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Tiemblo-Martín M, Pistorio V, Saake P, Mahdi L, Campanero-Rhodes MA, Di Girolamo R, Di Carluccio C, Marchetti R, Molinaro A, Solís D, Zuccaro A, Silipo A. Structure and properties of the exopolysaccharide isolated from Flavobacterium sp. Root935. Carbohydr Polym 2024; 343:122433. [PMID: 39174078 DOI: 10.1016/j.carbpol.2024.122433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/24/2024]
Abstract
Flavobacterium strains exert a substantial influence on roots and leaves of plants. However, there is still limited understanding of how the specific interactions between Flavobacterium and their plant hosts are and how these bacteria thrive in this competitive environment. A crucial step in understanding Flavobacterium - plant interactions is to unravel the structure of bacterial envelope components and the molecular features that facilitate initial contact with the host environment. Here, we have revealed structure and properties of the exopolysaccharides (EPS) produced by Flavobacterium sp. Root935. Chemical analyses revealed a complex and interesting branched heptasaccharidic repeating unit, containing a variety of sugar moieties, including Rha, Fuc, GlcN, Fuc4N, Gal, Man and QuiN and an important and extended substitution pattern, including acetyl and lactyl groups. Additionally, conformational analysis using molecular dynamics simulation showed an extended hydrophobic interface and a distinctly elongated, left-handed helicoidal arrangement. Furthermore, properties of the saccharide chain, and likely the huge substitution pattern prevented interaction and recognition by host lectins and possessed a low immunogenic potential, highlighting a potential role of Flavobacterium sp. Root935 in plant-microbial crosstalk.
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Affiliation(s)
- Marta Tiemblo-Martín
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Valeria Pistorio
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Pia Saake
- University of Cologne Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, D-50674 Cologne, Germany
| | - Lisa Mahdi
- University of Cologne Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, D-50674 Cologne, Germany
| | - María Asunción Campanero-Rhodes
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Avda Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Rocco Di Girolamo
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Dolores Solís
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Avda Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Alga Zuccaro
- University of Cologne Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, D-50674 Cologne, Germany
| | - Alba Silipo
- Department of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.
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2
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Nieto-Fabregat F, Lenza MP, Marseglia A, Di Carluccio C, Molinaro A, Silipo A, Marchetti R. Computational toolbox for the analysis of protein-glycan interactions. Beilstein J Org Chem 2024; 20:2084-2107. [PMID: 39189002 PMCID: PMC11346309 DOI: 10.3762/bjoc.20.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.
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Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Maria Pia Lenza
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Angela Marseglia
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
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3
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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4
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Cunha VLS, O'Doherty GA, Lowary TL. Exploring a De Novo Route to Bradyrhizose: Synthesis and Isomeric Equilibrium of Bradyrhizose Diastereomers ≠. Chemistry 2024; 30:e202400886. [PMID: 38590211 PMCID: PMC11168859 DOI: 10.1002/chem.202400886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/10/2024]
Abstract
A de novo asymmetric strategy for the synthesis of d-bradyrhizose diastereomers from an achiral ketoenolester precursor is described. Key transformations used in the stereodivergent approach include two Noyori asymmetric reductions, an Achmatowicz rearrangement, diastereoselective alkene oxidations, and the first example of a palladium(0)-catalyzed glycosylation of a vinylogous pyranone. The isomeric composition of the bicyclic reducing sugars obtained was analyzed and their behaviour was compared to the natural product, revealing key stereocentres that impact the overall distribution.
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Affiliation(s)
- Vitor L S Cunha
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, 11529, Taiwan
| | - George A O'Doherty
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, Taipei, 11529, Taiwan
- Institute of Biochemical Sciences, Institute of Biological Chemistry, National Taiwan University, Taipei, 106, Taiwan
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5
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Velichko NS, Kokoulin MS, Dmitrenok PS, Grinev VS, Kuchur PD, Komissarov AS, Fedonenko YP. Lipopolysaccharides of Herbaspirillum species and their relevance for bacterium-host interactions. Int J Biol Macromol 2024; 261:129516. [PMID: 38278393 DOI: 10.1016/j.ijbiomac.2024.129516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/14/2023] [Accepted: 01/13/2024] [Indexed: 01/28/2024]
Abstract
The lipopolysaccharides of Herbaspirillum lusitanum P6-12T (HlP6-12T) and H. frisingense GSF30T (HfGSF30T) was isolated by phenol-water extraction from bacterial cells and was characterized using chemical analysis and SDS-PAGE. It was shown that these bacteria produce LPSs that differ in their physicochemical properties and macromolecular organization. In this paper, the lipid A structure of the HlP6-12T LPS, was characterized through chemical analyses and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. To prove the effect of the size of micelles on their bioavailability, we examined the activity of both LPSs toward the morphology of wheat seedlings. Analysis of the HlP6-12T and HfGSF30T genomes showed no significant differences between the operons that encode proteins involved in the biosynthesis of the lipids A and core oligosaccharides. The difference may be due to the composition of the O-antigen operon. HfGSF30T has two copies of the rfb operon, with the main one divided into two fragments. In contrast, the HlP6-12T genome contains only a single rfb-containing operon, and the other O-antigen operons are not comparable at all. The integrity of O-antigen-related genes may also affect LPS variability of. Specifically, we have observed a hairpin structure in the middle of the O-antigen glycosyltransferase gene, which led to the division of the gene into two fragments, resulting in incorrect protein synthesis and potential abnormalities in O-antigen production.
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Affiliation(s)
- Natalya S Velichko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia.
| | - Maxim S Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - Pavel S Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - Vyacheslav S Grinev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia; Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov 410012, Russia
| | - Polina D Kuchur
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, St. Petersburg 191002, Russia
| | - Aleksey S Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, St. Petersburg 191002, Russia
| | - Yulia P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia; G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
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6
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Letarov AV. Bacterial Virus Forcing of Bacterial O-Antigen Shields: Lessons from Coliphages. Int J Mol Sci 2023; 24:17390. [PMID: 38139217 PMCID: PMC10743462 DOI: 10.3390/ijms242417390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In most Gram-negative bacteria, outer membrane (OM) lipopolysaccharide (LPS) molecules carry long polysaccharide chains known as the O antigens or O polysaccharides (OPS). The OPS structure varies highly from strain to strain, with more than 188 O serotypes described in E. coli. Although many bacteriophages recognize OPS as their primary receptors, these molecules can also screen OM proteins and other OM surface receptors from direct interaction with phage receptor-binding proteins (RBP). In this review, I analyze the body of evidence indicating that most of the E. coli OPS types robustly shield cells completely, preventing phage access to the OM surface. This shield not only blocks virulent phages but also restricts the acquisition of prophages. The available data suggest that OPS-mediated OM shielding is not merely one of many mechanisms of bacterial resistance to phages. Rather, it is an omnipresent factor significantly affecting the ecology, phage-host co-evolution and other related processes in E. coli and probably in many other species of Gram-negative bacteria. The phages, in turn, evolved multiple mechanisms to break through the OPS layer. These mechanisms rely on the phage RBPs recognizing the OPS or on using alternative receptors exposed above the OPS layer. The data allow one to forward the interpretation that, regardless of the type of receptors used, primary receptor recognition is always followed by the generation of a mechanical force driving the phage tail through the OPS layer. This force may be created by molecular motors of enzymatically active tail spikes or by virion structural re-arrangements at the moment of infection.
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Affiliation(s)
- Andrey V Letarov
- Winogradsky Institute of Micrbiology, Research Center Fundamentals of Biotechnology RAS, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow 117312, Russia
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7
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Di Lorenzo F, Nicolardi S, Marchetti R, Vanacore A, Gallucci N, Duda K, Nieto Fabregat F, Nguyen HNA, Gully D, Saenz J, Giraud E, Paduano L, Molinaro A, D’Errico G, Silipo A. Expanding Knowledge of Methylotrophic Capacity: Structure and Properties of the Rough-Type Lipopolysaccharide from Methylobacterium extorquens and Its Role on Membrane Resistance to Methanol. JACS AU 2023; 3:929-942. [PMID: 37006758 PMCID: PMC10052234 DOI: 10.1021/jacsau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
The ability of Methylobacterium extorquens to grow on methanol as the sole carbon and energy source has been the object of intense research activity. Unquestionably, the bacterial cell envelope serves as a defensive barrier against such an environmental stressor, with a decisive role played by the membrane lipidome, which is crucial for stress resistance. However, the chemistry and the function of the main constituent of the M. extorquens outer membrane, the lipopolysaccharide (LPS), is still undefined. Here, we show that M. extorquens produces a rough-type LPS with an uncommon, non-phosphorylated, and extensively O-methylated core oligosaccharide, densely substituted with negatively charged residues in the inner region, including novel monosaccharide derivatives such as O-methylated Kdo/Ko units. Lipid A is composed of a non-phosphorylated trisaccharide backbone with a distinctive, low acylation pattern; indeed, the sugar skeleton was decorated with three acyl moieties and a secondary very long chain fatty acid, in turn substituted by a 3-O-acetyl-butyrate residue. Spectroscopic, conformational, and biophysical analyses on M. extorquens LPS highlighted how structural and tridimensional features impact the molecular organization of the outer membrane. Furthermore, these chemical features also impacted and improved membrane resistance in the presence of methanol, thus regulating membrane ordering and dynamics.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Roberta Marchetti
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Adele Vanacore
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Noemi Gallucci
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Katarzyna Duda
- Research
Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Ferran Nieto Fabregat
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Ha Ngoc Anh Nguyen
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Djamel Gully
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - James Saenz
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Eric Giraud
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Luigi Paduano
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Gerardino D’Errico
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Alba Silipo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
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8
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Vanacore A, Forgione MC, Cavasso D, Nguyen HNA, Molinaro A, Saenz JP, D'Errico G, Paduano L, Marchetti R, Silipo A. Role of EPS in mitigation of plant abiotic stress: The case of Methylobacterium extorquens PA1. Carbohydr Polym 2022; 295:119863. [DOI: 10.1016/j.carbpol.2022.119863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022]
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9
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Singh A, Bansal K, Kumar S, Patil PB. Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane. Appl Environ Microbiol 2022; 88:e0055022. [PMID: 35916503 PMCID: PMC9397109 DOI: 10.1128/aem.00550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.
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Affiliation(s)
- Anu Singh
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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10
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Li S, Chen F, Li Y, Wang L, Li H, Gu G, Li E. Rhamnose-Containing Compounds: Biosynthesis and Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165315. [PMID: 36014553 PMCID: PMC9415975 DOI: 10.3390/molecules27165315] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Rhamnose-associated molecules are attracting attention because they are present in bacteria but not mammals, making them potentially useful as antibacterial agents. Additionally, they are also valuable for tumor immunotherapy. Thus, studies on the functions and biosynthetic pathways of rhamnose-containing compounds are in progress. In this paper, studies on the biosynthetic pathways of three rhamnose donors, i.e., deoxythymidinediphosphate-L-rhamnose (dTDP-Rha), uridine diphosphate-rhamnose (UDP-Rha), and guanosine diphosphate rhamnose (GDP-Rha), are firstly reviewed, together with the functions and crystal structures of those associated enzymes. Among them, dTDP-Rha is the most common rhamnose donor, and four enzymes, including glucose-1-phosphate thymidylyltransferase RmlA, dTDP-Glc-4,6-dehydratase RmlB, dTDP-4-keto-6-deoxy-Glc-3,5-epimerase RmlC, and dTDP-4-keto-Rha reductase RmlD, are involved in its biosynthesis. Secondly, several known rhamnosyltransferases from Geobacillus stearothermophilus, Saccharopolyspora spinosa, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Streptococcus pneumoniae are discussed. In these studies, however, the functions of rhamnosyltransferases were verified by employing gene knockout and radiolabeled substrates, which were almost impossible to obtain and characterize the products of enzymatic reactions. Finally, the application of rhamnose-containing compounds in disease treatments is briefly described.
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Affiliation(s)
- Siqiang Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Fujia Chen
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
| | - Lizhen Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, China
| | - Hongyan Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, 72 Binhai Road, Qingdao 266237, China
- Correspondence: (G.G.); (E.L.)
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian 463000, China
- Institute of Agricultural Products Fermentation Engineering and Application, Huanghuai University, Zhumadian 463000, China
- Correspondence: (G.G.); (E.L.)
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