1
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Ramos Figueroa J, Zhu L, van der Donk WA. Unexpected Transformations during Pyrroloiminoquinone Biosynthesis. J Am Chem Soc 2024; 146:14235-14245. [PMID: 38719200 PMCID: PMC11117183 DOI: 10.1021/jacs.4c03677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Pyrroloiminoquinone-containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP- and tRNA-dependent manner catalyzed by a PEptide Aminoacyl-tRNA Ligase (PEARL). The indole of Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes from two gene clusters, which show that the previously proposed pathway is incorrect and that Nature's route toward pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, amino groups in pyrroloiminoquinones are derived from (at least) three different sources, glycine, asparagine, and leucine, all introduced in a tRNA-dependent manner. We also show that an FAD-dependent putative glycine oxidase (Amm14) is required for the process that incorporates the nitrogens from glycine and leucine and that a quinone reductase is required for the incorporation of asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes, such as the glutamyl-tRNA-dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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2
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Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS. Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590974. [PMID: 38712170 PMCID: PMC11071452 DOI: 10.1101/2024.04.24.590974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here we identify C12orf29 as an atypical ATP-grasp enzyme that ligates RNA. Human C12orf29 and its homologs auto-adenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5'-phosphate and a 3'-hydroxyl. C12orf29 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Genetic depletion of c12orf29 in female mice alters global tRNA levels in brain. Furthermore, crystal structures of a C12orf29 homolog from Yasminevirus bound to nucleotides reveal a minimal and atypical RNA ligase fold with a unique active site architecture that participates in catalysis. Collectively, our results identify C12orf29 as an RNA ligase and suggest its involvement in tRNA biology.
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Affiliation(s)
- Yingjie Hu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Victor A. Lopez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - James P. Pfister
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bing Song
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Benjamin T. Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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3
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Figueroa JR, Zhu L, van der Donk WA. Unexpected transformations during pyrroloiminoquinone biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584671. [PMID: 38559119 PMCID: PMC10979984 DOI: 10.1101/2024.03.12.584671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pyrroloiminoquinone containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP and tRNA dependent manner catalyzed by a PEptide Amino-acyl tRNA ligase (PEARL). The indole of the Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes that show that the proposed pathway is incorrect and that Nature's route towards pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, the amino groups in pyrroloiminoquinones are derived from three different sources, glycine, asparagine, and leucine, all introduced in a tRNA dependent manner. We also show that an FAD-dependent putative glycine oxidase is required for the process that incorporates the nitrogens from glycine and leucine, and that a quinone reductase is required for the incorporation of the asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes such as the glutamyl-tRNA dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lingyang Zhu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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4
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Zheng R, Wang C, Liu R, Cai R, Sun C. Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria. eLife 2024; 12:RP89874. [PMID: 38265071 PMCID: PMC10945688 DOI: 10.7554/elife.89874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Planctomycetes bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea Planctomycetes members have been cultivated, limiting our understanding of Planctomycetes in the deep biosphere. Here, we have successfully cultured a novel strain of Planctomycetes (strain ZRK32) from a deep-sea cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3- or NH4+ promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid cycle and the Embden-Meyerhof-Parnas glycolysis pathway. Moreover, supplementation with NO3- or NH4+ induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes. Overall, these findings expand our understanding of deep-sea Planctomycetes bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
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5
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Lee H, Park SH, Kim J, Lee J, Koh MS, Lee JH, Kim S. Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305946. [PMID: 37987032 PMCID: PMC10787088 DOI: 10.1002/advs.202305946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiyoon Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehak Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min Sun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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6
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Yang M, Du S, Zhang Z, Xia Q, Liu H, Qin F, Wu Z, Ying H, Wu Y, Shao J, Zhao Y. Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria. Microbiol Spectr 2023; 11:e0494222. [PMID: 37607063 PMCID: PMC10580990 DOI: 10.1128/spectrum.04942-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/07/2023] [Indexed: 08/24/2023] Open
Abstract
The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns. IMPORTANCE OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.
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Affiliation(s)
- Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian Xia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanqi Ying
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yin Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiabing Shao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
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7
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Choi B, Link AJ. Discovery, Function, and Engineering of Graspetides. TRENDS IN CHEMISTRY 2023; 5:620-633. [PMID: 37614740 PMCID: PMC10443899 DOI: 10.1016/j.trechm.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Graspetides are a class of RiPPs (ribosomally synthesized and post-translationally modified peptides) defined by the presence of ester or amide side chain-side chain linkages resulting in peptide macrocycles. The graspetide name comes from the ATP-grasp enzymes that install the side chain-side chain linkages. This review covers the early, activity-based isolation of the first graspetides, marinostatins and microviridins, as well as the key genomics-driven experiments that established graspetide as RiPPs. The mechanism and structure of graspetide-associated ATP-grasp enzymes is discussed. Genome mining methods to discover new graspetides as well as the analytical techniques used to determine the linkages in graspetides are described. Extant knowledge on the bioactivity of graspetides as protease inhibitors is reviewed. Further chemical modifications to graspetides as well graspetide engineering studies are also described. We conclude with several suggestions about future directions of graspetide research.
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Affiliation(s)
- Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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8
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Ozhelvaci F, Steczkiewicz K. Identification and Classification of Papain-like Cysteine Proteinases. J Biol Chem 2023:104801. [PMID: 37164157 DOI: 10.1016/j.jbc.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, and cell wall remodeling. High sequence and structure diversity observed within these proteins hinders their comprehensive classification as well as the identification of new representatives. Moreover, in general protein databases, many families already classified as papain-like lack details regarding their mechanism of action or biological function. Here, we use transitive remote homology searches and 3D modeling to newly classify 21 families to the papain-like cysteine peptidase superfamily. We attempt to predict their biological function, and provide structural chacterization of 89 protein clusters defined based on sequence similarity altogether spanning 106 papain-like families. Moreover, we systematically discuss observed diversity in sequences, structures, and catalytic sites. Eventually, we expand the list of human papain-related proteins by seven representatives, including dopamine receptor-interacting protein (DRIP1) as potential deubiquitinase, and centriole duplication regulating CEP76 as retaining catalytically active peptidase-like domain. The presented results not only provide structure-based rationales to already existing peptidase databases but also may inspire further experimental research focused on peptidase-related biological processes.
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Affiliation(s)
- Fatih Ozhelvaci
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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9
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Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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10
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Elashal HE, Koos JD, Cheung-Lee WL, Choi B, Cao L, Richardson MA, White HL, Link AJ. Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide. Nat Chem 2022; 14:1325-1334. [PMID: 35982233 PMCID: PMC10078976 DOI: 10.1038/s41557-022-01022-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Microviridins and other ω-ester-linked peptides, collectively known as graspetides, are characterized by side-chain-side-chain linkages installed by ATP-grasp enzymes. Here we report the discovery of a family of graspetides, the gene clusters of which also encode an O-methyltransferase with homology to the protein repair catalyst protein L-isoaspartyl methyltransferase. Using heterologous expression, we produced fuscimiditide, a ribosomally synthesized and post-translationally modified peptide (RiPP). NMR analysis of fuscimiditide revealed that the peptide contains two ester cross-links forming a stem-loop macrocycle. Furthermore, an unusually stable aspartimide moiety is found within the loop macrocycle. We fully reconstituted fuscimiditide biosynthesis in vitro including formation of the ester and aspartimide moieties. The aspartimide moiety embedded in fuscimiditide hydrolyses regioselectively to isoaspartate. Surprisingly, this isoaspartate-containing peptide is also a substrate for the L-isoaspartyl methyltransferase homologue, thus driving any hydrolysis products back to the aspartimide form. Whereas an aspartimide is often considered a nuisance product in protein formulations, our data suggest that some RiPPs have aspartimide residues intentionally installed via enzymatic activity.
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Affiliation(s)
- Hader E Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Joseph D Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Brian Choi
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Michelle A Richardson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Heather L White
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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11
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Pederick JL, Horsfall AJ, Jovcevski B, Klose J, Abell AD, Pukala TL, Bruning JB. Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism. J Biol Chem 2022; 298:102392. [PMID: 35988643 PMCID: PMC9486568 DOI: 10.1016/j.jbc.2022.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl–ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate–ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jack Klose
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Tara L Pukala
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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12
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Chu L, Luo X, Zhu T, Cao Y, Zhang L, Deng Z, Gao J. Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate. Nat Commun 2022; 13:1736. [PMID: 35365617 PMCID: PMC8976061 DOI: 10.1038/s41467-022-29188-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/03/2022] [Indexed: 01/16/2023] Open
Abstract
Glyphosate is a widely used herbicide with an annual production of more than one million tons globally. Current commercialized production processes of glyphosate are generally associated with manufacturing hazards and toxic wastes. Recently, many countries have strengthened environmental supervision and law enforcement on glyphosate manufacturing. Therefore, a green source of glyphosate is required. Here, we characterize the genes required for producing aminomethylphosphonate (AMP), one of the intermediates in the biosynthesis of the potent antibiotics argolaphos. We apply a synthetic biology strategy to improve AMP production in Streptomyces lividans, with fermentation titers of 52 mg L-1, a 500-fold improvement over the original strain. Furthermore, we develop an efficient and practical chemical process for converting AMP to glyphosate. Our findings highlight one greenness-driven alternative in the production of glyphosate.
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Affiliation(s)
- Leixia Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Xiaoxia Luo
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science & Technology, Tarim University, Alar, Xinjiang, 843300, China
| | - Taoting Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Yingying Cao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lili Zhang
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
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13
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Makarova KS, Blackburne B, Wolf YI, Nikolskaya A, Karamycheva S, Espinoza M, Barry CE, Bewley CA, Koonin EV. Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis. Biol Direct 2022; 17:7. [PMID: 35313954 PMCID: PMC8939145 DOI: 10.1186/s13062-022-00320-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
Background Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified Peptides (RiPPs), and a major group of RiPPs are graspetides, so named after ATP-grasp ligases that catalyze the formation of lactam and lactone linkages in these peptides. The diversity of graspetides, the multiple proteins encoded in the respective Biosynthetic Gene Clusters (BGCs) and their evolution have not been studied in full detail. In this work, we attempt a comprehensive analysis of the graspetide-encoding BGCs and report a variety of novel graspetide groups as well as ancillary proteins implicated in graspetide biosynthesis and expression. Results We compiled a comprehensive, manually curated set of graspetides that includes 174 families including 115 new families with distinct patterns of amino acids implicated in macrocyclization and further modification, roughly tripling the known graspetide diversity. We derived signature motifs for the leader regions of graspetide precursors that could be used to facilitate graspetide prediction. Graspetide biosynthetic gene clusters and specific precursors were identified in bacterial divisions not previously known to encode RiPPs, in particular, the parasitic and symbiotic bacteria of the Candidate phyla radiation. We identified Bacteroides-specific biosynthetic gene clusters (BGC) that include remarkable diversity of graspetides encoded in the same loci which predicted to be modified by the same ATP-grasp ligase. We studied in details evolution of recently characterized chryseoviridin BGCs and showed that duplication and horizonal gene exchange both contribute to the diversification of the graspetides during evolution. Conclusions We demonstrate previously unsuspected diversity of graspetide sequences, even those associated with closely related ATP-grasp enzymes. Several previously unnoticed families of proteins associated with graspetide biosynthetic gene clusters are identified. The results of this work substantially expand the known diversity of RiPPs and can be harnessed to further advance approaches for their identification. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-022-00320-2.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Brittney Blackburne
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Anastasia Nikolskaya
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Marlene Espinoza
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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14
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Smith AJ, Advani J, Brock DC, Nellissery J, Gumerson J, Dong L, Aravind L, Kennedy B, Swaroop A. GATD3A, a mitochondrial deglycase with evolutionary origins from gammaproteobacteria, restricts the formation of advanced glycation end products. BMC Biol 2022; 20:68. [PMID: 35307029 PMCID: PMC8935817 DOI: 10.1186/s12915-022-01267-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
Functional complexity of the eukaryotic mitochondrial proteome is augmented by independent gene acquisition from bacteria since its endosymbiotic origins. Mammalian homologs of many ancestral mitochondrial proteins have uncharacterized catalytic activities. Recent forward genetic approaches attributed functions to proteins in established metabolic pathways, thereby limiting the possibility of identifying novel biology relevant to human disease. We undertook a bottom-up biochemistry approach to discern evolutionarily conserved mitochondrial proteins with catalytic potential.
Results
Here, we identify a Parkinson-associated DJ-1/PARK7-like protein—glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A), with bacterial evolutionary affinities although not from alphaproteobacteria. We demonstrate that GATD3A localizes to the mitochondrial matrix and functions as a deglycase. Through its amidolysis domain, GATD3A removes non-enzymatic chemical modifications produced during the Maillard reaction between dicarbonyls and amines of nucleotides and amino acids. GATD3A interacts with factors involved in mitochondrial mRNA processing and translation, suggestive of a role in maintaining integrity of important biomolecules through its deglycase activity. The loss of GATD3A in mice is associated with accumulation of advanced glycation end products (AGEs) and altered mitochondrial dynamics.
Conclusions
An evolutionary perspective helped us prioritize a previously uncharacterized but predicted mitochondrial protein GATD3A, which mediates the removal of early glycation intermediates. GATD3A restricts the formation of AGEs in mitochondria and is a relevant target for diseases where AGE deposition is a pathological hallmark.
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15
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Bhandari S, Bisht KS, Merkler DJ. The Biosynthesis and Metabolism of the N-Acylated Aromatic Amino Acids: N-Acylphenylalanine, N-Acyltyrosine, N-Acyltryptophan, and N-Acylhistidine. Front Mol Biosci 2022; 8:801749. [PMID: 35047560 PMCID: PMC8762209 DOI: 10.3389/fmolb.2021.801749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
The fatty acid amides are a family of lipids composed of two chemical moieties, a fatty acid and a biogenic amine linked together in an amide bond. This lipid family is structurally related to the endocannabinoid anandamide (N-arachidonoylethanolamine) and, thus, is frequently referred to as a family of endocannabinoid-related lipids. The fatty acid amide family is divided into different classes based on the conjugate amine; anandamide being a member of the N-acylethanolamine class (NAE). Another class within the fatty acid amide family is the N-acyl amino acids (NA-AAs). The focus of this review is a sub-class of the NA-AAs, the N-acyl aromatic amino acids (NA-ArAAs). The NA-ArAAs are not broadly recognized, even by those interested in the endocannabinoids and endocannabinoid-related lipids. Herein, the NA-ArAAs that have been identified from a biological source will be highlighted and pathways for their biosynthesis, degradation, enzymatic modification, and transport will be presented. Also, information about the cellular functions of the NA-ArAAs will be placed in context with the data regarding the identification and metabolism of these N-acylated amino acids. A review of the current state-of-knowledge about the NA-ArAAs is to stimulate future research about this underappreciated sub-class of the fatty acid amide family.
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Affiliation(s)
- Suzeeta Bhandari
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - Kirpal S Bisht
- Department of Chemistry, University of South Florida, Tampa, FL, United States
| | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, United States
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16
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Riegert AS, Narindoshvili T, Raushel FM. Discovery and Functional Characterization of a Clandestine ATP-Dependent Amidoligase in the Biosynthesis of the Capsular Polysaccharide from Campylobacter jejuni. Biochemistry 2022; 61:117-124. [PMID: 34951304 PMCID: PMC9619395 DOI: 10.1021/acs.biochem.1c00707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Campylobacter jejuni is a Gram-negative, pathogenic bacterium that is commensal in poultry. Infection of C. jejuni leads to campylobacteriosis, the leading cause of gastroenteritis worldwide. Coating the surface of C. jejuni is a thick layer of sugar molecules known as the capsular polysaccharide (CPS). The CPS of C. jejuni NCTC 11168 (HS:2) is composed of a repeating unit of d-glycero-l-gluco-heptose, d-glucuronate, d-N-acetyl-galactosamine, and d-ribose. The glucuronate is further amidated with either ethanolamine or serinol, but it is unknown how this new amide bond is formed. Sequence similarity networks were used to identify a candidate enzyme for amide bond formation during the biosynthesis of the CPS of C. jejuni. The C-terminal domain of Cj1438 was shown to catalyze amide bond formation using MgATP and d-glucuronate in the presence of either ethanolamine phosphate or (S)-serinol phosphate. Product formation was verified using 31P NMR spectroscopy and ESI mass spectrometry, and the kinetic constants determined using a coupled enzyme assay by measuring the rate of ADP formation. This work represents the first functional characterization of an ATP-dependent amidoligase in the formation of amide bonds in the biosynthetic pathway for the assembly of the CPS in C. jejuni.
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Affiliation(s)
- Alexander S. Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, United States
| | - Frank M. Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, United States.,Department of Chemistry, Texas A&M University, College Station, TX, 77843, United States.,Corresponding Author: Frank M. Raushel – Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States; , phone: 1-979-845-3373
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17
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Ramesh S, Guo X, DiCaprio AJ, De Lio AM, Harris LA, Kille BL, Pogorelov TV, Mitchell DA. Bioinformatics-Guided Expansion and Discovery of Graspetides. ACS Chem Biol 2021; 16:2787-2797. [PMID: 34766760 DOI: 10.1021/acschembio.1c00672] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.
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Affiliation(s)
- Sangeetha Ramesh
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Xiaorui Guo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashley M. De Lio
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Bryce L. Kille
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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18
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Dell M, Dunbar KL, Hertweck C. Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature. Nat Prod Rep 2021; 39:453-459. [PMID: 34586117 DOI: 10.1039/d1np00019e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.
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Affiliation(s)
- Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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19
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Riegert AS, Narindoshvili T, Coricello A, Richards NGJ, Raushel FM. Functional Characterization of Two PLP-Dependent Enzymes Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni. Biochemistry 2021; 60:2836-2843. [PMID: 34505775 DOI: 10.1021/acs.biochem.1c00439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a Gram-negative, pathogenic bacterium that causes campylobacteriosis, a form of gastroenteritis. C. jejuni is the most frequent cause of food-borne illness in the world, surpassing Salmonella and E. coli. Coating the surface of C. jejuni is a layer of sugar molecules known as the capsular polysaccharide that, in C. jejuni NCTC 11168, is composed of a repeating unit of d-glycero-l-gluco-heptose, d-glucuronic acid, d-N-acetyl-galactosamine, and d-ribose. The d-glucuronic acid moiety is further amidated with either serinol or ethanolamine. It is unknown how these modifications are synthesized and attached to the polysaccharide. Here, we report the catalytic activities of two previously uncharacterized, pyridoxal phosphate (PLP)-dependent enzymes, Cj1436 and Cj1437, from C. jejuni NCTC 11168. Using a combination of mass spectrometry and nuclear magnetic resonance, we determined that Cj1436 catalyzes the decarboxylation of l-serine phosphate to ethanolamine phosphate. Cj1437 was shown to catalyze the transamination of dihydroxyacetone phosphate to (S)-serinol phosphate in the presence of l-glutamate. The probable routes to the ultimate formation of the glucuronamide substructures in the capsular polysaccharides of C. jejuni are discussed.
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Affiliation(s)
- Alexander S Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Adriana Coricello
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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20
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Hecht N, Monteil CL, Perrière G, Vishkautzan M, Gur E. Exploring Protein Space: From Hydrolase to Ligase by Substitution. Mol Biol Evol 2021; 38:761-776. [PMID: 32870983 PMCID: PMC7947786 DOI: 10.1093/molbev/msaa215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The understanding of how proteins evolve to perform novel functions has long been sought by biologists. In this regard, two homologous bacterial enzymes, PafA and Dop, pose an insightful case study, as both rely on similar mechanistic properties, yet catalyze different reactions. PafA conjugates a small protein tag to target proteins, whereas Dop removes the tag by hydrolysis. Given that both enzymes present a similar fold and high sequence similarity, we sought to identify the differences in the amino acid sequence and folding responsible for each distinct activity. We tackled this question using analysis of sequence–function relationships, and identified a set of uniquely conserved residues in each enzyme. Reciprocal mutagenesis of the hydrolase, Dop, completely abolished the native activity, at the same time yielding a catalytically active ligase. Based on the available Dop and PafA crystal structures, this change of activity required a conformational change of a critical loop at the vicinity of the active site. We identified the conserved positions essential for stabilization of the alternative loop conformation, and tracked alternative mutational pathways that lead to a change in activity. Remarkably, all these pathways were combined in the evolution of PafA and Dop, despite their redundant effect on activity. Overall, we identified the residues and structural elements in PafA and Dop responsible for their activity differences. This analysis delineated, in molecular terms, the changes required for the emergence of a new catalytic function from a preexisting one.
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Affiliation(s)
- Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Caroline L Monteil
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard - Lyon 1, Villeurbanne, France
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard - Lyon 1, Villeurbanne, France
| | - Marina Vishkautzan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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21
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Riegert AS, Raushel FM. Functional and Structural Characterization of the UDP-Glucose Dehydrogenase Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni. Biochemistry 2021; 60:725-734. [PMID: 33621065 DOI: 10.1021/acs.biochem.0c00953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Campylobacter jejuni is a pathogenic organism that can cause campylobacteriosis in children and adults. Most commonly, campylobacter infection is brought on by consumption of raw or undercooked poultry, unsanitary drinking water, or pet feces. Surrounding the C. jejuni bacterium is a coat of sugar molecules known as the capsular polysaccharide (CPS). The capsular polysaccharide can be very diverse among the different strains of C. jejuni, and this diversity is considered important for evading the host immune system. Modifications to the CPS of C. jejuni NCTC 11168 include O-methylation, phosphoramidylation, and amidation of glucuronate with either serinol or ethanolamine. The enzymes responsible for amidation of glucuronate are currently unknown. In this study, Cj1441, an enzyme expressed from the CPS biosynthetic gene cluster in C. jejuni NCTC 11168, was shown to catalyze the oxidation of UDP-α-d-glucose into UDP-α-d-glucuronic acid with NAD+ as the cofactor. No amide products were found in an attempt to determine whether the putative thioester intermediate formed during the oxidation of UDP-glucose by Cj1441 could be captured in the presence of added amines. The three-dimensional crystal structure of Cj1441 was determined in the presence of NAD+ and UDP-glucose bound in the active site of the enzyme (Protein Data Bank entry 7KWS). A more thorough bioinformatic analysis of the CPS gene cluster suggests that the amidation activity is localized to the t-terminal half of Cj1438, a bifunctional enzyme that is currently annotated as a sugar transferase.
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Affiliation(s)
- Alexander S Riegert
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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22
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M. Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. Viruses 2021; 13:v13010063. [PMID: 33466489 PMCID: PMC7824862 DOI: 10.3390/v13010063] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.
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Affiliation(s)
- Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Arunkumar Krishnan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, India;
| | - A. Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
- Correspondence:
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23
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Evolutionary genetic analysis of unassigned peptidase clan-associated microbial virulence and pathogenesis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00529-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Lee H, Choi M, Park JU, Roh H, Kim S. Genome Mining Reveals High Topological Diversity of ω-Ester-Containing Peptides and Divergent Evolution of ATP-Grasp Macrocyclases. J Am Chem Soc 2020; 142:3013-3023. [PMID: 31961152 DOI: 10.1021/jacs.9b12076] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ω-Ester-containing peptides (OEPs) are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) containing intramolecular ω-ester or ω-amide bonds. Although their distinct side-to-side connections may create considerable topological diversity of multicyclic peptides, it is largely unknown how diverse ring patterns have been developed in nature. Here, using genome mining of biosynthetic enzymes of OEPs, we identified genes encoding nine new groups of putative OEPs with novel core consensus sequences, disclosing a total of ∼1500 candidate OEPs in 12 groups. Connectivity analysis revealed that OEPs from three different groups contain novel tricyclic structures, one of which has a distinct biosynthetic pathway where a single ATP-grasp enzyme produces both ω-ester and ω-amide linkages. Analysis of the enzyme cross-reactivity showed that, while enzymes are promiscuous to nonconserved regions of the core peptide, they have high specificity to the cognate core consensus sequence, suggesting that the enzyme-core pair has coevolved to create a unique ring topology within the same group and has sufficiently diversified across different groups. Collectively, our results demonstrate that the diverse ring topologies, in addition to diverse sequences, have been developed in nature with multiple ω-ester or ω-amide linkages in the OEP family of RiPPs.
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Mingyu Choi
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Jung-Un Park
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Heejin Roh
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Seokhee Kim
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
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25
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Black MH, Osinski A, Gradowski M, Servage KA, Pawłowski K, Tomchick DR, Tagliabracci VS. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Science 2019; 364:787-792. [PMID: 31123136 DOI: 10.1126/science.aaw7446] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/01/2019] [Indexed: 12/11/2022]
Abstract
Enzymes with a protein kinase fold transfer phosphate from adenosine 5'-triphosphate (ATP) to substrates in a process known as phosphorylation. Here, we show that the Legionella meta-effector SidJ adopts a protein kinase fold, yet unexpectedly catalyzes protein polyglutamylation. SidJ is activated by host-cell calmodulin to polyglutamylate the SidE family of ubiquitin (Ub) ligases. Crystal structures of the SidJ-calmodulin complex reveal a protein kinase fold that catalyzes ATP-dependent isopeptide bond formation between the amino group of free glutamate and the γ-carboxyl group of an active-site glutamate in SidE. We show that SidJ polyglutamylation of SidE, and the consequent inactivation of Ub ligase activity, is required for successful Legionella replication in a viable eukaryotic host cell.
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Affiliation(s)
- Miles H Black
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Kelly A Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, Dallas, TX 75390, USA
| | - Krzysztof Pawłowski
- Warsaw University of Life Sciences, Warsaw, Poland.,Lund University, Lund, Sweden
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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26
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinoline A–C: neuartige bakterielle Tetrahydroisochinoline mit einer bemerkenswerten Biosynthese. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuriy Rebets
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Suvd Nadmid
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Constanze Paulus
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Charlotte Dahlem
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Jennifer Herrmann
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Harald Hübner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Christian Rückert
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Alexandra K. Kiemer
- Department of Pharmacy Pharmaceutical Biology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy Friedrich-Alexander-Universität Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Jörn Kalinowski
- Center for Biotechnology – CeBiTec University of Bielefeld Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Rolf Müller
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
| | - Andriy Luzhetskyy
- Department of Pharmacy Pharmaceutical Biotechnology University of Saarland Campus, Bld. C2 3 Saarbrucken 66123 Deutschland
- Department Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Campus, Bld. 8 1 Saarbrucken 66123 Deutschland
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27
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Sharma A, Sharma D, Verma SK. Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190369. [PMID: 31598288 PMCID: PMC6774946 DOI: 10.1098/rsos.190369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/21/2019] [Indexed: 05/15/2023]
Abstract
Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.
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28
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Rebets Y, Nadmid S, Paulus C, Dahlem C, Herrmann J, Hübner H, Rückert C, Kiemer AK, Gmeiner P, Kalinowski J, Müller R, Luzhetskyy A. Perquinolines A-C: Unprecedented Bacterial Tetrahydroisoquinolines Involving an Intriguing Biosynthesis. Angew Chem Int Ed Engl 2019; 58:12930-12934. [PMID: 31310031 DOI: 10.1002/anie.201905538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Indexed: 01/15/2023]
Abstract
Metabolic profiling of Streptomyces sp. IB2014/016-6 led to the identification of three new tetrahydroisoquinoline natural products, perquinolines A-C (1-3). Labelled precursor feeding studies and the cloning of the pqr biosynthetic gene cluster revealed that 1-3 are assembled by the action of several unusual enzymes. The biosynthesis starts with the condensation of succinyl-CoA and l-phenylalanine catalyzed by the amino-7-oxononanoate synthase-like enzyme PqrA, representing rare chemistry in natural product assembly. The second condensation and cyclization events are conducted by PqrG, an enzyme resembling an acyl-CoA ligase. Last, ATP-grasp RimK-type ligase PqrI completes the biosynthesis by transferring a γ-aminobutyric acid or β-alanine moiety. The discovered pathway represents a new route for assembling the tetrahydroisoquinoline cores of natural products.
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Affiliation(s)
- Yuriy Rebets
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Suvd Nadmid
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Constanze Paulus
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Jennifer Herrmann
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Christian Rückert
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology-CeBiTec, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, University of Saarland, Campus, Bld. C2 3, Saarbrucken, 66123, Germany.,Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus, Bld. 8 1, Saarbrucken, 66123, Germany
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29
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Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019; 294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD-Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD-Memo families.
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Affiliation(s)
- A Maxwell Burroughs
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Margaret E Glasner
- the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, and
| | - Kevin P Barry
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Erika A Taylor
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - L Aravind
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,
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30
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Iradi-Serrano M, Tola-García L, Cortese MS, Ugalde U. The Early Asexual Development Regulator fluG Codes for a Putative Bifunctional Enzyme. Front Microbiol 2019; 10:778. [PMID: 31057506 PMCID: PMC6478659 DOI: 10.3389/fmicb.2019.00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
FluG is a long recognized early regulator of asexual development in Aspergillus nidulans. fluG null mutants show profuse aerial growth and no conidial production. Initial studies reported sequence homology of FluG with a prokaryotic type I glutamine synthetase, but catalytic activity has not been demonstrated. In this study, we conducted an in-depth analysis of the FluG sequence, which revealed a single polypeptide containing a putative N-terminal amidohydrolase region linked to a putative C-terminal γ-glutamyl ligase region. Each region corresponded, separately and completely, to respective single function bacterial enzymes. Separate expression of these regions confirmed that the C-terminal region was essential for asexual development. The N-terminal region alone did not support conidial development, but contributed to increased conidial production under high nutrient availability. Point mutations directed at respective key catalytic residues in each region demonstrated that they were essential for biological function. Moreover, the substitution of the N- and C-terminal regions with homologs from Lactobacillus paracasei and Pseudomonas aeruginosa, respectively, maintained functionality, albeit with altered characteristics. Taken together, the results lead us to conclude that FluG is a bifunctional enzyme that participates in an as yet unidentified metabolic or signaling pathway involving a γ-glutamylated intermediate that contributes to developmental fate.
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Affiliation(s)
| | | | | | - Unai Ugalde
- Microbial Biochemistry Laboratory, Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastian, Spain
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31
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Roh H, Han Y, Lee H, Kim S. A Topologically Distinct Modified Peptide with Multiple Bicyclic Core Motifs Expands the Diversity of Microviridin‐Like Peptides. Chembiochem 2019; 20:1051-1059. [DOI: 10.1002/cbic.201800678] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Heejin Roh
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Yeji Han
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Hyunbin Lee
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
| | - Seokhee Kim
- Department of ChemistrySeoul National University 1 Gwanak-ro Gwanak-gu Seoul 08826 South Korea
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32
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Complete Genome Sequence of Sinorhizobium Phage ΦM6, the First Terrestrial Phage of a Marine Phage Group. Microbiol Resour Announc 2018; 7:MRA01143-18. [PMID: 30533689 PMCID: PMC6256558 DOI: 10.1128/mra.01143-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/06/2018] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium phage ΦM6 infects the nitrogen-fixing rhizobial bacterium Sinorhizobium meliloti. ΦM6 most closely resembles marine phages, such as Puniceispirillum phage HMO-2011, rather than previously sequenced rhizobial phages. Sinorhizobium phage ΦM6 infects the nitrogen-fixing rhizobial bacterium Sinorhizobium meliloti. ΦM6 most closely resembles marine phages, such as Puniceispirillum phage HMO-2011, rather than previously sequenced rhizobial phages. The 68,176-bp genome is predicted to encode 121 open reading frames, only 10 of which have similarity to those of otherwise-unrelated Sinorhizobium phages.
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33
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Exploration of the Biosynthetic Potential of the Populus Microbiome. mSystems 2018; 3:mSystems00045-18. [PMID: 30320216 PMCID: PMC6172771 DOI: 10.1128/msystems.00045-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/17/2018] [Indexed: 01/13/2023] Open
Abstract
The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents. Natural products (NPs) isolated from bacteria have dramatically advanced human society, especially in medicine and agriculture. The rapidity and ease of genome sequencing have enabled bioinformatics-guided NP discovery and characterization. As a result, NP potential and diversity within a complex community, such as the microbiome of a plant, are rapidly expanding areas of scientific exploration. Here, we assess biosynthetic diversity in the Populus microbiome by analyzing both bacterial isolate genomes and metagenome samples. We utilize the fully sequenced genomes of isolates from the Populus root microbiome to characterize a subset of organisms for NP potential. The more than 3,400 individual gene clusters identified in 339 bacterial isolates, including 173 newly sequenced organisms, were diverse across NP types and distinct from known NP clusters. The ribosomally synthesized and posttranslationally modified peptides were both widespread and divergent from previously characterized molecules. Lactones and siderophores were prevalent in the genomes, suggesting a high level of communication and pressure to compete for resources. We then consider the overall bacterial diversity and NP variety of metagenome samples compared to the sequenced isolate collection and other plant microbiomes. The sequenced collection, curated to reflect the phylogenetic diversity of the Populus microbiome, also reflects the overall NP diversity trends seen in the metagenomic samples. In our study, only about 1% of all clusters from sequenced isolates were positively matched to a previously characterized gene cluster, suggesting a great opportunity for the discovery of novel NPs involved in communication and control in the Populus root microbiome. IMPORTANCE The plant root microbiome is one of the most diverse and abundant biological communities known. Plant-associated bacteria can have a profound effect on plant growth and development, and especially on protection from disease and environmental stress. These organisms are also known to be a rich source of antibiotic and antifungal drugs. In order to better understand the ways bacterial communities influence plant health, we evaluated the diversity and uniqueness of the natural product gene clusters in bacteria isolated from poplar trees. The complex molecule clusters are abundant, and the majority are unique, suggesting a great potential to discover new molecules that could not only affect plant health but also could have applications as antibiotic agents.
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34
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A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate. Nat Commun 2018; 9:1780. [PMID: 29725007 PMCID: PMC5934393 DOI: 10.1038/s41467-018-04154-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 02/23/2018] [Indexed: 11/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important family of natural products. Their biosynthesis follows a common scheme in which the leader peptide of a precursor peptide guides the modifications of a single core peptide. Here we describe biochemical studies of the processing of multiple core peptides within a precursor peptide, rare in RiPP biosynthesis. In a cyanobacterial microviridin pathway, an ATP-grasp ligase, AMdnC, installs up to two macrolactones on each of the three core peptides within AMdnA. The enzyme catalysis occurs in a distributive fashion and follows an unstrict N-to-C overall directionality, but a strict order in macrolactonizing each core peptide. Furthermore, AMdnC is catalytically versatile to process unnatural substrates carrying one to four core peptides, and kinetic studies provide insights into its catalytic properties. Collectively, our results reveal a distinct biosynthetic logic of RiPPs, opening up the possibility of modular production via synthetic biology approaches. Microviridins belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, the authors discover a microviridin-synthesizing enzyme in a cyanobacterium that modifies multiple core peptides from a single substrate in a distributive and unstrictly directional manner, an unusual biosynthetic logic for RiPPs.
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Markley JL, Morse TL, Rath NP, Wencewicz TA. Stream-lined synthesis of 3-hydroxy-β-lactams: Norrish-Yang type II photocyclizations of β-ketoformamides. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.04.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu. J Mol Biol 2018; 430:628-640. [DOI: 10.1016/j.jmb.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/30/2017] [Accepted: 01/04/2018] [Indexed: 11/20/2022]
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37
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Dorr BM, Fuerst DE. Enzymatic amidation for industrial applications. Curr Opin Chem Biol 2018; 43:127-133. [PMID: 29414531 DOI: 10.1016/j.cbpa.2018.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/21/2017] [Accepted: 01/11/2018] [Indexed: 11/18/2022]
Abstract
Nature has developed a robust toolbox for the formation of amide bonds, enabling a variety of disconnections applicable to small molecule synthesis. In spite of this, the exploitation of biocatalytic techniques for industrial synthesis remains limited to a few very important cases. This review discusses previously demonstrated techniques for the biocatalytic synthesis of amide bonds, reviews examples of industrial scale-up of these techniques, and identifies a number of limitations to the scalability within the current state of the art.
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Affiliation(s)
- Brent M Dorr
- Advanced Manufacturing Technologies, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, United States
| | - Douglas E Fuerst
- Advanced Manufacturing Technologies, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, United States.
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38
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Patrick GJ, Fang L, Schaefer J, Singh S, Bowman GR, Wencewicz TA. Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam. Biochemistry 2018; 57:117-135. [PMID: 29039929 PMCID: PMC5934995 DOI: 10.1021/acs.biochem.7b00838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tabtoxinine-β-lactam (TβL), also known as wildfire toxin, is a time- and ATP-dependent inhibitor of glutamine synthetase produced by plant pathogenic strains of Pseudomonas syringae. Here we demonstrate that recombinant glutamine synthetase from Escherichia coli phosphorylates the C3-hydroxyl group of the TβL 3-(S)-hydroxy-β-lactam (3-HβL) warhead. Phosphorylation of TβL generates a stable, noncovalent enzyme-ADP-inhibitor complex that resembles the glutamine synthetase tetrahedral transition state. The TβL β-lactam ring remains intact during enzyme inhibition, making TβL mechanistically distinct from traditional β-lactam antibiotics such as penicillin. Our findings could enable the design of new 3-HβL transition state inhibitors targeting enzymes in the ATP-dependent carboxylate-amine ligase superfamily with broad therapeutic potential in many disease areas.
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Affiliation(s)
- Garrett J. Patrick
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Luting Fang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
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The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers. J Mol Biol 2017; 430:611-627. [PMID: 29258816 PMCID: PMC6376114 DOI: 10.1016/j.jmb.2017.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 12/11/2022]
Abstract
Ancestral β-subunit (Anbu) is homologous to HslV and 20S proteasomes. Based on its phylogenetic distribution and sequence clustering, Anbu has been proposed as the “ancestral” form of proteasomes. Here, we report biochemical data, small-angle X-ray scattering results, negative-stain electron microscopy micrographs and a crystal structure of the Anbu particle from Yersinia bercovieri (YbAnbu). All data are consistent with YbAnbu forming defined 12–14 subunit multimers that differ in shape from both HslV and 20S proteasomes. The crystal structure reveals that YbAnbu subunits form tight dimers, held together in part by the Anbu specific C-terminal helices. These dimers (“protomers”) further assemble into a low-rise left-handed staircase. The lock-washer shape of YbAnbu is consistent with the presence of defined multimers, X-ray diffraction data in solution and negative-stain electron microscopy images. The presented structure suggests a possible evolutionary pathway from helical filaments to highly symmetric or pseudosymmetric multimer structures. YbAnbu subunits have the Ntn-hydrolase fold, a putative S1 pocket and conserved candidate catalytic residues Thr1, Asp17 and Lys32(33). Nevertheless, we did not detect any YbAnbu peptidase or amidase activity. However, we could document orthophosphate production from ATP catalyzed by the ATP-grasp protein encoded in the Y. bercovieri Anbu operon.
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40
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Fields RN, Roy H. Deciphering the tRNA-dependent lipid aminoacylation systems in bacteria: Novel components and structural advances. RNA Biol 2017; 15:480-491. [PMID: 28816600 PMCID: PMC6103681 DOI: 10.1080/15476286.2017.1356980] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
tRNA-dependent addition of amino acids to lipids on the outer surface of the bacterial membrane results in decreased effectiveness of antimicrobials such as cationic antimicrobial peptides (CAMPs) that target the membrane, and increased virulence of several pathogenic species. After a brief introduction to CAMPs and the various bacterial resistance mechanisms used to counteract these compounds, this review focuses on recent advances in tRNA-dependent pathways for lipid modification in bacteria. Phenotypes associated with amino acid lipid modifications and regulation of their expression will also be discussed.
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Affiliation(s)
- Rachel N Fields
- a Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando , Florida , United States of America
| | - Hervé Roy
- a Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando , Florida , United States of America
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41
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Lee H, Park Y, Kim S. Enzymatic Cross-Linking of Side Chains Generates a Modified Peptide with Four Hairpin-like Bicyclic Repeats. Biochemistry 2017; 56:4927-4930. [DOI: 10.1021/acs.biochem.7b00808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Youngseon Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System. Structure 2017; 25:834-845.e5. [PMID: 28479063 PMCID: PMC5666114 DOI: 10.1016/j.str.2017.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/23/2016] [Accepted: 04/14/2017] [Indexed: 11/22/2022]
Abstract
Proteasomes are self-compartmentalizing proteases that function at the core of the cellular protein degradation machinery in eukaryotes, archaea, and some bacteria. Although their evolutionary history is under debate, it is thought to be linked to that of the bacterial protease HslV and the hypothetical bacterial protease Anbu (ancestral beta subunit). Here, together with an extensive bioinformatic analysis, we present the first biophysical characterization of Anbu. Anbu forms a dodecameric complex with a unique architecture that was only accessible through the combination of X-ray crystallography and small-angle X-ray scattering. While forming continuous helices in crystals and electron microscopy preparations, refinement of sections from the crystal structure against the scattering data revealed a helical open-ring structure in solution, contrasting the ring-shaped structures of proteasome and HslV. Based on this primordial architecture and exhaustive sequence comparisons, we propose that Anbu represents an ancestral precursor at the origin of self-compartmentalization. The crystal structure of the bacterial proteasome homolog Anbu has been solved The dodecameric architecture reveals unique features compared with classical proteasomes Bioinformatic analysis places Anbu at the root of the proteasome family
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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45
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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46
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Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Nat Chem Biol 2016; 12:973-979. [PMID: 27669417 PMCID: PMC5117808 DOI: 10.1038/nchembio.2200] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/03/2016] [Indexed: 11/08/2022]
Abstract
Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides whose members target proteases with potent reversible inhibition. The product structure is constructed by three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here, we describe the detailed structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases, MdnC and MdnB, interact with a conserved α-helix of the precursor peptide using a novel precursor peptide recognition mechanism. The results provide insight into the unique protein/protein interactions key to the chemistry, suggest an origin of the natural combinatorial synthesis of microviridin peptides and provide a framework for future engineering efforts to generate designed compounds.
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47
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Chang PK, Scharfenstein LL, Ehrlich KC, Diana Di Mavungu J. The Aspergillus flavus fluP-associated metabolite promotes sclerotial production. Fungal Biol 2016; 120:1258-68. [PMID: 27647242 DOI: 10.1016/j.funbio.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 12/22/2022]
Abstract
Aspergillus flavus is able to synthesize a variety of polyketide-derived secondary metabolites including the hepatocarcinogen, aflatoxin B1. The fungus reproduces and disseminates predominantly by production of conidia. It also produces hardened mycelial aggregates called sclerotia that are used to cope with unfavourable growth environments. In the present study, we examined the role of A. flavus fluP, the backbone polyketide synthase gene of secondary metabolite gene cluster 41, on fungal development. The A. flavus CA14 fluP deletion mutant (AfΔfluP) grew and accumulated aflatoxin normally but produced a lower amount of sclerotia than the parental strain. This was also true for the Aspergillus parasiticus BN9 fluP deletion mutant (ApΔfluP). The A. flavus fluP gene was positively regulated by developmental regulators of VeA and VelB but not by the global regulator of secondary metabolism, LaeA. Overexpression of fluP in AfΔfluP (OEfluP) elevated its ability to produce sclerotia compared to that of the parental strain. Coculture of OEfluP with CA14, AfΔfluP, ApΔfluP, or an A. flavus pptA deletion mutant incapable of producing functional polyketide synthases also allowed increased sclerotial production of the respective strains at edges where colonies made contact. Acetone extracts of OEfluP but not of AfΔfluP exhibited the same effect in promoting sclerotial production of AfΔfluP. These results suggest that FluP polyketide synthase is involved in the synthesis of a diffusible metabolite that could serve as a signal molecule to regulate sclerotiogenesis.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, United States.
| | - Leslie L Scharfenstein
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, United States
| | - Kenneth C Ehrlich
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, United States
| | - José Diana Di Mavungu
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 460 Ottergemsesteenweg, 9000 Ghent, Belgium
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Imkamp F, Ziemski M, Weber-Ban E. Pupylation-dependent and -independent proteasomal degradation in mycobacteria. Biomol Concepts 2016; 6:285-301. [PMID: 26352358 DOI: 10.1515/bmc-2015-0017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/08/2015] [Indexed: 02/02/2023] Open
Abstract
Bacteria make use of compartmentalizing protease complexes, similar in architecture but not homologous to the eukaryotic proteasome, for the selective and processive removal of proteins. Mycobacteria as members of the actinobacteria harbor proteasomes in addition to the canonical bacterial degradation complexes. Mycobacterial proteasomal degradation, although not essential during normal growth, becomes critical for survival under particular environmental conditions, like, for example, during persistence of the pathogenic Mycobacterium tuberculosis in host macrophages or of environmental mycobacteria under starvation. Recruitment of protein substrates for proteasomal degradation is usually mediated by pupylation, the post-translational modification of lysine side chains with the prokaryotic ubiquitin-like protein Pup. This substrate recruitment strategy is functionally reminiscent of ubiquitination in eukaryotes, but is the result of convergent evolution, relying on chemically and structurally distinct enzymes. Pupylated substrates are recognized by the ATP-dependent proteasomal regulator Mpa that associates with the 20S proteasome core. A pupylation-independent proteasome degradation pathway has recently been discovered that is mediated by the ATP-independent bacterial proteasome activator Bpa (also referred to as PafE), and that appears to play a role under stress conditions. In this review, mechanistic principles of bacterial proteasomal degradation are discussed and compared with functionally related elements of the eukaryotic ubiquitin-proteasome system. Special attention is given to an understanding on the molecular level based on structural and biochemical analysis. Wherever available, discussion of in vivo studies is included to highlight the biological significance of this unusual bacterial degradation pathway.
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Abstract
Amides are widespread in biologically active compounds with a broad range of applications in biotechnology, agriculture and medicine. Therefore, as alternative to chemical synthesis the biocatalytic amide synthesis is a very interesting field of research. As usual, Nature can serve as guide in the quest for novel biocatalysts. Several mechanisms for carboxylate activation involving mainly acyl-adenylate, acyl-phosphate or acyl-enzyme intermediates have been discovered, but also completely different pathways to amides are found. In addition to ribosomes, selected enzymes of almost all main enzyme classes are able to synthesize amides. In this review we give an overview about amide synthesis in Nature, as well as biotechnological applications of these enzymes. Moreover, several examples of biocatalytic amide synthesis are given.
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