB42 as a surrogate host for the heterologous expression of the loc gene cluster for locillomycins. The fosmid N13 containing whole loc gene cluster was screened from the B. velezensis 916 genomic library. Subsequently, a spectinomycin resistance cassette, and the cassette fused with an IPTG inducible promoter Pspac, was introduced in the fosmid N13 using λ Red recombination system, respectively. The resulting fosmids, designated N13+Spec and N13+PSSpec, were used for the transformation of B. velezensis FZB42 to obtain derivative strains FZBNPLOC and FZBPSLOC. RT-PCR and qRT-PCR results revealed the efficient heterologous expression of the loc gene cluster in both derivative strains. Particularly, there was positive correlation between the derivative FZBPSLOC strain and the enhanced production of locillomycins upon addition of the inducer IPTG with the highest production of locillomycins at 15-fold more than that of B. velezensis 916. This overproduction of locillomycins was also related to the enhancement of antibacterial activity against methicillin-resistant Staphylococcus aureus, and exhibited moderate changes in its hemolytic activity. Together our findings demonstrate that the nonlinear hexamodular NRPS, encoded by the loc gene cluster from B. velezensis 916, is sufficient for the biosynthesis of cyclic lipononapeptide locillomycins in the surrogate host B. velezensis FZB42. Moreover, the FZBPSLOC strain will also be useful for further development of novel locillomycins derivatives with improved antibacterial activity.
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Affiliation(s)
- Chuping Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China.
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
| | - Yongxing Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Xuehui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Xiaoyu Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiangqian Li
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
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32
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Xu WF, Ren HS, Ou T, Lei T, Wei JH, Huang CS, Li T, Strobel G, Zhou ZY, Xie J. Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose. Microb Ecol 2019; 77:651-663. [PMID: 30178387 DOI: 10.1007/s00248-018-1247-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.
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Affiliation(s)
- Wei-Fang Xu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Hui-Shuang Ren
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ting Ou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ting Lei
- Institute of Sericulture Science and Technology Research, Chongqing, 400700, People's Republic of China
| | - Jun-Hong Wei
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chuan-Shu Huang
- Institute of Sericulture Science and Technology Research, Chongqing, 400700, People's Republic of China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China
| | - Gary Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Ze-Yang Zhou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- College of Life Science, Chongqing Normal University, Chongqing, 400047, People's Republic of China.
| | - Jie Xie
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing, 400715, People's Republic of China.
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Bóka B, Manczinger L, Kocsubé S, Shine K, Alharbi NS, Khaled JM, Münsterkötter M, Vágvölgyi C, Kredics L. Genome analysis of a Bacillus subtilis strain reveals genetic mutations determining biocontrol properties. World J Microbiol Biotechnol 2019; 35:52. [PMID: 30868269 PMCID: PMC6435635 DOI: 10.1007/s11274-019-2625-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/01/2019] [Indexed: 11/03/2022]
Abstract
Several Bacillus strains are used as biocontrol agents, as they frequently have strong antagonistic effects against microbial plant pathogens. Bacillus strain SZMC 6179J, isolated from tomato rhizosphere, was previously shown to have excellent in vitro antagonistic properties against the most important fungal pathogens of tomato (Alternaria solani, Botrytis cinerea, Phytophthora infestans and Sclerotinia sclerotiorum) as well as several Fusarium species. Taxonomic investigations revealed that it is a member of the B. subtilis subsp. subtilis group and very closely related with the reference type strain B. subtilis subsp. subtilis 168. The sequenced genome of strain SZMC 6179J contains the genes responsible for the synthesis of the extracellular antibiotics surfactin, fengycin and bacilysin. Compared to strain 168, a prophage-like region is missing from the genome of SZMC 6179J, while there are 106 single nucleotide polymorphisms and 23 deletion-insertion polymorphisms. The high biocontrol potential of strain SZMC 6179J may results from a single base deletion in the sfp gene encoding the transcription factor of the surfactin and fengycin operons. Hypermutated regions reflecting short-time evolutionary processes could be detected in SZMC 6179J. The deletion-insertion polymorphism in the sfp gene and the detected hypermutations can be suggested as genetic determinants of biocontrol features in B. subtilis.
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Affiliation(s)
- Bettina Bóka
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - László Manczinger
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Kadaikunnan Shine
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky u. 4, Sopron, 9401, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.
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Jahanshah G, Yan Q, Gerhardt H, Pataj Z, Lämmerhofer M, Pianet I, Josten M, Sahl HG, Silby MW, Loper JE, Gross H. Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1. J Nat Prod 2019; 82:301-308. [PMID: 30666877 DOI: 10.1021/acs.jnatprod.8b00747] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.
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Affiliation(s)
- Gahzaleh Jahanshah
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Qing Yan
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Heike Gerhardt
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Zoltán Pataj
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Isabelle Pianet
- CESAMO-ISM, UMR 5255, CNRS , Université Bordeaux I , 351 Cours de la Libération , F-33405 Talence , France
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Mark W Silby
- Department of Biology , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
- Agricultural Research Service , U.S. Department of Agriculture , Corvallis , Oregon 97331 , United States
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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Li H, Ali Z, Liu X, Jiang L, Tang Y, Dai J. Expression of recombinant tachyplesin I in Pichia pastoris. Protein Expr Purif 2019; 157:50-56. [PMID: 30711625 DOI: 10.1016/j.pep.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/20/2019] [Accepted: 01/30/2019] [Indexed: 11/19/2022]
Abstract
The development of antibiotic-resistant bacteria has become a major public health problem, prompting the search for alternative solutions. Tachyplesin I (TP-I) is an antimicrobial peptide, which exhibits potent and broad-spectrum activities against bacteria, fungi, viruses, and tumor cells. However, limited amounts of TP-I produced in horseshoe crab restrict its large-scale use. In order to solve this problem, a eukaryotic expression system of Pichia pastoris with high TP-I expression was constructed by gene engineering. To achieve high expression of TP-I, 74 amino acid-long peptide (4TP-1) was designed containing 4 copies of TP-I, and specific cleavage sites for pancreatic elastase (-Ala↓ or -Gly↓) and carboxypeptidase A (cleaves C terminal amino acid); these cleavage sites for enzymes were located between the four copies of TP-I. The gene sequence for the designed peptide was synthesized taking into consideration codon preferences for P. pastoris, and cloned into the highly efficient expression vector pGAPZα B. Host Pichia pastoris strain GS115 cells were transfected by the constructed expression vector pGAPZα B-4tp-I by electroporation. Tricine-SDS-PAGE electrophoresis was carried out to detect the expression of target peptides in the fermentation medium. This analysis showed a protein band of 3.3 kDa, identical to that of chemically synthesized TP-I, verifying that successful synthesis and secretion of TP-I by genetically engineered P. pastoris. The concentration of TP-I in the fermentation broth was 27.24-29.53 mg/L. High-resolution mass spectrometry analysis documented that the TP-I monomer had the same molecular weight, 2262.85, as the designed 17-amino acid sequence. The recombinant TP-I peptide displayed different levels of bactericidal activity against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, and Staphylococcus aureus. Thus, the present study demonstrated the feasibility of achieving high levels of expression of TP-I in P. pastoris.
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Affiliation(s)
- Hanmei Li
- Shenzhen Key Laboratory of Fermentation, Purification and Analysis, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Zeeshan Ali
- Shenzhen Key Laboratory of Fermentation, Purification and Analysis, Shenzhen Polytechnic, Shenzhen, 518055, China; School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xiaolong Liu
- Shenzhen Key Laboratory of Fermentation, Purification and Analysis, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Li Jiang
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yongjun Tang
- Shenzhen Key Laboratory of Fermentation, Purification and Analysis, Shenzhen Polytechnic, Shenzhen, 518055, China.
| | - Jianguo Dai
- Shenzhen Key Laboratory of Fermentation, Purification and Analysis, Shenzhen Polytechnic, Shenzhen, 518055, China.
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Nanjundan J, Ramasamy R, Uthandi S, Ponnusamy M. Antimicrobial activity and spectroscopic characterization of surfactin class of lipopeptides from Bacillus amyloliquefaciens SR1. Microb Pathog 2019; 128:374-380. [PMID: 30695712 DOI: 10.1016/j.micpath.2019.01.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 11/18/2022]
Abstract
A bacterial isolate screened from wet land soil sample, found to posses antimicrobial activity against an array of fungal plant pathogens viz., Rhizoctonia solani, Sclerotium rolfsii, Alternaria solani, Fusarium oxysporum under in vitro dual culture plate assay. Further the isolate was identified into Bacillus amyloliquefaciens based on 16S rRNA sequencing. The antimicrobial fraction from the extracellular supernatant of the isolate comprises chiefly of surfactin molecules and also iturin and fengycin group of compounds. The surfactins were partially purified by tangential flow ultra-filtration and quantified with liquid chromatography yielding 316.1 mg L-1. Further the surfactin molecules were characterized by HPLC separation, FT-IR, LC-MS spectroscopy and PCR amplification of antibiotic genes. The surfactin molecule with m/z 1022 performed for MS-MS fragmentation and produced two different patterns of ion dissociation.
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MESH Headings
- Alternaria/pathogenicity
- Anti-Infective Agents/chemistry
- Anti-Infective Agents/isolation & purification
- Anti-Infective Agents/pharmacology
- Antifungal Agents/chemistry
- Antifungal Agents/isolation & purification
- Antifungal Agents/pharmacology
- Ascomycota/pathogenicity
- Bacillus amyloliquefaciens/classification
- Bacillus amyloliquefaciens/genetics
- Bacillus amyloliquefaciens/isolation & purification
- Bacillus amyloliquefaciens/metabolism
- Chromatography, High Pressure Liquid
- Chromatography, Liquid
- DNA, Bacterial
- Fusarium/pathogenicity
- Genes, Bacterial/genetics
- Lipopeptides/chemistry
- Lipopeptides/genetics
- Lipopeptides/isolation & purification
- Lipopeptides/pharmacology
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/genetics
- Peptides, Cyclic/isolation & purification
- Peptides, Cyclic/pharmacology
- Plant Diseases/microbiology
- RNA, Ribosomal, 16S/genetics
- Rhizoctonia/pathogenicity
- Soil Microbiology
- Spectroscopy, Fourier Transform Infrared
- Tandem Mass Spectrometry
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Affiliation(s)
- Jaivel Nanjundan
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India.
| | - Rajesh Ramasamy
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Sivakumar Uthandi
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
| | - Marimuthu Ponnusamy
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India
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Grady EN, MacDonald J, Ho MT, Weselowski B, McDowell T, Solomon O, Renaud J, Yuan ZC. Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6. BMC Microbiol 2019; 19:5. [PMID: 30621587 PMCID: PMC6325804 DOI: 10.1186/s12866-018-1380-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/25/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Bacillus velezensis is an endospore-forming, free-living soil bacterium with potential as a biopesticide against a broad spectrum of microbial pathogens of plants. Its potential for commercial development is enhanced by rapid replication and resistance to adverse environmental conditions, typical of Bacillus species. However, the use of beneficial microbes against phytopathogens has not gained dominance due to limitations that may be overcome with new biopesticidal strains and/or new biological knowledge. RESULTS Here, we isolated B. velezensis strain 9D-6 and showed that it inhibits the in vitro growth of prokaryotic and eukaryotic pathogens, including the bacteria Bacillus cereus , Clavibacter michiganensis, Pantoea agglomerans, Ralstonia solanacearum, Xanthomonas campestris, and Xanthomonas euvesicatoria; and the fungi Alternaria solani, Cochliobolus carbonum, Fusarium oxysporum, Fusarium solani, Gibberella pulicaris, Gibberella zeae, Monilinia fructicola, Pyrenochaeta terrestris and Rhizoctonia solani. Antimicrobial compounds with activity against Clavibacter michiganensis were isolated from B. velezensis 9D-6 and characterized by high resolution LC-MS/MS, yielding formulae of C52H91N7O13 and C53H93N7O13, which correspond to [Leu7] surfactins C14 and C15 (also called surfactin B and surfactin C), respectively. We further sequenced the B. velezensis 9D-6 genome which consists of a single circular chromosome and revealed 13 gene clusters expected to participate in antimicrobial metabolite production, including surfactin and two metabolites that have not typically been found in this species - ladderane and lantipeptide. Despite being unable to inhibit the growth of Pseudomonas syringae DC3000 in an in vitro plate assay, B. velezensis 9D-6 significantly reduced root colonization by DC3000, suggesting that 9D-6 uses methods other than antimicrobials to control phytopathogens in the environment. Finally, using in silico DNA-DNA hybridization (isDDH), we confirm previous findings that many strains currently classified as B. amyloliquefaciens are actually B. velezensis. CONCLUSIONS The data presented here suggest B. velezensis 9D-6 as a candidate plant growth promoting bacterium (PGPB) and biopesticide, which uses a unique complement of antimicrobials, as well as other mechanisms, to protect plants against phytopathogens. Our results may contribute to future utilization of this strain, and will contribute to a knowledge base that will help to advance the field of microbial biocontrol.
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Affiliation(s)
- Elliot Nicholas Grady
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Margaret T. Ho
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ori Solomon
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Justin Renaud
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
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Cabalteja CC, Mihalko DS, Seth Horne W. Heterogeneous-Backbone Foldamer Mimics of a Computationally Designed, Disulfide-Rich Miniprotein. Chembiochem 2019; 20:103-110. [PMID: 30326175 PMCID: PMC6314896 DOI: 10.1002/cbic.201800558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/29/2022]
Abstract
Disulfide-rich peptides have found widespread use in the development of bioactive agents; however, low proteolytic stability and the difficulty of exerting synthetic control over chain topology present barriers to their application in some systems. Herein, we report a method that enables the creation of artificial backbone ("foldamer") mimics of compact, disulfide-rich tertiary folds. Systematic replacement of a subset of natural α-residues with various artificial building blocks in the context of a computationally designed prototype sequence leads to "heterogeneous-backbone" variants that undergo clean oxidative folding, adopt tertiary structures indistinguishable from that of the prototype, and enjoy proteolytic protection beyond that inherent to the topologically constrained scaffold. Collectively, these results demonstrate systematic backbone substitution to be a viable method to engineer the properties of disulfide-rich sequences and expands the repertoire of protein mimicry by foldamers to an exciting new structural class.
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Affiliation(s)
- Chino C. Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
| | - Daniel S. Mihalko
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
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Quintero D, Carrafa J, Vincent L, Kim HJ, Wohlschlegel J, Bermudes D. Co-Expression of a Chimeric Protease Inhibitor Secreted by a Tumor-Targeted Salmonella Protects Therapeutic Proteins from Proteolytic Degradation. J Microbiol Biotechnol 2018; 28:2079-2094. [PMID: 30661346 PMCID: PMC6883771 DOI: 10.4014/jmb.1807.08036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Sunflower trypsin inhibitor (SFTI) is a 14-amino-acid bicyclic peptide that contains a single internal disulfide bond. We initially constructed chimeras of SFTI with N-terminal secretion signals from the Escherichia coli OmpA and Pseudomonas aeruginosa ToxA, but only detected small amounts of protease inhibition resulting from these constructs. A substantially higher degree of protease inhibition was detected from a C-terminal SFTI fusion with E. coli YebF, which radiated more than a centimeter from an individual colony of E. coli using a culture-based inhibitor assay. Inhibitory activity was further improved in YebF-SFTI fusions by the addition of a trypsin cleavage signal immediately upstream of SFTI, and resulted in production of a 14-amino-acid, disulfide-bonded SFTI free in the culture supernatant. To assess the potential of the secreted SFTI to protect the ability of a cytotoxic protein to kill tumor cells, we utilized a tumor-selective form of the Pseudomonas ToxA (OTG-PE38K) alone and expressed as a polycistronic construct with YebF-SFTI in the tumor-targeted Salmonella VNP20009. When we assessed the ability of toxin-containing culture supernatants to kill MDA-MB-468 breast cancer cells, the untreated OTG-PE38K was able to eliminate all detectable tumor cells, while pretreatment with trypsin resulted in the complete loss of anticancer cytotoxicity. However, when OTG-PE38K was co-expressed with YebF-SFTI, cytotoxicity was completely retained in the presence of trypsin. These data demonstrate SFTI chimeras are secreted in a functional form and that co-expression of protease inhibitors with therapeutic proteins by tumor-targeted bacteria has the potential to enhance the activity of therapeutic proteins by suppressing their degradation within a proteolytic environment.
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Affiliation(s)
- David Quintero
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University, College of Science and Math, California State University, Northridge, Northridge, CA 91330-8303
| | - Jamie Carrafa
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
| | - Lena Vincent
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Current Address, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California at Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - David Bermudes
- Department of Biology, California State University Northridge, Northridge, CA 91330-8303, USA
- Interdisciplinary Research Institute for the Sciences (IRIS), California State University, College of Science and Math, California State University, Northridge, Northridge, CA 91330-8303
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Abstract
Thiopeptides are members of the ribosomally synthesized and post-translationally modified peptide family of natural products. Most characterized thiopeptides display nanomolar potency toward Gram-positive bacteria by blocking protein translation with several being produced at the industrial scale for veterinary and livestock applications. Employing our custom bioinformatics program, RODEO, we expand the thiopeptide family of natural products by a factor of four. This effort revealed many new thiopeptide biosynthetic gene clusters with products predicted to be distinct from characterized thiopeptides and identified gene clusters for previously characterized molecules of unknown biosynthetic origin. To further validate our data set of predicted thiopeptide biosynthetic gene clusters, we isolated and characterized a structurally unique thiopeptide featuring a central piperidine and rare thioamide moiety. Termed saalfelduracin, this thiopeptide displayed potent antibiotic activity toward several drug-resistant Gram-positive pathogens. A combination of whole-genome sequencing, comparative genomics, and heterologous expression experiments confirmed that the thioamide moiety of saalfelduracin is installed post-translationally by the joint action of two proteins, TfuA and YcaO. These results reconcile the previously unknown origin of the thioamide in two long-known thiopeptides, thiopeptin and Sch 18640. Armed with these new insights into thiopeptide chemical-genomic space, we provide a roadmap for the discovery of additional members of this natural product family.
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Affiliation(s)
- Christopher J. Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Bryce Kille
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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Kang X, Zhang W, Cai X, Zhu T, Xue Y, Liu C. Bacillus velezensis CC09: A Potential 'Vaccine' for Controlling Wheat Diseases. Mol Plant Microbe Interact 2018; 31:623-632. [PMID: 29372814 DOI: 10.1094/mpmi-09-17-0227-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biocontrol bacteria that can act like a "vaccine", stimulating plant resistance to pathogenic diseases, are still not fully elucidated. In this study, an endophytic bacterium, Bacillus velezensis CC09, labeled with green fluorescent protein, was tested for its colonization, migration, and expression of genes encoding iturin A synthetase within wheat tissues and organs as well as for protective effects against wheat take-all and spot blotch diseases. The results showed that strain CC09 not only formed biofilm on the root surface but was also widely distributed in almost every tissue, including the epidermis, cortex, and xylem vessels, and even migrated to stems and leaves, resulting in 66.67% disease-control efficacy (DCE) of take-all and 21.64% DCE of spot blotch. Moreover, the gene cluster encoding iturin A synthase under the control of the pitu promoter is expressed in B. velezensis CC09 in wheat tissues, which indicates that iturin A might contribute to the in-vivo antifungal activity and leads to the disease control. All these data suggested that strain CC09 can act like a 'vaccine' in the control of wheat diseases, with a single treatment inoculated on roots through multiple mechanisms.
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Affiliation(s)
- Xingxing Kang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wanling Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xunchao Cai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tong Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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Burnett PGG, Young LW, Olivia CM, Jadhav PD, Okinyo-Owiti DP, Reaney MJT. Novel flax orbitide derived from genetic deletion. BMC Plant Biol 2018; 18:90. [PMID: 29783946 PMCID: PMC5963108 DOI: 10.1186/s12870-018-1303-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Flaxseed orbitides are homodetic plant cyclic peptides arising from ribosomal synthesis and post-translation modification (N to C cyclization), and lacking cysteine double bonds (Nat Prod Rep 30:108-160, 2013). Screening for orbitide composition was conducted on the flax core collection (FCC) grown at both Saskatoon, Saskatchewan and Morden, Manitoba over three growing seasons (2009-2011). Two flax (Linum usitatissimum L.) accessions 'Hollandia' (CN 98056) and 'Z 11637' (CN 98150) produce neither [1-9-NαC]-linusorb B2 (3) nor [1-9-NαC]-linusorb B3 (1). Mass spectrometry was used to identify novel compounds and elucidate their structure. NMR spectroscopy was used to corroborate structural information. RESULTS Experimental findings indicated that these accessions produce a novel orbitide, identified in three oxidation states having quasimolecular ion peaks at m/z 1072.6 (18), 1088.6 (19), and 1104.6 (20) [M + H]+ corresponding to molecular formulae C57H86N9O9S, C57H86N9O10S, and C57H86N9O11S, respectively. The structure of 19 was confirmed unequivocally as [1-9-NαC]-OLIPPFFLI. PCR amplification and sequencing of the gene coding for 18, using primers developed for 3 and 1, identified the putative linear precursor protein of 18 as being comprised of the first three amino acid residues of 3 (MLI), four conserved amino acid residues of 3 and/or 1 (PPFF), and the last two residues of 1 (LI). CONCLUSION Comparison of gene sequencing data revealed that a 117 base pair deletion had occurred that resulted in truncation of both 3 and 1 to produce a sequence encoding for the novel orbitide precursor of 18. This observation suggests that repeat units of flax orbitide genes are conserved and suggests a novel mechanism for evolution of orbitide gene diversity. Orbitides 19 and 20 contain MetO and MetO2, respectively, and are not directly encoded, but are products of post-translation modification of Met present in 18 ([1-9-NαC]-MLIPPFFLI).
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Affiliation(s)
- Peta-Gaye Gillian Burnett
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Lester Warren Young
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Clara Marisa Olivia
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Pramodkumar Dinkar Jadhav
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Denis Paskal Okinyo-Owiti
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Martin John Tarsisius Reaney
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, Guangzhou, 510632 Guangdong China
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Kritzer JA, Freyzon Y, Lindquist S. Yeast can accommodate phosphotyrosine: v-Src toxicity in yeast arises from a single disrupted pathway. FEMS Yeast Res 2018; 18:4931722. [PMID: 29546391 PMCID: PMC6454501 DOI: 10.1093/femsyr/foy027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/08/2018] [Indexed: 12/29/2022] Open
Abstract
Tyrosine phosphorylation is a key biochemical signal that controls growth and differentiation in multicellular organisms. Saccharomyces cerevisiae and nearly all other unicellular eukaryotes lack intact phosphotyrosine signaling pathways. However, many of these organisms have primitive phosphotyrosine-binding proteins and tyrosine phosphatases, leading to the assumption that the major barrier for emergence of phosphotyrosine signaling was the negative consequences of promiscuous tyrosine kinase activity. In this work, we reveal that the classic oncogene v-Src, which phosphorylates many dozens of proteins in yeast, is toxic because it disrupts a specific spore wall remodeling pathway. Using genetic selections, we find that expression of a specific cyclic peptide, or overexpression of SMK1, a MAP kinase that controls spore wall assembly, both lead to robust growth despite a continuous high level of phosphotyrosine in the yeast proteome. Thus, minimal genetic manipulations allow yeast to tolerate high levels of phosphotyrosine. These results indicate that the introduction of tyrosine kinases within single-celled organisms may not have been a major obstacle to the evolution of phosphotyrosine signaling.
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Affiliation(s)
- Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford MA 02155, USA
| | - Yelena Freyzon
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA
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44
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Rajasekaran K, Sayler RJ, Sickler CM, Majumdar R, Jaynes JM, Cary JW. Control of Aspergillus flavus growth and aflatoxin production in transgenic maize kernels expressing a tachyplesin-derived synthetic peptide, AGM182. Plant Sci 2018; 270:150-156. [PMID: 29576068 DOI: 10.1016/j.plantsci.2018.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Aspergillus flavus is an opportunistic, saprophytic fungus that infects maize and other fatty acid-rich food and feed crops and produces toxic and carcinogenic secondary metabolites known as aflatoxins. Contamination of maize with aflatoxin poses a serious threat to human health in addition to reducing the crop value leading to a substantial economic loss. Here we report designing a tachyplesin1-derived synthetic peptide AGM182 and testing its antifungal activity both in vitro and in planta. In vitro studies showed a five-fold increase in antifungal activity of AGM182 (vs. tachyplesin1) against A. flavus. Transgenic maize plants expressing AGM182 under maize Ubiquitin-1 promoter were produced through Agrobacterium-mediated transformation. PCR products confirmed integration of the AGM182 gene, while RT-PCR of maize RNA confirmed the presence of AGM182 transcripts. Maize kernel screening assay using a highly aflatoxigenic A. flavus strain (AF70) showed up to 72% reduction in fungal growth in the transgenic AGM182 seeds compared to isogenic negative control seeds. Reduced fungal growth in the AGM182 transgenic seeds resulted in a significant reduction in aflatoxin levels (76-98%). The results presented here show the power of computational and synthetic biology to rationally design and synthesize an antimicrobial peptide against A. flavus that is effective in reducing fungal growth and aflatoxin contamination in an economically important food and feed crop such as maize.
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Affiliation(s)
- Kanniah Rajasekaran
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States.
| | - Ronald J Sayler
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, United States
| | - Christine M Sickler
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
| | - Rajtilak Majumdar
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
| | - Jesse M Jaynes
- College of Agriculture, Environment and Nutrition Sciences, Tuskegee University, Tuskegee, AL 36088, United States
| | - Jeffrey W Cary
- Food and Feed Safety Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124, United States
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45
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Karathanasi G, Bojer MS, Baldry M, Johannessen BA, Wolff S, Greco I, Kilstrup M, Hansen PR, Ingmer H. Linear peptidomimetics as potent antagonists of Staphylococcus aureus agr quorum sensing. Sci Rep 2018; 8:3562. [PMID: 29476092 PMCID: PMC5824847 DOI: 10.1038/s41598-018-21951-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/14/2018] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is an important pathogen causing infections in humans and animals. Increasing problems with antimicrobial resistance has prompted the development of alternative treatment strategies, including antivirulence approaches targeting virulence regulation such as the agr quorum sensing system. agr is naturally induced by cyclic auto-inducing peptides (AIPs) binding to the AgrC receptor and cyclic peptide inhibitors have been identified competing with AIP binding to AgrC. Here, we disclose that small, linear peptidomimetics can act as specific and potent inhibitors of the S. aureus agr system via intercepting AIP-AgrC signal interaction at low micromolar concentrations. The corresponding linear peptide did not have this ability. This is the first report of a linear peptide-like molecule that interferes with agr activation by competitive binding to AgrC. Prospectively, these peptidomimetics may be valuable starting scaffolds for the development of new inhibitors of staphylococcal quorum sensing and virulence gene expression.
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Affiliation(s)
- Georgia Karathanasi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Martin Saxtorph Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Bárdur Andréson Johannessen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Sanne Wolff
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Ines Greco
- Department of Drug Design and Farmacology, Faculty of Health and Medical Sciences University of Copenhagen, Universitetsparken 2, 2100, København, Denmark
| | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Metabolic Signaling and Regulation, Technical University of Denmark, Matematiktorvet, 2800, Lyngby, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Farmacology, Faculty of Health and Medical Sciences University of Copenhagen, Universitetsparken 2, 2100, København, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark.
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Kawahara T, Izumikawa M, Kozone I, Hashimoto J, Kagaya N, Koiwai H, Komatsu M, Fujie M, Sato N, Ikeda H, Shin-Ya K. Neothioviridamide, a Polythioamide Compound Produced by Heterologous Expression of a Streptomyces sp. Cryptic RiPP Biosynthetic Gene Cluster. J Nat Prod 2018; 81:264-269. [PMID: 29381067 DOI: 10.1021/acs.jnatprod.7b00607] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During genome mining for thioviridamide-like biosynthetic gene clusters that could produce polythioamide RiPP (ribosomally synthesized and post-translationally modified peptides), we discovered a novel cryptic biosynthetic gene cluster. During efforts to express this biosynthetic gene using heterologous expression of this biosynthetic gene cluster, a novel compound designated as neothioviridamide was produced. We report herein the cloning and heterologous expression of the neothioviridamide biosynthetic gene cluster and the isolation, structure determination, and cytotoxic activity of neothioviridamide.
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Affiliation(s)
- Teppei Kawahara
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hanae Koiwai
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Mamoru Komatsu
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Noriyuki Sato
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University , 1-15-1 Kitasato Sagamihara, Kanagawa 228-8555, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- The Biotechnology Research Center, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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47
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Xu Y, Zhang H, Pan B, Zhang S, Wang S, Niu Q. Transcriptome-Wide Identification of Differentially Expressed Genes and Long Non-coding RNAs in Aluminum-Treated Rat Hippocampus. Neurotox Res 2018; 34:220-232. [PMID: 29460113 DOI: 10.1007/s12640-018-9879-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/20/2018] [Accepted: 02/02/2018] [Indexed: 12/14/2022]
Abstract
Aluminum (Al) is an environmental neurotoxicant with a wide exposure, but the molecular mechanism underlying its toxicity remains unclear. We used RNA sequencing (RNA-seq) in the hippocampus of Al-treated rats to identify 96 upregulated and 652 downregulated mRNAs, and 37 dysregulated long non-coding (lnc)RNAs. Gene ontology analysis showed that dysregulated genes were involved in glial cell differentiation, neural transmission, and vesicle trafficking. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed clustering of differentially expressed mRNAs and lncRNA target genes in several pathways, including the "adenosine monophosphate-activated protein kinase signaling pathway," "extracellular matrix receptor interaction," "the phosphatidylinositol 3 kinase-protein kinase B signaling pathway," and "focal adhesion" signaling pathway. RNA-seq results were validated by reverse transcription (RT)-PCR. Additionally, Al induced changes to the number and morphology of glial cells in the hippocampus of rats, as shown by glial fibrillary acidic protein (GFAP) and ionized calcium binding adaptor molecule 1 (Iba1) immunochemistry. RT-PCR and western blotting validated the significant increase in expression of glial cell-related genes GFAP and SOX10 following Al exposure compared with control rats, consistent with RNA-seq results. Collectively, these results suggest that aberrant mRNAs and lncRNAs respond to Al neurotoxicity, and that glial cell-related genes play important roles in the Al neurotoxicity mechanism. These findings provide the basis for designing targeted approaches for the treatment or prevention of Al-induced neurotoxicity.
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Affiliation(s)
- Yirong Xu
- Pathology Department, Shanxi Medical University Fenyang College, Fenyang, Shanxi, 032200, China
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Huifang Zhang
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Baolong Pan
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shuhui Zhang
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shan Wang
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Qiao Niu
- College of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
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48
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Poon S, Harris KS, Jackson MA, McCorkelle OC, Gilding EK, Durek T, van der Weerden NL, Craik DJ, Anderson MA. Co-expression of a cyclizing asparaginyl endopeptidase enables efficient production of cyclic peptides in planta. J Exp Bot 2018; 69:633-641. [PMID: 29309615 PMCID: PMC5853369 DOI: 10.1093/jxb/erx422] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/04/2017] [Indexed: 05/18/2023]
Abstract
Cyclotides are ultra-stable, backbone-cyclized plant defence peptides that have attracted considerable interest in the pharmaceutical industry. This is due to their range of native bioactivities as well as their ability to stabilize other bioactive peptides within their framework. However, a hindrance to their widespread application is the lack of scalable, cost-effective production strategies. Plant-based production is an attractive, benign option since all biosynthetic steps are performed in planta. Nonetheless, cyclization in non-cyclotide-producing plants is poor. Here, we show that cyclic peptides can be produced efficiently in Nicotiana benthamiana, one of the leading plant-based protein production platforms, by co-expressing cyclotide precursors with asparaginyl endopeptidases that catalyse peptide backbone cyclization. This approach was successful in a range of other plants (tobacco, bush bean, lettuce, and canola), either transiently or stably expressed, and was applicable to both native and engineered cyclic peptides. We also describe the use of the transgenic system to rapidly identify new asparaginyl endopeptidase cyclases and interrogate their substrate sequence requirements. Our results pave the way for exploiting cyclotides for pest protection in transgenic crops as well as large-scale production of cyclic peptide pharmaceuticals in plants.
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Affiliation(s)
- Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Karen S Harris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mark A Jackson
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Owen C McCorkelle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Edward K Gilding
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L van der Weerden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David J Craik
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Schwalen CJ, Hudson GA, Kosol S, Mahanta N, Challis GL, Mitchell DA. In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily. J Am Chem Soc 2017; 139:18154-18157. [PMID: 29200283 PMCID: PMC5915351 DOI: 10.1021/jacs.7b09899] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bottromycins belong to the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Bottromycins exhibit unique structural features, including a hallmark macrolactamidine ring and thiazole heterocycle for which divergent members of the YcaO superfamily have been biosynthetically implicated. Here we report the in vitro reconstitution of two YcaO proteins, BmbD and BmbE, responsible for the ATP-dependent cyclodehydration reactions that yield thiazoline- and macrolactamidine-functionalized products, respectively. We also establish the substrate tolerance for BmbD and BmbE and systematically dissect the role of the follower peptide, which we show serves a purpose similar to canonical leader peptides in directing the biosynthetic enzymes to the substrate. Lastly, we leverage the expanded capabilities of YcaO proteins to conduct an extensive bioinformatic survey to classify known YcaO chemistry. This analysis predicts new functions remain to be uncovered within the superfamily.
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Affiliation(s)
- Christopher J. Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Simone Kosol
- Department of Chemistry and Warwick Integrative Synthetic Biology Center, University of Warwick, Coventry CV4 7AL, UK
| | - Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Center, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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50
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Imjongjirak C, Amphaiphan P, Charoensapsri W, Amparyup P. Characterization and antimicrobial evaluation of SpPR-AMP1, a proline-rich antimicrobial peptide from the mud crab Scylla paramamosain. Dev Comp Immunol 2017; 74:209-216. [PMID: 28479344 DOI: 10.1016/j.dci.2017.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Antimicrobial peptide (AMP) is an important molecule in the innate immune system. Here, we report the cloning and functional studies of proline-rich AMPs (PR-AMPs) from the three species of mud crab: Scylla paramamosain, S. serrata, and the swimming crab Portunus pelagicus. The deduced peptides revealed that they contain the putative signal peptides and encode for mature peptides, which contain sequence architecture similar to a 6.5-kDa proline-rich AMP of the shore crab, Carcinus maenas which showed similarity with the bactenecin7. Tissue distribution analysis indicated that the SpPR-AMP1 was expressed in a wide range of adult tissues, with the highest expression levels in the crab hemocyte. Challenge experiments showed that the levels of SpPR-AMP1 mRNA expression were up-regulated in the hemocyte after peptidoglycan stimulation. To evaluate the biological properties of mature SpPR-AMP1, peptides were chemically synthesized and recombinantly expressed. SpPR-AMP1 showed strong antibacterial activity against both Gram-positive bacteria Micrococcus luteus and Gram-negative bacteria Vibrio harveyi. The results indicate that the SpPR-AMP1 plays a role in crab immunity.
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Affiliation(s)
- Chanprapa Imjongjirak
- Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
| | - Pawanrat Amphaiphan
- Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - Walaiporn Charoensapsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Piti Amparyup
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand.
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