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Daitch AK, Smith EL, Goley ED. OpgH is an essential regulator of Caulobacter morphology. mBio 2024; 15:e0144324. [PMID: 39145657 PMCID: PMC11389396 DOI: 10.1128/mbio.01443-24] [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: 05/15/2024] [Accepted: 06/20/2024] [Indexed: 08/16/2024] Open
Abstract
Bacterial growth and division rely on intricate regulation of morphogenetic complexes to remodel the cell envelope without compromising envelope integrity. Significant progress has been made in recent years towards understanding the regulation of cell wall metabolic enzymes. However, other cell envelope components play a role in morphogenesis as well. A primary factor required to protect envelope integrity in low osmolarity environments is OpgH, the synthase of osmoregulated periplasmic glucans (OPGs). Here, we demonstrate that OpgH is essential in the α-proteobacterium Caulobacter crescentus. Unexpectedly, depletion of OpgH or attempted complementation with a catalytically dead OpgH variant results in striking asymmetric bulging and cell lysis. These shape defects are accompanied by reduced cell wall synthesis and mislocalization of morphogenetic complexes. Interestingly, overactivation of the CenKR two-component system that has been implicated in cell envelope stress homeostasis in α-proteobacteria phenocopies the morphogenetic defects associated with OpgH depletion. Each of these perturbations leads to an increase in the levels of the elongasome protein, MreB, and decreases in the levels of divisome proteins FtsZ and MipZ as well as OpgH, itself. Constitutive production of OpgH during CenKR overactivation prevents cell bulging, but cells still exhibit morphogenetic defects. We propose that OPG depletion activates CenKR, leading to changes in the expression of cell envelope-related genes, but that OPGs also exert CenKR-independent effects on morphogenesis. Our data establish a surprising function for an OpgH homolog in morphogenesis and reveal an essential role of OpgH in maintaining cell morphology in Caulobacter.IMPORTANCEBacteria must synthesize and fortify the cell envelope in a tightly regulated manner to orchestrate growth and adaptation. Osmoregulated periplasmic glucans (OPGs) are important, but poorly understood, constituents of Gram-negative cell envelopes that contribute to envelope integrity and protect against osmotic stress. Here, we determined that the OPG synthase OpgH plays a surprising, essential role in morphogenesis in Caulobacter crescentus. Loss of OpgH causes asymmetric cell bulging and lysis via misregulation of the localization and activity of morphogenetic complexes. Overactivation of the CenKR two-component system involved in envelope homeostasis phenocopies OpgH depletion, suggesting that depletion of OpgH activates CenKR. Because cell envelope integrity is critical for bacterial survival, understanding how OpgH activity contributes to morphogenesis and maintenance of envelope integrity could aid in the development of antibiotic therapies.
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Affiliation(s)
- Allison K Daitch
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Wang Y, Zhang P, Luo Z, Huang C. Insights into the role of glycosyltransferase in the targeted treatment of gastric cancer. Biomed Pharmacother 2024; 178:117194. [PMID: 39137647 DOI: 10.1016/j.biopha.2024.117194] [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: 05/20/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024] Open
Abstract
Gastric cancer is a remarkably heterogeneous tumor. Despite some advances in the diagnosis and treatment of gastric cancer in recent years, the precise treatment and curative outcomes remain unsatisfactory. Poor prognosis continues to pose a major challenge in gastric cancer. Therefore, it is imperative to identify effective targets to improve the treatment and prognosis of gastric cancer patients. It should be noted that glycosylation, a novel form of posttranslational modification, is a process capable of regulating protein function and influencing cellular activities. Currently, numerous studies have shown that glycosylation plays vital roles in the occurrence and progression of gastric cancer. As crucial enzymes that regulate glycan synthesis in glycosylation processes, glycosyltransferases are potential targets for treating GC. Hence, investigating the regulation of glycosyltransferases and the expression of associated proteins in gastric cancer cells is highly important. In this review, the related glycosyltransferases and their related signaling pathways in gastric cancer, as well as the existing inhibitors of glycosyltransferases, provide more possibilities for targeted therapies for gastric cancer.
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Affiliation(s)
- Yueling Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi 214028, China; Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Pengshan Zhang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zai Luo
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Chen Huang
- Wuxi School of Medicine, Jiangnan University, Wuxi 214028, China; Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China.
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3
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Kortsinoglou AM, Wood MJ, Myridakis AI, Andrikopoulos M, Roussis A, Eastwood D, Butt T, Kouvelis VN. Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity. G3 (BETHESDA, MD.) 2024:jkae190. [PMID: 39210673 DOI: 10.1093/g3journal/jkae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Entomopathogenic fungi belonging to the Order Hypocreales are renowned for their ability to infect and kill insect hosts, while their endophytic mode of life and the beneficial rhizosphere effects on plant hosts have only been recently recognized. Understanding the molecular mechanisms underlying their different lifestyles could optimize their potential as both biocontrol and biofertilizer agents, as well as the wider appreciation of niche plasticity in fungal ecology. This study describes the comprehensive whole genome sequencing and analysis of one of the most effective entomopathogenic and endophytic EPF strains, Metarhizium brunneum V275 (commercially known as Lalguard Met52), achieved through Nanopore and Illumina reads. Comparative genomics for exploring intraspecies variability and analyses of key gene sets were conducted with a second effective EPF strain, M. brunneum ARSEF 4556. The search for strain- or species-specific genes was extended to M. brunneum strain ARSEF 3297 and other species of genus Metarhizium, to identify molecular mechanisms and putative key genome adaptations associated with mode of life differences. Genome size differed significantly, with M. brunneum V275 having the largest genome amongst M. brunneum strains sequenced to date. Genome analyses revealed an abundance of plant-degrading enzymes, plant colonization-associated genes, and intriguing intraspecies variations regarding their predicted secondary metabolic compounds and the number and localization of Transposable Elements. The potential significance of the differences found between closely related endophytic and entomopathogenic fungi, regarding plant growth-promoting and entomopathogenic abilities, are discussed, enhancing our understanding of their diverse functionalities and putative applications in agriculture and ecology.
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Affiliation(s)
- Alexandra M Kortsinoglou
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Martyn J Wood
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Singleton Park, SA2 8PP, Swansea, UK
| | - Antonis I Myridakis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Marios Andrikopoulos
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Andreas Roussis
- Section of Botany, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Dan Eastwood
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Singleton Park, SA2 8PP, Swansea, UK
| | - Tariq Butt
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Singleton Park, SA2 8PP, Swansea, UK
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15771 Athens, Greece
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Teppa RE, Galuska SP, Harduin-Lepers A. Molecular dynamics simulations shed light into the donor substrate specificity of vertebrate poly-alpha-2,8-sialyltransferases ST8Sia IV. Biochim Biophys Acta Gen Subj 2024; 1868:130647. [PMID: 38801837 DOI: 10.1016/j.bbagen.2024.130647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Sialic acids are essential monosaccharides influencing several biological processes and disease states. The sialyltransferases catalyze the transfer of Sia residues to glycoconjugates playing critical roles in cellular recognition and signaling. Despite their importance, the molecular mechanisms underlying their substrate specificity, especially between different organisms, remain poorly understood. Recently, the human ST8Sia IV, a key enzyme in the synthesis of polysialic acids, was found to accept only CMP-Neu5Ac as a sugar-donor, whereas the whitefish Coregonus maraena enzyme showed a wider donor substrate specificity, accepting CMP-Neu5Ac, CMP-Neu5Gc, and CMP-Kdn. However, what causes these differences in donor substrate specificity is unknown. METHODS Computational approaches were used to investigate the structural and biochemical determinants of the donor substrate specificity in ST8Sia IV. Accurate structural models of the human and fish ST8Sia IV catalytic domains and their complexes with three sialic acid donors (CMP-Neu5Ac, CMP-Neu5Gc, and CMP-Kdn) were generated. Subsequently, molecular dynamics simulations were conducted to analyze the stability and interactions within these complexes and identify differences in complex stability and substrate binding sites between the two ST8Sia IV. RESULTS Our MD simulations revealed that the human enzyme effectively stabilizes CMP-Neu5Ac, whereas CMP-Neu5Gc and CMP-Kdn are unstable and explore different conformations. In contrast, the fish ST8Sia IV stabilizes all three donor substrates. Based on these data, we identified the key interacting residues for the different Sias parts of the substrate donors. GENERAL SIGNIFICANCE This work advances our knowledge of the enzymatic mechanisms governing sialic acid transfer, shedding light on the evolutionary adaptations of sialyltransferases.
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Affiliation(s)
- Roxana Elin Teppa
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France.
| | - Sebastian Peter Galuska
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Anne Harduin-Lepers
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France; Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Faculté des sciences et Technologies, Univ. Lille, 59655 Villeneuve d'Ascq, France.
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5
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Putkaradze N, Dato L, Kırtel O, Hansen J, Welner DH. Enzymatic glycosylation of aloesone performed by plant UDP-dependent glycosyltransferases. Glycobiology 2024; 34:cwae050. [PMID: 38995933 PMCID: PMC11273223 DOI: 10.1093/glycob/cwae050] [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: 02/02/2024] [Revised: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 07/14/2024] Open
Abstract
Aloesone is a bioactive natural product and biosynthetic precursor of rare glucosides found in rhubarb and some aloe plants including Aloe vera. This study aimed to investigate biocatalytic aloesone glycosylation and more than 400 uridine diphosphate-dependent glycosyltransferase (UGT) candidates, including multifunctional and promiscuous enzymes from a variety of plant species were assayed. As a result, 137 selective aloesone UGTs were discovered, including four from the natural producer rhubarb. Rhubarb UGT72B49 was further studied and its catalytic constants (kcat = 0.00092 ± 0.00003 s-1, KM = 30 ± 2.5 μM) as well as temperature and pH optima (50 °C and pH 7, respectively) were determined. We further aimed to find an efficient aloesone glycosylating enzyme with potential application for biocatalytic production of the glucoside. We discovered UGT71C1 from Arabidopsis thaliana as an efficient aloesone UGT showing a 167-fold higher catalytic efficiency compared to that of UGT72B49. Interestingly, sequence analysis of all the 137 newly identified aloesone UGTs showed that they belong to different phylogenetic groups, with the highest representation in groups B, D, E, F and L. Finally, our study indicates that aloesone C-glycosylation is highly specific and rare, since it was not possible to achieve in an efficient manner with any of the 422 UGTs assayed, including multifunctional GTs and 28 known C-UGTs.
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Affiliation(s)
- Natalia Putkaradze
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads 220, Lyngby DK-2800, Denmark
| | - Laura Dato
- River Stone Biotech ISG, Fruebjergvej 3, Copenhagen DK-2100, Denmark
| | - Onur Kırtel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads 220, Lyngby DK-2800, Denmark
| | - Jørgen Hansen
- River Stone Biotech ISG, Fruebjergvej 3, Copenhagen DK-2100, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads 220, Lyngby DK-2800, Denmark
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Zhong C, Nidetzky B. Bottom-Up Synthesized Glucan Materials: Opportunities from Applied Biocatalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400436. [PMID: 38514194 DOI: 10.1002/adma.202400436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Linear d-glucans are natural polysaccharides of simple chemical structure. They are comprised of d-glucosyl units linked by a single type of glycosidic bond. Noncovalent interactions within, and between, the d-glucan chains give rise to a broad variety of macromolecular nanostructures that can assemble into crystalline-organized materials of tunable morphology. Structure design and functionalization of d-glucans for diverse material applications largely relies on top-down processing and chemical derivatization of naturally derived starting materials. The top-down approach encounters critical limitations in efficiency, selectivity, and flexibility. Bottom-up approaches of d-glucan synthesis offer different, and often more precise, ways of polymer structure control and provide means of functional diversification widely inaccessible to top-down routes of polysaccharide material processing. Here the natural and engineered enzymes (glycosyltransferases, glycoside hydrolases and phosphorylases, glycosynthases) for d-glucan polymerization are described and the use of applied biocatalysis for the bottom-up assembly of specific d-glucan structures is shown. Advanced material applications of the resulting polymeric products are further shown and their important role in the development of sustainable macromolecular materials in a bio-based circular economy is discussed.
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Affiliation(s)
- Chao Zhong
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
- Austrian Centre of Industrial Biotechnology (acib), Krenngasse 37, Graz, 8010, Austria
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7
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 2024; 9:e0008124. [PMID: 38837404 PMCID: PMC11332178 DOI: 10.1128/msphere.00081-24] [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: 02/01/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides difficile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter the viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and the predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight flexibility in metabolism that may influence pathogenesis. IMPORTANCE Clostridioides difficile results in upward of 250,000 infections and 12,000 deaths annually in the United States. Community-acquired infections continue to rise, and recurrent disease is common, emphasizing a vital need to understand C. difficile pathogenesis. C. difficile undoubtedly interacts with colonic mucus, but the extent to which the pathogen can independently respond to and take advantage of this niche has not been explored extensively. Moreover, the metabolic complexity of C. difficile remains poorly understood but likely impacts its capacity to grow and persist in the host. Here, we demonstrate that C. difficile uses native colonic mucus for growth, indicating C. difficile possesses mechanisms to exploit the mucosal niche. Furthermore, mucus induces metabolic shifts and biofilm formation in C. difficile, which has potential ramifications for intestinal colonization. Overall, our work is crucial to better understand the dynamics of C. difficile-mucus interactions in the context of the human gut.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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Zhu X, Wen S, Gul H, Xu P, Yang Y, Liao X, Ye Y, Xu Z, Zhang X, Wu L. Exploring regulatory network of icariin synthesis in Herba Epimedii through integrated omics analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1409601. [PMID: 38933461 PMCID: PMC11203402 DOI: 10.3389/fpls.2024.1409601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Herba Epimedii's leaves are highly valued in traditional Chinese medicine for their substantial concentration of flavonoids, which play a crucial role in manifesting the plant's therapeutic properties. This study investigated the metabolomic, transcriptomic and proteomic profiles of leaves from two Herba Epimedii cultivars, Epipremnum sagittatum (J) and Epipremnum pubescens (R), at three different developmental stages. Metabolite identification and analysis revealed a total of 1,412 and 1,421 metabolites with known structures were found. Flavonoids made up of 33%, including 10 significant accumulated icariin analogues. Transcriptomic analysis unveiled totally 41,644 differentially expressed genes (DEGs) containing five encoded genes participated in icariin biosynthesis pathways. Totally, 9,745 differentially expressed proteins (DEPs) were found, including Cluster-47248.2.p1 (UDP-glucuronosy/UDP-glucosyltransferase), Cluster-30441.2.p1 (O-glucosyltransferase), and Cluster-28344.9.p1 (anthocyanidin 3-O-glucoside 2 "-O-glucosyltransferase-like) through proteomics analysis which are involved to icariin biosynthesis. Protein-protein interaction (PPI) assay exhibited, totally 12 proteins showing a strong relationship of false discovery rate (FDR) <0.05 with these three proteins containing 2 leucine-rich repeat receptor kinase-like protein SRF7, and 5 methyl jasmonate esterase 1. Multi-omics connection networks uncovered 237 DEGs and 72 DEPs exhibited significant associations with the 10 icariin analogues. Overall, our integrated omics approach provides comprehensive insights into the regulatory network underlying icariin synthesis in Herba Epimedii, offering valuable resources for further research and development in medicinal plant cultivation and pharmaceutical applications.
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Affiliation(s)
- Xuedong Zhu
- Fuling Academy of Southwest University/Southeast Chongqing Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hameed Gul
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Pan Xu
- Fuling Academy of Southwest University/Southeast Chongqing Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yang Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ximei Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Yunling Ye
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Germplasm Innovation of Upper Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Zijian Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Germplasm Innovation of Upper Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Xiaofang Zhang
- Fuling Academy of Southwest University/Southeast Chongqing Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lin Wu
- Fuling Academy of Southwest University/Southeast Chongqing Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Germplasm Innovation of Upper Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
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9
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Pei C, Peng X, Wu Y, Jiao R, Li T, Jiao S, Zhou L, Li J, Du Y, Qian EW. Characterization and application of active human α2,6-sialyltransferases ST6GalNAc V and ST6GalNAc VI recombined in Escherichia coli. Enzyme Microb Technol 2024; 177:110426. [PMID: 38503081 DOI: 10.1016/j.enzmictec.2024.110426] [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: 01/09/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Eukaryotic sialyltransferases play key roles in many physiological and pathological events. The expression of active human recombinant sialyltransferases in bacteria is still challenging. In the current study, the genes encoding human N-acetylgalactosaminide α2,6-sialyltransferase V (hST6GalNAc V) and N-acetylgalactosaminide α2,6-sialyltransferase VI (hST6GalNAc VI) lacking the N-terminal transmembrane domains were cloned into the expression vectors, pET-32a and pET-22b, respectively. Soluble and active forms of recombinant hST6GalNAc V and hST6GalNAc VI when coexpressed with the chaperone plasmid pGro7 were successfully achieved in Escherichia coli. Further, lactose (Lac), Lacto-N-triose II (LNT II), lacto-N-tetraose (LNT), and sialyllacto-N-tetraose a (LSTa) were used as acceptor substrates to investigate their activities and substrate specificities. Unexpectedly, both can transfer sialic acid onto all those substrates. Compared with hST6GalNAc V expressed in the mammalian cells, the recombinant two α2,6-sialyltransferases in bacteria displayed flexible substrate specificities and lower enzymatic efficiency. In addition, an important human milk oligosaccharide disialyllacto-N-tetraose (DSLNT) can be synthesized by both human α2,6-sialyltransferases expressed in E. coli using LSTa as an acceptor substrate. To the best of our knowledge, these two active human α2,6-sialyltransferases enzymes were expressed in bacteria for the first time. They showed a high potential to be applied in biotechnology and investigating the molecular mechanisms of biological and pathological interactions related to sialylated glycoconjugates.
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Affiliation(s)
- Caixia Pei
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Nakacho 2-24-16, Koganei, Tokyo 184-8588, Japan; State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
| | - Xinlv Peng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runmiao Jiao
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Nakacho 2-24-16, Koganei, Tokyo 184-8588, Japan; State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Siming Jiao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing 100190, China
| | - Lei Zhou
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing 100190, China.
| | - Eika W Qian
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Nakacho 2-24-16, Koganei, Tokyo 184-8588, Japan.
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10
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Zhang X, Wang W, Wang Y, Cao Z, Yang H, Li S. Metagenomic and metabolomic analyses reveal differences in rumen microbiota between grass- and grain-fed Sanhe heifers. Front Microbiol 2024; 15:1336278. [PMID: 38803375 PMCID: PMC11128563 DOI: 10.3389/fmicb.2024.1336278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers. Methods Metagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers (n = 20) with similar body weights and ages from grass-fed and grain-fed systems. Results The grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system. Conclusion These results could help manipulate and regulate feed efficiency in Sanhe cattle.
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Affiliation(s)
| | | | | | | | | | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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11
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Li Z, Tu M, Qin F, Shui G, Xu D, Zang X. Identification of Indicator Genes for Agar Accumulation in Gracilariopsis lemaneiformis (Rhodophyta). Int J Mol Sci 2024; 25:4606. [PMID: 38731824 PMCID: PMC11083068 DOI: 10.3390/ijms25094606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
Agar, as a seaweed polysaccharide mainly extracted from Gracilariopsis lemaneiformis, has been commercially applied in multiple fields. To investigate factors indicating the agar accumulation in G. lemaneiformis, the agar content, soluble polysaccharides content, and expression level of 11 genes involved in the agar biosynthesis were analysed under 4 treatments, namely salinity, temperature, and nitrogen and phosphorus concentrations. The salinity exerted the greatest impact on the agar content. Both high (40‱) and low (10‱, 20‱) salinity promoted agar accumulation in G. lemaneiformis by 4.06%, 2.59%, and 3.00%, respectively. The content of agar as a colloidal polysaccharide was more stable than the soluble polysaccharide content under the treatments. No significant correlation was noted between the two polysaccharides, and between the change in the agar content and the relative growth rate of the algae. The expression of all 11 genes was affected by the 4 treatments. Furthermore, in the cultivar 981 with high agar content (21.30 ± 0.95%) compared to that (16.23 ± 1.59%) of the wild diploid, the transcriptional level of 9 genes related to agar biosynthesis was upregulated. Comprehensive analysis of the correlation between agar accumulation and transcriptional level of genes related to agar biosynthesis in different cultivation conditions and different species of G. lemaneiformis, the change in the relative expression level of glucose-6-phosphate isomerase II (gpiII), mannose-6-phosphate isomerase (mpi), mannose-1-phosphate guanylyltransferase (mpg), and galactosyltransferase II (gatII) genes was highly correlated with the relative agar accumulation. This study lays a basis for selecting high-yield agar strains, as well as for targeted breeding, by using gene editing tools in the future.
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Affiliation(s)
| | | | | | | | - Di Xu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Z.L.); (M.T.); (F.Q.); (G.S.)
| | - Xiaonan Zang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Z.L.); (M.T.); (F.Q.); (G.S.)
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12
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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (BETHESDA, MD.) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [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: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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13
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Li G, Wang W, Guo H, Yi S, Wang F, Huang S, Hu N, Xu Q, Zang Y, Han B, Yin X. Mutability landscape guided engineering of a promiscuous microbial glycosyltransferase for regioselective synthesis of salidroside and icariside D2. Int J Biol Macromol 2024; 263:130229. [PMID: 38378110 DOI: 10.1016/j.ijbiomac.2024.130229] [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: 10/22/2023] [Revised: 01/28/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Microbial glycosyltransferases efficiently synthesize glucosides and have garnered increasing interest. However, limited regioselectivity has impeded their broad application, particularly in the pharmaceutical industry. In this study, the UDP-glycosyltransferase YjiC from Bacillus licheniformis (BlYjiC) was engineered to achieve the bidirectional regioselective glycosylation of tyrosol and its derivatives. Initially, site-directed saturation mutagenesis was performed on two newly identified substrate-binding cavities in the acceptor pocket of BlYjiC to provide a comprehensive blueprint of the interplay between mutations and function (mutability landscape). Iterative saturation mutagenesis was performed, guided by the mutability landscape. Two highly regioselective mutants M6 (M112L/I325Y/L70R/Q136E/I67E/M77R) and M2' (M112D/I62L) were generated, exhibiting >99 % regioselectivity toward the alcoholic and phenolic hydroxyl of tyrosol, respectively, compared with the wild-type (product mixture: 51:49 %). Both mutants exhibited excellent regioselectivity toward several dihydroxy phenolic substrates, offering valuable biocatalysts for the regioselective synthesis of glucosides. Their application was confirmed in a short synthesis of salidroside (3.6 g/L) and icariside D2 (2.4 g/L), which exhibited near-perfect regioselectivity. This study provides valuable insights into future protein engineering of similar enzymes and opens new avenues for their practical applications.
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Affiliation(s)
- Guosi Li
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Wei Wang
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Heng Guo
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519080, China
| | - Shanyong Yi
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Fang Wang
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Shiping Huang
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Nan Hu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Qilin Xu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Yongjun Zang
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China
| | - Bangxing Han
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, West Anhui University, Lu'an 237012, Anhui, China; Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Traditional Chinese Medicine Institute of Anhui Dabie Mountain, Lu'an 237012, Anhui, China
| | - Xinjian Yin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519080, China.
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14
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Tvaroška I. Glycosylation Modulates the Structure and Functions of Collagen: A Review. Molecules 2024; 29:1417. [PMID: 38611696 PMCID: PMC11012932 DOI: 10.3390/molecules29071417] [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: 02/26/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Collagens are fundamental constituents of the extracellular matrix and are the most abundant proteins in mammals. Collagens belong to the family of fibrous or fiber-forming proteins that self-assemble into fibrils that define their mechanical properties and biological functions. Up to now, 28 members of the collagen superfamily have been recognized. Collagen biosynthesis occurs in the endoplasmic reticulum, where specific post-translational modification-glycosylation-is also carried out. The glycosylation of collagens is very specific and adds β-d-galactopyranose and β-d-Glcp-(1→2)-d-Galp disaccharide through β-O-linkage to hydroxylysine. Several glycosyltransferases, namely COLGALT1, COLGALT2, LH3, and PGGHG glucosidase, were associated the with glycosylation of collagens, and recently, the crystal structure of LH3 has been solved. Although not fully understood, it is clear that the glycosylation of collagens influences collagen secretion and the alignment of collagen fibrils. A growing body of evidence also associates the glycosylation of collagen with its functions and various human diseases. Recent progress in understanding collagen glycosylation allows for the exploitation of its therapeutic potential and the discovery of new agents. This review will discuss the relevant contributions to understanding the glycosylation of collagens. Then, glycosyltransferases involved in collagen glycosylation, their structure, and catalytic mechanism will be surveyed. Furthermore, the involvement of glycosylation in collagen functions and collagen glycosylation-related diseases will be discussed.
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Affiliation(s)
- Igor Tvaroška
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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15
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Katz M, Diskin R. The underlying mechanisms of arenaviral entry through matriglycan. Front Mol Biosci 2024; 11:1371551. [PMID: 38516183 PMCID: PMC10955480 DOI: 10.3389/fmolb.2024.1371551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
Matriglycan, a recently characterized linear polysaccharide, is composed of alternating xylose and glucuronic acid subunits bound to the ubiquitously expressed protein α-dystroglycan (α-DG). Pathogenic arenaviruses, like the Lassa virus (LASV), hijack this long linear polysaccharide to gain cellular entry. Until recently, it was unclear through what mechanisms LASV engages its matriglycan receptor to initiate infection. Additionally, how matriglycan is synthesized onto α-DG by the Golgi-resident glycosyltransferase LARGE1 remained enigmatic. Recent structural data for LARGE1 and for the LASV spike complex informs us about the synthesis of matriglycan as well as its usage as an entry receptor by arenaviruses. In this review, we discuss structural insights into the system of matriglycan generation and eventual recognition by pathogenic viruses. We also highlight the unique usage of matriglycan as a high-affinity host receptor compared with other polysaccharides that decorate cells.
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Affiliation(s)
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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16
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Yang L, Yang M, Deng Z, Hou X, Zheng X, Ping Q, Rao Y, Shi J, Zhang Y. Selective synthesis of rebaudioside M2 through structure-guided engineering of glycosyltransferase UGT94D1. Front Bioeng Biotechnol 2024; 12:1334427. [PMID: 38375456 PMCID: PMC10875103 DOI: 10.3389/fbioe.2024.1334427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/12/2024] [Indexed: 02/21/2024] Open
Abstract
Rebaudioside M2 (Reb M2), a novel steviol glycoside derivative, has limited industrial applications due to its low synthetic yield and selectivity. Herein, we identify UGT94D1 as a selective glycosyltransferase for rebaudioside D (Reb D), leading to the production of a mono β-1,6-glycosylated derivative, Reb M2. A variant UGT94D1-F119I/D188P was developed through protein engineering. This mutant exhibited a 6.33-fold improvement in catalytic efficiency, and produced Reb M2 with 92% yield. Moreover, molecular dynamics simulations demonstrated that UGT94D1-F119I/D188P exhibited a shorter distance between the nucleophilic oxygen (OH6) of the substrate Reb D and uridine diphosphate glucose, along with an increased Ophosphate-C1-Oacceptor angle, thus improving the catalytic activity of the enzyme. Therefore, this study provides an efficient method for the selective synthesis of Reb M2 and paves the way for its applications in various fields.
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Affiliation(s)
- Lifeng Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, China
| | - Mengliang Yang
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiwei Deng
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaodong Hou
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiangting Zheng
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Qian Ping
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yijian Rao
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jinsong Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yan Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
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17
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578425. [PMID: 38352512 PMCID: PMC10862863 DOI: 10.1101/2024.02.01.578425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight a flexibility in metabolism that may influence pathogenesis.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
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18
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Wang Y, Peng Q, Liu Y, Wu N, He Y, Cui X, Dan T. Genomic and transcriptomic analysis of genes involved in exopolysaccharide biosynthesis by Streptococcus thermophilus IMAU20561 grown on different sources of nitrogen. Front Microbiol 2024; 14:1328824. [PMID: 38348305 PMCID: PMC10859522 DOI: 10.3389/fmicb.2023.1328824] [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: 10/27/2023] [Accepted: 12/31/2023] [Indexed: 02/15/2024] Open
Abstract
Exopolysaccharides (EPSs), which are produced by lactic acid bacteria, have been found to improve the texture and functionality of fermented dairy products. In a previous study, four nitrogen sources were identified as affecting the yield, molecular weight and structure of EPSs produced by Streptococcus thermophilus IMAU20561 in M17 medium. In this genomic and transcriptomics study, a novel eps gene cluster responsible for assembly of repeating units of EPS is reported. This eps cluster (22.3 kb), consisting of 24 open reading frames, is located in the chromosomal DNA. To explore the biosynthetic mechanisms in EPS, we completed RNA-seq analysis of S. thermophilus IMAU20561 grown in four different nitrogen sources for 5 h (log phase) or 10 h (stationary phase). GO functional annotation showed that there was a significant enrichment of differentially expressed genes (DEGs) involved in: amino acid biosynthesis and metabolism; ribonucleotide biosynthesis and metabolism; IMP biosynthesis and metabolism; and phosphorus metabolism. KEGG functional annotation also indicated enrichment of DEGs involved in amino acid biosynthesis, glycolysis, phosphotransferase system, fructose, and mannose metabolism. Our findings provide a better understanding the genetic traits of S. thermophilus, the biosynthetic pathways needed for the production of EPS, and a theoretical basis for screening dairy starter cultures.
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Affiliation(s)
- Yuenan Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Qingting Peng
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yang Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Na Wu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanyan He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xinrui Cui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Tong Dan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
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19
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Vuksanovic N, Clasman JR, Imperiali B, Allen KN. Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Protein Sci 2024; 33:e4848. [PMID: 38019455 PMCID: PMC10731488 DOI: 10.1002/pro.4848] [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: 09/09/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
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Affiliation(s)
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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20
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Ireland K, Kayrouz CM, Huang J, Seyedsayamdost MR, Davis KM. Structural Characterization and Ligand-Induced Conformational Changes of SenB, a Se-Glycosyltransferase Involved in Selenoneine Biosynthesis. Biochemistry 2023; 62:3337-3342. [PMID: 37966244 PMCID: PMC10702425 DOI: 10.1021/acs.biochem.3c00452] [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: 08/26/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Selenium (Se) is an essential micronutrient that is found naturally in proteins, nucleic acids, and natural products. Unlike selenoproteins and selenonucleic acids, little is known about the structures of biosynthetic enzymes that incorporate Se into small molecules. Here, we report the X-ray crystal structure of SenB, the first known Se-glycosyltransferase that was recently found to be involved in the biosynthesis of the Se-containing metabolite selenoneine. SenB catalyzes C-Se bond formation using selenophosphate and an activated uridine diphosphate sugar as a Se and glycosyl donor, respectively, making it the first known selenosugar synthase and one of only four bona fide C-Se bond-forming enzymes discovered to date. Our crystal structure, determined to 2.25 Å resolution, reveals that SenB is a type B glycosyltransferase, displaying the prototypical fold with two globular Rossmann-like domains and a catalytic interdomain cleft. By employing complementary structural biology techniques, we find that SenB undergoes both local and global substrate-induced conformational changes, demonstrating a significant increase in α-helicity and a transition to a more compact conformation. Our results provide the first structure of SenB and set the stage for further biochemical characterization in the future.
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Affiliation(s)
- Kendra
A. Ireland
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Chase M. Kayrouz
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jonathan Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Katherine M. Davis
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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21
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Arriaza RH, Abiskaroon B, Patel M, Daneshian L, Kluza A, Snoeck S, Watkins MB, Hopkins JB, Van Leeuwen T, Grbic M, Grbic V, Borowski T, Chruszcz M. Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest. J Biol Chem 2023; 299:105421. [PMID: 37923139 PMCID: PMC10731231 DOI: 10.1016/j.jbc.2023.105421] [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: 09/18/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for UDP glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism; however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site-directed mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor-binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.
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Affiliation(s)
- Ricardo Hernandez Arriaza
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Brendan Abiskaroon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Megha Patel
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Krakow, Poland
| | - Simon Snoeck
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario, Canada; University of La Rioja, Logrono, Spain
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario, Canada
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Krakow, Poland
| | - Maksymilian Chruszcz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA.
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22
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Shao Z, Wang S, Liu N, Wang W, Zhu L. Interactions between sulfonamide homologues and glycosyltransferase induced metabolic disorders in rice (Oryza sativa L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122486. [PMID: 37669699 DOI: 10.1016/j.envpol.2023.122486] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/24/2023] [Accepted: 08/30/2023] [Indexed: 09/07/2023]
Abstract
Sulfadiazine and its derivatives (sulfonamides, SAs) could induce distinct biotoxic, metabolic and physiological abnormalities, potentially due to their subtle structural differences. This study conducted an in-depth investigation on the interactions between SA homologues, i.e. sulfadiazine (SD), sulfamerazine (SD1), and sulfamethazine (SD2), and the key metabolic enzyme (glycosyltransferase, GT) in rice (Oryza sativa L.). Untargeted screening of SA metabolites revealed that GT-catalyzed glycosylation was the primary transformation pathway of SAs in rice. Molecular docking identified that the binding sites of SAs on GT (D0TZD6) were responsible for transferring sugar moiety to synthesize polysaccharides and detoxify SAs. Specifically, amino acids in the GT-binding cavity (e.g., GLY487 and CYS486) formed stable hydrogen bonds with SAs (e.g., the sulfonamide group of SD). Molecular dynamics simulations revealed that SAs induced conformational changes in GT ligand binding domain, which was supported by the significantly decreased GT activity and gene expression level. As evidenced by proteomics and metabolomics, SAs inhibited the transfer and synthesis of sugar but stimulated sugar decomposition in rice leaves, leading to the accumulation of mono- and disaccharides in rice leaves. While the differences in the increased sugar content by SD (24.3%, compared with control), SD1 (11.1%), and SD2 (6.24%) can be attributed to their number of methyl groups (0, 1, 2, respectively), which determined the steric hindrance and hydrogen bonds formation with GT. This study suggested that the disturbances on crop sugar metabolism by homologues contaminants are determined by the interaction between the contaminants and the target enzyme, and are greatly dependent on the steric hindrance effects contributed by their side chains. The results are of importance to identify priority pollutants and ensure crop quality in contaminated fields.
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Affiliation(s)
- Zexi Shao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Shuyuan Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Na Liu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang, 310058, China.
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23
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Wang S, Chen D, Liu Q, Zang L, Zhang G, Sui M, Dai Y, Zhou C, Li Y, Yang Y, Ding F. Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118889. [PMID: 37666128 DOI: 10.1016/j.jenvman.2023.118889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.
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Affiliation(s)
- Shasha Wang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Danmei Chen
- College of Forestry, Guizhou University, Guiyang, 550025, China.
| | - Qingfu Liu
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Lipeng Zang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Guangqi Zhang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Mingzhen Sui
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yu Dai
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Chunjie Zhou
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yujuan Li
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yousu Yang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Fangjun Ding
- Guizhou Libo Observation and Research Station for Karst Forest Ecosystem, National Forestry and Grassland Administration, Libo, 558400, China
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24
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Jiang S, Shi H, Zhang Q, Wang ZY, Zhang Y, Zhang CY. Rolling circle transcription amplification-directed construction of tandem spinach-based fluorescent light-up biosensor for label-free sensing of β-glucosyltransferase activity. Biosens Bioelectron 2023; 237:115513. [PMID: 37419074 DOI: 10.1016/j.bios.2023.115513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/17/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
β-glucosyltransferase (β-GT) can specifically catalyze the conversion of 5-hydroxymethylcytosine (5-hmC) to 5-glucosylhydroxy methylcytosine (5-ghmC), and it is associated with the control of phage-specific gene expression by affecting transcription process in vivo and in vitro. The current strategies for β-GT assay usually involve expensive equipment, laborious treatment, radioactive hazard, and poor sensitivity. Here, we report a Spinach-based fluorescent light-up biosensor for label-free measurement of β-GT activity by utilizing 5-hmC glucosylation-initiated rolling circle transcription amplification (RCTA). We design a 5-hmC-modified multifunctional circular detection probe (5-hmC-MCDP) that integrates the functions of target-recognition, signal transduction, and transcription amplification in one probe. The introduction of β-GT catalyzes 5-hmC glucosylation of 5-hmC-MCDP probe, protecting the glucosylated 5-mC-MCDP probe from the cleavage by MspI. The remaining 5-hmC-MCDP probe can initiate RCTA reaction with the aid of T7 RNA polymerase, generating tandem Spinach RNA aptamers. The tandem Spinach RNA aptamers can be lightened up by fluorophore 3,5-difluoro-4-hydroxybenzylidene imidazolinone, facilitating label-free measurement of β-GT activity. Notably, the high specificity of MspI-catalyzed cleavage of nonglucosylated probe can efficiently inhibit nonspecific amplification, endowing this assay with a low background. Due to the higher efficiency of RCTA than the canonical promoter-initiated RNA synthesis, the signal-to-noise ratio of RCTA is 4.6-fold higher than that of linear template-based transcription amplification. This method is capable of sensitively detecting β-GT activity with a limit of detection of 2.03 × 10-5 U/mL, and it can be used for the screening of inhibitors and determination of kinetic parameters, with great potential in epigenetic research and drug discovery.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Huanhuan Shi
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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25
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Jawaharraj K, Peta V, Dhiman SS, Gnimpieba EZ, Gadhamshetty V. Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria. Sci Rep 2023; 13:16181. [PMID: 37758719 PMCID: PMC10533852 DOI: 10.1038/s41598-023-43089-8] [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: 03/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.
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Affiliation(s)
- Kalimuthu Jawaharraj
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Vincent Peta
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA
| | - Saurabh Sudha Dhiman
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Chemistry, Biology and Health Sciences, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Etienne Z Gnimpieba
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA.
| | - Venkataramana Gadhamshetty
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
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26
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Wei X, Wang P, Liu F, Ye X, Xiong D. Drug Discovery Based on Fluorine-Containing Glycomimetics. Molecules 2023; 28:6641. [PMID: 37764416 PMCID: PMC10536126 DOI: 10.3390/molecules28186641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Glycomimetics, which are synthetic molecules designed to mimic the structures and functions of natural carbohydrates, have been developed to overcome the limitations associated with natural carbohydrates. The fluorination of carbohydrates has emerged as a promising solution to dramatically enhance the metabolic stability, bioavailability, and protein-binding affinity of natural carbohydrates. In this review, the fluorination methods used to prepare the fluorinated carbohydrates, the effects of fluorination on the physical, chemical, and biological characteristics of natural sugars, and the biological activities of fluorinated sugars are presented.
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Affiliation(s)
- Xingxing Wei
- Department of Pharmacy, Changzhi Medical College, No. 161, Jiefang East Street, Changzhi 046012, China
| | - Pengyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Fen Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Xinshan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
| | - Decai Xiong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Rd. No. 38, Beijing 100191, China (F.L.); (X.Y.)
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27
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Al Saoud R, Hamrouni A, Idris A, Mousa WK, Abu Izneid T. Recent advances in the development of sialyltransferase inhibitors to control cancer metastasis: A comprehensive review. Biomed Pharmacother 2023; 165:115091. [PMID: 37421784 DOI: 10.1016/j.biopha.2023.115091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023] Open
Abstract
Metastasis accounts for the majority of cancer-associated mortalities, representing a huge health and economic burden. One of the mechanisms that enables metastasis is hypersialylation, characterized by an overabundance of sialylated glycans on the tumor surface, which leads to repulsion and detachment of cells from the original tumor. Once the tumor cells are mobilized, sialylated glycans hijack the natural killer T-cells through self-molecular mimicry and activatea downstream cascade of molecular events that result in inhibition of cytotoxicity and inflammatory responses against cancer cells, ultimately leading to immune evasion. Sialylation is mediated by a family of enzymes known as sialyltransferases (STs), which catalyse the transfer of sialic acid residue from the donor, CMP-sialic acid, onto the terminal end of an acceptor such as N-acetylgalactosamine on the cell-surface. Upregulation of STs increases tumor hypersialylation by up to 60% which is considered a distinctive hallmark of several types of cancers such as pancreatic, breast, and ovarian cancer. Therefore, inhibiting STs has emerged as a potential strategy to prevent metastasis. In this comprehensive review, we discuss the recent advances in designing novel sialyltransferase inhibitors using ligand-based drug design and high-throughput screening of natural and synthetic entities, emphasizing the most successful approaches. We analyse the limitations and challenges of designing selective, potent, and cell-permeable ST inhibitors that hindered further development of ST inhibitors into clinical trials. We conclude by analysing emerging opportunities, including advanced delivery methods which further increase the potential of these inhibitors to enrich the clinics with novel therapeutics to combat metastasis.
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Affiliation(s)
- Ranim Al Saoud
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, P.O. Box 112612, Al Ain, Abu Dhabi, United Arab Emirates; AAU Health and Biomedical Research Center, Al Ain University, P.O. Box 112612, Abu Dhabi, United Arab Emirates
| | - Amar Hamrouni
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, P.O. Box 112612, Al Ain, Abu Dhabi, United Arab Emirates; AAU Health and Biomedical Research Center, Al Ain University, P.O. Box 112612, Abu Dhabi, United Arab Emirates
| | - Adi Idris
- School of Biomedical Sciences, Queensland University of Technology, Gardens Point, QLD, Australia; School of Pharmacy and Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
| | - Walaa K Mousa
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, P.O. Box 112612, Al Ain, Abu Dhabi, United Arab Emirates; AAU Health and Biomedical Research Center, Al Ain University, P.O. Box 112612, Abu Dhabi, United Arab Emirates
| | - Tareq Abu Izneid
- Pharmaceutical Sciences Program, College of Pharmacy, Al Ain University, P.O. Box 112612, Al Ain, Abu Dhabi, United Arab Emirates; AAU Health and Biomedical Research Center, Al Ain University, P.O. Box 112612, Abu Dhabi, United Arab Emirates.
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28
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Liu G, Zhang K, Gong H, Yang K, Wang X, Zhou G, Cui W, Chen Y, Yang Y. Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:130. [PMID: 37598218 PMCID: PMC10439612 DOI: 10.1186/s13068-023-02375-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/25/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Lignocellulosic biomass is the most abundant and renewable terrestrial raw material for conversion into bioproducts and biofuels. However, the low utilization efficiency of lignocellulose causes environmental pollution and resource waste, which limits the large-scale application of bioconversion. The degradation of lignocellulose by microorganisms is an efficient and cost-effective way to overcome the challenge of utilizing plant biomass resources. This work aimed to screen valuable cellulolytic bacteria, explore its molecular mechanism from genomic insights, and investigate the ability of the strain to biodegrade wheat straw. RESULTS Bacillus subtilis (B. subtilis) RLI2019 was isolated from the intestine of Reticulitermes labralis. The strain showed comprehensive enzyme activities related to lignocellulose degradation, which were estimated as 4.06, 1.97, 4.12, 0.74, and 17.61 U/mL for endoglucanase, β-glucosidase, PASC enzyme, filter paper enzyme, and xylanase, respectively. Whole genome sequencing was performed to better understand the genetic mechanism of cellulose degradation. The genome size of B. subtilis RLI2019 was 4,195,306 bp with an average GC content of 43.54%, and the sequence characteristics illustrated an extremely high probability (99.41%) as a probiotic. The genome contained 4,381 protein coding genes with an average GC content of 44.20%, of which 145 genes were classified into six carbohydrate-active enzyme (CAZyme) families and 57 subfamilies. Eight cellulose metabolism enzyme-related genes and nine hemicellulose metabolism enzyme-related genes were annotated by the CAZyme database. The starch and sucrose metabolic pathway (ko00500) was the most enriched with 46 genes in carbohydrate metabolism. B. subtilis RLI2019 was co-cultured with wheat straw for 7 days of fermentation, the contents of neutral detergent fiber, acid detergent fiber, hemicellulose, and lignin were significantly reduced by 5.8%, 10.3%, 1.0%, and 4.7%, respectively. Moreover, the wheat straw substrate exhibited 664.9 μg/mL of reducing sugars, 1.22 U/mL and 6.68 U/mL of endoglucanase and xylanase activities, respectively. Furthermore, the fiber structures were effectively disrupted, and the cellulose crystallinity was significantly reduced from 40.2% to 36.9%. CONCLUSIONS The complex diversity of CAZyme composition mainly contributed to the strong cellulolytic attribute of B. subtilis RLI2019. These findings suggest that B. subtilis RLI2019 has favorable potential for biodegradation applications, thus it can be regarded as a promising candidate bacterium for lignocellulosic biomass degradation.
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Affiliation(s)
- Gongwei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hanxuan Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kaiyao Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoyu Wang
- Qinling Giant Panda Breeding Research Center, Shaanxi Academy of Forestry Sciences, Zhouzhi, 710402, Shaanxi, China
| | - Guangchen Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenyuan Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Jiang W, Chen J, Duan X, Li Y, Tao Z. Comparative Transcriptome Profiling Reveals Two WRKY Transcription Factors Positively Regulating Polysaccharide Biosynthesis in Polygonatum cyrtonema. Int J Mol Sci 2023; 24:12943. [PMID: 37629123 PMCID: PMC10454705 DOI: 10.3390/ijms241612943] [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: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Polygonatum cyrtonema (P. cyrtonema) is a valuable rhizome-propagating traditional Chinese medical herb. Polysaccharides (PCPs) are the major bioactive constituents in P. cyrtonema. However, the molecular basis of PCP biosynthesis in P. cyrtonema remains unknown. In this study, we measured the PCP contents of 11 wild P. cyrtonema germplasms. The results showed that PCP content was the highest in Lishui Qingyuan (LSQY, 11.84%) and the lowest in Hangzhou Lin'an (HZLA, 7.18%). We next analyzed the transcriptome profiles of LSQY and HZLA. Through a qRT-PCR analysis of five differential expression genes from the PCP biosynthesis pathway, phosphomannomutase, UDP-glucose 4-epimerase (galE), and GDP-mannose 4,6-dehydratase were determined as the key enzymes. A protein of a key gene, galE1, was localized in the chloroplast. The PCP content in the transiently overexpressed galE1 tobacco leaves was higher than in the wild type. Moreover, luciferase and Y1H assays indicated that PcWRKY31 and PcWRKY34 could activate galE1 by binding to its promoter. Our research uncovers the novel regulatory mechanism of PCP biosynthesis in P. cyrtonema and is critical to molecular-assisted breeding.
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Affiliation(s)
- Wu Jiang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; (W.J.); (J.C.); (X.D.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Jiadong Chen
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; (W.J.); (J.C.); (X.D.)
| | - Xiaojing Duan
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; (W.J.); (J.C.); (X.D.)
| | - Yaping Li
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Zhengming Tao
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; (W.J.); (J.C.); (X.D.)
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Santos-Pereira C, Sousa J, Costa ÂMA, Santos AO, Rito T, Soares P, Franco-Duarte R, Silvério SC, Rodrigues LR. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12627-9. [PMID: 37417976 PMCID: PMC10390414 DOI: 10.1007/s00253-023-12627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
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Affiliation(s)
- Cátia Santos-Pereira
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Joana Sousa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Ângela M A Costa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Andréia O Santos
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Teresa Rito
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal.
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
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Wang B, Abubakar YS, Wang Z. Special Issue "Genomics of Fungal Plant Pathogens". J Fungi (Basel) 2023; 9:713. [PMID: 37504702 PMCID: PMC10381389 DOI: 10.3390/jof9070713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023] Open
Abstract
Plant diseases can be classified according to pathogenic organisms, and 70-80% of them are fungal diseases [...].
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Affiliation(s)
- Baohua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Trait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Trait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Biochemistry, Faculty of Life Science, Ahmadu Bello University, Zaria 810281, Nigeria
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Trait Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
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Spiers AJ, Dorfmueller HC, Jerdan R, McGregor J, Nicoll A, Steel K, Cameron S. Bioinformatics characterization of BcsA-like orphan proteins suggest they form a novel family of pseudomonad cyclic-β-glucan synthases. PLoS One 2023; 18:e0286540. [PMID: 37267309 PMCID: PMC10237404 DOI: 10.1371/journal.pone.0286540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/18/2023] [Indexed: 06/04/2023] Open
Abstract
Bacteria produce a variety of polysaccharides with functional roles in cell surface coating, surface and host interactions, and biofilms. We have identified an 'Orphan' bacterial cellulose synthase catalytic subunit (BcsA)-like protein found in four model pseudomonads, P. aeruginosa PA01, P. fluorescens SBW25, P. putida KT2440 and P. syringae pv. tomato DC3000. Pairwise alignments indicated that the Orphan and BcsA proteins shared less than 41% sequence identity suggesting they may not have the same structural folds or function. We identified 112 Orphans among soil and plant-associated pseudomonads as well as in phytopathogenic and human opportunistic pathogenic strains. The wide distribution of these highly conserved proteins suggest they form a novel family of synthases producing a different polysaccharide. In silico analysis, including sequence comparisons, secondary structure and topology predictions, and protein structural modelling, revealed a two-domain transmembrane ovoid-like structure for the Orphan protein with a periplasmic glycosyl hydrolase family GH17 domain linked via a transmembrane region to a cytoplasmic glycosyltransferase family GT2 domain. We suggest the GT2 domain synthesises β-(1,3)-glucan that is transferred to the GH17 domain where it is cleaved and cyclised to produce cyclic-β-(1,3)-glucan (CβG). Our structural models are consistent with enzymatic characterisation and recent molecular simulations of the PaPA01 and PpKT2440 GH17 domains. It also provides a functional explanation linking PaPAK and PaPA14 Orphan (also known as NdvB) transposon mutants with CβG production and biofilm-associated antibiotic resistance. Importantly, cyclic glucans are also involved in osmoregulation, plant infection and induced systemic suppression, and our findings suggest this novel family of CβG synthases may provide similar range of adaptive responses for pseudomonads.
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Affiliation(s)
- Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Helge C. Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Robyn Jerdan
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Jessica McGregor
- Nuffield Research Placement Students, School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Abbie Nicoll
- Nuffield Research Placement Students, School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Kenzie Steel
- Nuffield Research Placement Students, School of Applied Sciences, Abertay University, Dundee, United Kingdom
| | - Scott Cameron
- School of Applied Sciences, Abertay University, Dundee, United Kingdom
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Hao C, Yang W, Dong G, Yu Y, Liu Y, Zhang J, Zhu Y, Wei X, Chen S. Visualization and identification of benzylisoquinoline alkaloids in various nelumbo nucifera tissues. Heliyon 2023; 9:e16138. [PMID: 37251486 PMCID: PMC10220311 DOI: 10.1016/j.heliyon.2023.e16138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023] Open
Abstract
Benzylisoquinoline alkaloids in lotus (Nelumbo nucifera) seed plumules and leaves exhibit significant tissue specificity for their pharmacological effects and potential nutritional properties. Herein, 46 benzylisoquinoline alkaloids were identified via UPLC-QTOF-HRMS, of which 9 were annotated as glycosylated monobenzylisoquinoline alkaloids concentrated in the seed plumules. The spatial distribution of targeted benzylisoquinoline alkaloids in leaves, seed plumules, and milky sap was determined via MALDI-MSI. Furthermore, 37 Nelumbo cultivars were investigated using targeted metabolomics to provide insights into functional tea development. While aporphine alkaloids comprised the main compounds present in lotus leaves, bisbenzylisoquinoline alkaloids were the main compounds in lotus plumules, where glycosylation primarily occurs. These findings can help understand the distribution of benzylisoquinoline alkaloids in lotus tissue and the directional breeding of varieties enriched with specific chemical functional groups for nutritional and pharmacological applications.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Wei Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | | | - Yuetong Yu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Yan Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Jun Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Yongping Zhu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Xiaolu Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Sha Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
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Dukes HE, Tinker KA, Ottesen EA. Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics. Front Microbiol 2023; 14:1156809. [PMID: 37323917 PMCID: PMC10266427 DOI: 10.3389/fmicb.2023.1156809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including-but not limited to-polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.
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Affiliation(s)
- Helen E Dukes
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Kara A Tinker
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, United States
| | - Elizabeth A Ottesen
- Department of Microbiology, University of Georgia, Athens, GA, United States
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Liao J, Sun G, Kurze E, Steinchen W, Hoffmann TD, Song C, Zou Z, Hoffmann T, Schwab WG. Subfunctionalization of a monolignol to a phytoalexin glucosyltransferase is accompanied by substrate inhibition. PLANT COMMUNICATIONS 2023; 4:100506. [PMID: 36566353 DOI: 10.1016/j.xplc.2022.100506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 05/11/2023]
Abstract
Uridine diphosphate-dependent glycosyltransferases (UGTs) mediate the glycosylation of plant metabolites, thereby altering their physicochemical properties and bioactivities. Plants possess numerous UGT genes, with the encoded enzymes often glycosylating multiple substrates and some exhibiting substrate inhibition kinetics, but the biological function and molecular basis of these phenomena are not fully understood. The promiscuous monolignol/phytoalexin glycosyltransferase NbUGT72AY1 exhibits substrate inhibition (Ki) at 4 μM scopoletin, whereas the highly homologous monolignol StUGT72AY2 is inhibited at 190 μM. We therefore used hydrogen/deuterium exchange mass spectrometry and structure-based mutational analyses of both proteins and introduced NbUGT72AY1 residues into StUGT72AY2 and vice versa to study promiscuity and substrate inhibition of UGTs. A single F87I and chimeric mutant of NbUGT72AY1 showed significantly reduced scopoletin substrate inhibition, whereas its monolignol glycosylation activity was almost unaffected. Reverse mutations in StUGT72AY2 resulted in increased scopoletin glycosylation, leading to enhanced promiscuity, which was accompanied by substrate inhibition. Studies of 3D structures identified open and closed UGT conformers, allowing visualization of the dynamics of conformational changes that occur during catalysis. Previously postulated substrate access tunnels likely serve as drainage channels. The results suggest a two-site model in which the second substrate molecule binds near the catalytic site and blocks product release. Mutational studies showed that minor changes in amino acid sequence can enhance the promiscuity of the enzyme and add new capabilities such as substrate inhibition without affecting existing functions. The proposed subfunctionalization mechanism of expanded promiscuity may play a role in enzyme evolution and highlights the importance of promiscuous enzymes in providing new functions.
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Affiliation(s)
- Jieren Liao
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Guangxin Sun
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Elisabeth Kurze
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036 Hefei, Anhui, P. R. China
| | - Zhiwei Zou
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wilfried G Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
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Wozniak K, Brzezinski K. Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life. Biomolecules 2023; 13:biom13050782. [PMID: 37238652 DOI: 10.3390/biom13050782] [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: 03/06/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
| | - Krzysztof Brzezinski
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
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Kunoh T, Yamamoto T, Ono E, Sugimoto S, Takabe K, Takeda M, Utada AS, Nomura N. Identification of lthB, a Gene Encoding a Putative Glycosyltransferase Family 8 Protein Required for Leptothrix Sheath Formation. Appl Environ Microbiol 2023; 89:e0191922. [PMID: 36951572 PMCID: PMC10132092 DOI: 10.1128/aem.01919-22] [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: 12/01/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023] Open
Abstract
The bacterium Leptothrix cholodnii generates cell chains encased in sheaths that are composed of woven nanofibrils. The nanofibrils are mainly composed of glycoconjugate repeats, and several glycosyltransferases (GTs) are required for its biosynthesis. However, only one GT (LthA) has been identified to date. In this study, we screened spontaneous variants of L. cholodnii SP6 to find those that form smooth colonies, which is one of the characteristics of sheathless variants. Genomic DNA sequencing of an isolated variant revealed an insertion in the locus Lcho_0972, which encodes a putative GT family 8 protein. We thus designated this protein LthB and characterized it using deletion mutants and antibodies. LthB localized adjacent to the cell envelope. ΔlthB cell chains were nanofibril free and thus sheathless, indicating that LthB is involved in nanofibril biosynthesis. Unlike the ΔlthA mutant and the wild-type strain, which often generate planktonic cells, most ΔlthB organisms presented as long cell chains under static conditions, resulting in deficient pellicle formation, which requires motile planktonic cells. These results imply that sheaths are not required for elongation of cell chains. Finally, calcium depletion, which induces cell chain breakage due to sheath loss, abrogated the expression of LthA, but not LthB, suggesting that these GTs cooperatively participate in glycoconjugate biosynthesis under different signaling controls. IMPORTANCE In recent years, the regulation of cell chain elongation of filamentous bacteria via extracellular signals has attracted attention as a potential strategy to prevent clogging of water distribution systems and filamentous bulking of activated sludge in industrial settings. However, a fundamental understanding of the ecology of filamentous bacteria remains elusive. Since sheath formation is associated with cell chain elongation in most of these bacteria, the molecular mechanisms underlying nanofibril sheath formation, including the intracellular signaling cascade in response to extracellular stimuli, must be elucidated. Here, we isolated a sheathless variant of L. cholodnii SP6 and thus identified a novel glycosyltransferase, LthB. Although mutants with deletions of lthA, encoding another GT, and lthB were both defective for nanofibril formation, they exhibited different phenotypes of cell chain elongation and pellicle formation. Moreover, LthA expression, but not LthB expression, was influenced by extracellular calcium, which is known to affect nanofibril formation, indicating the functional diversities of LthA and LthB. Such molecular insights are critical for a better understanding of ecology of filamentous bacteria, which, in turn, can be used to improve strategies to control filamentous bacteria in industrial facilities.
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Affiliation(s)
- Tatsuki Kunoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Erika Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kyosuke Takabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Minoru Takeda
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Andrew S. Utada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Fukunaga T, Watanabe M, Nakamichi Y, Morita T, Higuchi Y, Maekawa H, Takegawa K. Mechanistic insights into Schizosaccharomyces pombe GT-A family protein Pvg3 in the biosynthesis of pyruvylated β1,3-galactose of N-linked oligosaccharides. J Biosci Bioeng 2023; 135:423-432. [DOI: 10.1016/j.jbiosc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/24/2023] [Accepted: 03/04/2023] [Indexed: 03/31/2023]
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Belmok A, de Almeida FM, Rocha RT, Vizzotto CS, Tótola MR, Ramada MHS, Krüger RH, Kyaw CM, Pappas GJ. Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid. Braz J Microbiol 2023; 54:239-258. [PMID: 36701110 PMCID: PMC9944591 DOI: 10.1007/s42770-022-00900-4] [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: 01/29/2022] [Accepted: 10/02/2022] [Indexed: 01/27/2023] Open
Abstract
A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).
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Affiliation(s)
- Aline Belmok
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Felipe Marques de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Rodrigo Theodoro Rocha
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Carla Simone Vizzotto
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Faculdade de Tecnologia, Universidade de Brasília, Brasilia, DF, Brazil
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Cynthia Maria Kyaw
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
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Kint N, Dubois T, Viollier PH. Stereoisomer-specific reprogramming of a bacterial flagellin sialyltransferase. EMBO J 2023; 42:e112880. [PMID: 36636824 PMCID: PMC9975948 DOI: 10.15252/embj.2022112880] [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: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly pseudaminic acid (Pse) and its stereoisomer legionaminic acid (Leg), which decorate eubacterial and archaeal surface layers or protein appendages. FlmG, a recently identified protein sialyltransferase, O-glycosylates flagellins, the subunits of the flagellar filament. We show that flagellin glycosylation and motility in Caulobacter crescentus and Brevundimonas subvibrioides is conferred by functionally insulated Pse and Leg biosynthesis pathways, respectively, and by specialized FlmG orthologs. We established a genetic glyco-profiling platform for the classification of Pse or Leg biosynthesis pathways, discovered a signature determinant of eubacterial and archaeal Leg biosynthesis, and validated it by reconstitution experiments in a heterologous host. Finally, by rewiring FlmG glycosylation using chimeras, we defined two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that either donates Leg or Pse and a specialized flagellin-binding domain that identifies the acceptor.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
| | - Thomas Dubois
- University of Lille, CNRS, INRAE, Centrale Lille, UMR 8207‐UMET‐Unité Matériaux et TransformationsLilleFrance
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
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Exopolysaccharide Biosynthesis in Rhizobium leguminosarum bv. trifolii Requires a Complementary Function of Two Homologous Glycosyltransferases PssG and PssI. Int J Mol Sci 2023; 24:ijms24044248. [PMID: 36835659 PMCID: PMC9961541 DOI: 10.3390/ijms24044248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
The Pss-I region of Rhizobium leguminosarum bv. trifolii TA1 comprises more than 20 genes coding for glycosyltransferases, modifying enzymes, and polymerization/export proteins, altogether determining the biosynthesis of symbiotically relevant exopolysaccharides. In this study, the role of homologous PssG and PssI glycosyltransferases in exopolysaccharide subunit synthesis were analyzed. It was shown that the glycosyltransferase-encoding genes of the Pss-I region were part of a single large transcriptional unit with potential downstream promoters activated in specific conditions. The ΔpssG and ΔpssI mutants produced significantly lower amounts of the exopolysaccharide, while the double deletion mutant ΔpssIΔpssG produced no exopolysaccharide. Complementation of double mutation with individual genes restored exopolysaccharide synthesis, but only to the level similar to that observed for the single ΔpssI or ΔpssG mutants, indicating that PssG and PssI serve complementary functions in the process. PssG and PssI interacted with each other in vivo and in vitro. Moreover, PssI displayed an expanded in vivo interaction network comprising other GTs involved in subunit assembly and polymerization/export proteins. PssG and PssI proteins were shown to interact with the inner membrane through amphipathic helices at their C-termini, and PssG also required other proteins involved in exopolysaccharide synthesis to localize in the membrane protein fraction.
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Taugt17b1 Overexpression in Trichoderma atroviride Enhances Its Ability to Colonize Roots and Induce Systemic Defense of Plants. Pathogens 2023; 12:pathogens12020264. [PMID: 36839536 PMCID: PMC9959489 DOI: 10.3390/pathogens12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Trichoderma atroviride, a soil fungus, has important applications in the biocontrol of plant diseases. Glycosyltransferases enhance the root colonization ability of Trichoderma spp. This study aimed to functionally characterize glycosyltransferase Taugt17b1 in T. atroviride. We investigated the effect of Taugt17b1 overexpression in T. atroviride H18-1-1 on its biocontrol properties, especially its ability to colonize roots. Our results demonstrated that the overexpression of the Taugt17b1 increases the T. atroviride colony growth rate, improves its root colonization ability, promotes the growth and activity of the defensive enzymatic system of plants, and prevents plant diseases. This study put forth a new role of T. atroviride glycosyltransferase and furthered the understanding of the mechanisms by which fungal biocontrol agents exert their effect.
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Liu W, Tang S, Peng J, Zhu Y, Pan L, Wang J, Peng X, Cheng H, Chen Z, Wang Y, Zhou H. Enhancing lactose recognition of a key enzyme in 2'-fucosyllactose synthesis: α-1,2-fucosyltransferase. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1303-1314. [PMID: 36116126 DOI: 10.1002/jsfa.12224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND 2'-Fucosyllactose, a representative oligosaccharide in human milk, is an emerging and promising food and pharmaceutical ingredient due to its powerful health benefits, such as participating in immune regulation, regulation of intestinal flora, etc. To enable economically viable production of 2'-fucosyllactose, different biosynthesis strategies using precursors and pathway enzymes have been developed. The α-1,2-fucosyltransferases are an essential part involved in these strategies, but their strict substrate selectivity and unsatisfactory substrate tolerance are one of the key roadblocks limiting biosynthesis. RESULTS To tackle this issue, a semi-rational manipulation combining computer-aided designing and screening with biochemical experiments were adopted. The mutant had a 100-fold increase in catalytic efficiency compared to the wild-type. The highest 2'-fucosyllactose yield was up to 0.65 mol mol-1 lactose with a productivity of 2.56 g mL-1 h-1 performed by enzymatic catalysis in vitro. Further analysis revealed that the interactions between the mutant and substrates were reduced. The crucial contributions of wild-type and mutant to substrate recognition ability were closely related to their distinct phylotypes in terms of amino acid preference. CONCLUSION It is envisioned that the engineered α-1,2-fucosyltransferase could be harnessed to relieve constraints imposed on the bioproduction of 2'-fucosyllactose and lay a theoretical foundation for elucidating the substrate recognition mechanisms of fucosyltransferases. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Wenxian Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Shizhe Tang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Jing Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
| | - Yuling Zhu
- Changsha Yunkang Biotechnology Co Ltd, Changsha, P. R. China
| | - Lina Pan
- Ausnutria Institute Food & Nutrition, Ausnutria Dairy China Co Ltd, Changsha, P. R. China
| | - Jiaqi Wang
- Ausnutria Institute Food & Nutrition, Ausnutria Dairy China Co Ltd, Changsha, P. R. China
| | - Xiaoyu Peng
- Ausnutria Institute Food & Nutrition, Ausnutria Dairy China Co Ltd, Changsha, P. R. China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, P. R. China
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Maranha A, Costa M, Ripoll-Rozada J, Manso JA, Miranda V, Mendes VM, Manadas B, Macedo-Ribeiro S, Ventura MR, Pereira PJB, Empadinhas N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 2023; 6:108. [PMID: 36707645 PMCID: PMC9883506 DOI: 10.1038/s42003-023-04448-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The steep increase in nontuberculous mycobacteria (NTM) infections makes understanding their unique physiology an urgent health priority. NTM synthesize two polysaccharides proposed to modulate fatty acid metabolism: the ubiquitous 6-O-methylglucose lipopolysaccharide, and the 3-O-methylmannose polysaccharide (MMP) so far detected in rapidly growing mycobacteria. The recent identification of a unique MMP methyltransferase implicated the adjacent genes in MMP biosynthesis. We report a wide distribution of this gene cluster in NTM, including slowly growing mycobacteria such as Mycobacterium avium, which we reveal to produce MMP. Using a combination of MMP purification and chemoenzymatic syntheses of intermediates, we identified the biosynthetic mechanism of MMP, relying on two enzymes that we characterized biochemically and structurally: a previously undescribed α-endomannosidase that hydrolyses MMP into defined-sized mannoligosaccharides that prime the elongation of new daughter MMP chains by a rare α-(1→4)-mannosyltransferase. Therefore, MMP biogenesis occurs through a partially conservative replication mechanism, whose disruption affected mycobacterial growth rate at low temperature.
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Affiliation(s)
- Ana Maranha
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mafalda Costa
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jorge Ripoll-Rozada
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal ,grid.507090.b0000 0004 5303 6218Present Address: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, Santander, Spain
| | - José A. Manso
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Vanessa Miranda
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Vera M. Mendes
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - M. Rita Ventura
- grid.10772.330000000121511713Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro José Barbosa Pereira
- grid.5808.50000 0001 1503 7226IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Nuno Empadinhas
- grid.8051.c0000 0000 9511 4342CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342IIIUC - Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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Mulenga A, Radulovic Z, Porter L, Britten TH, Kim TK, Tirloni L, Gaithuma AK, Adeniyi-Ipadeola GO, Dietrich JK, Moresco JJ, Yates JR. Identification and characterization of proteins that form the inner core Ixodes scapularis tick attachment cement layer. Sci Rep 2022; 12:21300. [PMID: 36494396 PMCID: PMC9734129 DOI: 10.1038/s41598-022-24881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Ixodes scapularis long-term blood feeding behavior is facilitated by a tick secreted bio adhesive (tick cement) that attaches tick mouthparts to skin tissue and prevents the host from dislodging the attached tick. Understanding tick cement formation is highly sought after as its disruption will prevent tick feeding. This study describes proteins that form the inner core layer of I. scapularis tick cement as disrupting these proteins will likely stop formation of the outer cortical layer. The inner core cement layer completes formation by 24 h of tick attachment. Thus, we used laser-capture microdissection to isolate cement from cryosections of 6 h and 24 h tick attachment sites and to distinguish between early and late inner core cement proteins. LC-MS/MS analysis identified 138 tick cement proteins (TCPs) of which 37 and 35 were unique in cement of 6 and 24 h attached ticks respectively. We grouped TCPs in 14 functional categories: cuticular protein (16%), tick specific proteins of unknown function, cytoskeletal proteins, and enzymes (13% each), enzymes (10%), antioxidant, glycine rich, scaffolding, heat shock, histone, histamine binding, proteases and protease inhibitors, and miscellaneous (3-6% each). Gene ontology analysis confirm that TCPs are enriched for bio adhesive properties. Our data offer insights into tick cement bonding patterns and set the foundation for understanding the molecular basis of I. scapularis tick cement formation.
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Affiliation(s)
- Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA.
| | - Zeljko Radulovic
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, USA
| | - Lindsay Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, USA
| | - Taylor Hollman Britten
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Alex Kiarie Gaithuma
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Grace O Adeniyi-Ipadeola
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jolene K Dietrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Leisico F, Omeiri J, Le Narvor C, Beaudouin J, Hons M, Fenel D, Schoehn G, Couté Y, Bonnaffé D, Sadir R, Lortat-Jacob H, Wild R. Structure of the human heparan sulfate polymerase complex EXT1-EXT2. Nat Commun 2022; 13:7110. [PMID: 36402845 PMCID: PMC9675754 DOI: 10.1038/s41467-022-34882-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Heparan sulfates are complex polysaccharides that mediate the interaction with a broad range of protein ligands at the cell surface. A key step in heparan sulfate biosynthesis is catalyzed by the bi-functional glycosyltransferases EXT1 and EXT2, which generate the glycan backbone consisting of repeating N-acetylglucosamine and glucuronic acid units. The molecular mechanism of heparan sulfate chain polymerization remains, however, unknown. Here, we present the cryo-electron microscopy structure of human EXT1-EXT2, which reveals the formation of a tightly packed hetero-dimeric complex harboring four glycosyltransferase domains. A combination of in vitro and in cellulo mutational studies is used to dissect the functional role of the four catalytic sites. While EXT1 can catalyze both glycosyltransferase reactions, our results indicate that EXT2 might only have N-acetylglucosamine transferase activity. Our findings provide mechanistic insight into heparan sulfate chain elongation as a nonprocessive process and lay the foundation for future studies on EXT1-EXT2 function in health and disease.
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Affiliation(s)
- Francisco Leisico
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Juneina Omeiri
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Christine Le Narvor
- grid.462047.30000 0004 0382 4005Université Paris-Saclay, CNRS, Institut de chimie moléculaire et des matériaux d’Orsay, 91405 Orsay, France
| | - Joël Beaudouin
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Michael Hons
- grid.418923.50000 0004 0638 528XEuropean Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Daphna Fenel
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Guy Schoehn
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Yohann Couté
- grid.457348.90000 0004 0630 1517University Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - David Bonnaffé
- grid.462047.30000 0004 0382 4005Université Paris-Saclay, CNRS, Institut de chimie moléculaire et des matériaux d’Orsay, 91405 Orsay, France
| | - Rabia Sadir
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Hugues Lortat-Jacob
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - Rebekka Wild
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
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Chen H, Hu Y, Li P, Feng X, Jiang M, Sui Z. Single-cell transcriptome sequencing revealing the difference in photosynthesis and carbohydrate metabolism between epidermal cells and non-epidermal cells of Gracilariopsis lemaneiformis (Rhodophyta). FRONTIERS IN PLANT SCIENCE 2022; 13:968158. [PMID: 36466256 PMCID: PMC9714639 DOI: 10.3389/fpls.2022.968158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
The allocation of photoassimilates is considered as a key factor for determining plant productivity. The difference in photosynthesis and carbohydrate metabolism between source and sink cells provide the driven force for photoassimilates' allocation. However, photosynthesis and carbohydrate metabolism of different cells and the carbon allocation between these cells have not been elucidated in Gracilariopsis lemaneiformis. In the present study, transcriptome analysis of epidermal cells (EC) and non-epidermal cells (NEC) of G. lemaneiformis under normal light conditions was carried out. There were 3436 differentially expressed genes (DEGs) identified, and most of these DEGs were related to photosynthesis and metabolism. Based on a comprehensive analysis both at physiological and transcriptional level, the activity of photosynthesis and carbohydrate metabolism of EC and NEC were revealed. Photosynthesis activity and the synthesis activity of many low molecular weight carbohydrates (floridoside, sucrose, and others) in EC were significantly higher than those in NEC. However, the main carbon sink, floridean starch and agar, had higher levels in NEC. Moreover, the DEGs related to transportation of photoassimilates were found in this study. These results suggested that photoassimilates of EC could be transported to NEC. This study will contribute to our understanding of the source and sink relationship between the cells in G. lemaneiformis.
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Pereira de Sa N, Del Poeta M. Sterylglucosides in Fungi. J Fungi (Basel) 2022; 8:1130. [PMID: 36354897 PMCID: PMC9698648 DOI: 10.3390/jof8111130] [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: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Sterylglucosides (SGs) are sterol conjugates widely distributed in nature. Although their universal presence in all living organisms suggests the importance of this kind of glycolipids, they are yet poorly understood. The glycosylation of sterols confers a more hydrophilic character, modifying biophysical properties of cell membranes and altering immunogenicity of the cells. In fungi, SGs regulate different cell pathways to help overcome oxygen and pH challenges, as well as help to accomplish cell recycling and other membrane functions. At the same time, the level of these lipids is highly controlled, especially in wild-type fungi. In addition, modulating SGs metabolism is becoming a novel tool for vaccine and antifungal development. In the present review, we bring together multiple observations to emphasize the underestimated importance of SGs for fungal cell functions.
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Affiliation(s)
- Nivea Pereira de Sa
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
- Institute of Chemical Biology and Drug Discovery (ICB&DD), Stony Brook, NY 11794, USA
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
- Veterans Administration Medical Center, Northport, NY 11768, USA
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49
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Warring SL, Malone LM, Jayaraman J, Easingwood RA, Rigano LA, Frampton RA, Visnovsky SB, Addison SM, Hernandez L, Pitman AR, Lopez Acedo E, Kleffmann T, Templeton MD, Bostina M, Fineran PC. A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environ Microbiol 2022; 24:4834-4852. [PMID: 35912527 PMCID: PMC9796965 DOI: 10.1111/1462-2920.16106] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.
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Affiliation(s)
- Suzanne L. Warring
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Lucia M. Malone
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
| | | | - Luciano A. Rigano
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Plant Health & Environment Laboratory, Biosecurity New ZealandMinistry for Primary IndustriesAucklandNew Zealand
| | - Rebekah A. Frampton
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Sandra B. Visnovsky
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Shea M. Addison
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Loreto Hernandez
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand
| | - Andrew R. Pitman
- The New Zealand Institute for Plant & Food Research LimitedChristchurchNew Zealand,Foundation for Arable Research (FAR), TempletonChristchurchNew Zealand
| | - Elena Lopez Acedo
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | | | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited, Mt AlbertAucklandNew Zealand,Bioprotection AotearoaCanterburyNew Zealand,School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Mihnea Bostina
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Otago Centre for Electron MicroscopyUniversity of OtagoDunedinNew Zealand
| | - Peter C. Fineran
- Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand,Bioprotection AotearoaCanterburyNew Zealand
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50
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Anderson AC, Stangherlin S, Pimentel KN, Weadge JT, Clarke AJ. The SGNH hydrolase family: a template for carbohydrate diversity. Glycobiology 2022; 32:826-848. [PMID: 35871440 PMCID: PMC9487903 DOI: 10.1093/glycob/cwac045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
The substitution and de-substitution of carbohydrate materials are important steps in the biosynthesis and/or breakdown of a wide variety of biologically important polymers. The SGNH hydrolase superfamily is a group of related and well-studied proteins with a highly conserved catalytic fold and mechanism composed of 16 member families. SGNH hydrolases can be found in vertebrates, plants, fungi, bacteria, and archaea, and play a variety of important biological roles related to biomass conversion, pathogenesis, and cell signaling. The SGNH hydrolase superfamily is chiefly composed of a diverse range of carbohydrate-modifying enzymes, including but not limited to the carbohydrate esterase families 2, 3, 6, 12 and 17 under the carbohydrate-active enzyme classification system and database (CAZy.org). In this review, we summarize the structural and functional features that delineate these subfamilies of SGNH hydrolases, and which generate the wide variety of substrate preferences and enzymatic activities observed of these proteins to date.
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Affiliation(s)
- Alexander C Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Stefen Stangherlin
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo N2L3C5, Canada
| | - Kyle N Pimentel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
| | - Joel T Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo N2L3C5, Canada
| | - Anthony J Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G2W1, Canada
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo N2L3C5, Canada
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