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Tian X, Zheng L, Wang C, Han Y, Li Y, Cui T, Liu J, Liu C, Jia G, Yang L, Hsu Y, Zeng C, Ding L, Wang C, Cheng B, Wang M, Xie R. Selenium-based metabolic oligosaccharide engineering strategy for quantitative glycan detection. Nat Commun 2023; 14:8281. [PMID: 38092825 PMCID: PMC10719347 DOI: 10.1038/s41467-023-44118-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and the background signal readout makes it challenging to achieve glycan quantification. Here we develop SeMOE, a selenium-based metabolic oligosaccharide engineering strategy that concisely combines elemental analysis and MOE,enabling the mass spectrometric imaging of glycome. We also demonstrate that the new-to-nature SeMOE probes allow for detection, quantitative measurement and visualization of glycans in diverse biological contexts. We also show that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. SeMOE thus provides a convenient and simplified method to explore the glyco-world.
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Affiliation(s)
- Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Lingna Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yida Han
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yujie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jialin Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chuanming Liu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Guogeng Jia
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lujie Yang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yi Hsu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Chen Zeng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Lijun Ding
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bo Cheng
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Meng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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Mathew BJ, Gupta P, Naaz T, Rai R, Gupta S, Gupta S, Chaurasiya SK, Purwar S, Biswas D, Vyas AK, Singh AK. Role of Streptococcus pneumoniae extracellular glycosidases in immune evasion. Front Cell Infect Microbiol 2023; 13:1109449. [PMID: 36816580 PMCID: PMC9937060 DOI: 10.3389/fcimb.2023.1109449] [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: 11/27/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) typically colonizes the human upper airway asymptomatically but upon reaching other sites of the host body can cause an array of diseases such as pneumonia, bacteremia, otitis media, and meningitis. Be it colonization or progression to disease state, pneumococcus faces multiple challenges posed by host immunity ranging from complement mediated killing to inflammation driven recruitment of bactericidal cells for the containment of the pathogen. Pneumococcus has evolved several mechanisms to evade the host inflicted immune attack. The major pneumococcal virulence factor, the polysaccharide capsule helps protect the bacteria from complement mediated opsonophagocytic killing. Another important group of pneumococcal proteins which help bacteria to establish and thrive in the host environment is surface associated glycosidases. These enzymes can hydrolyze host glycans on glycoproteins, glycolipids, and glycosaminoglycans and consequently help bacteria acquire carbohydrates for growth. Many of these glycosidases directly or indirectly facilitate bacterial adherence and are known to modulate the function of host defense/immune proteins likely by removing glycans and thereby affecting their stability and/or function. Furthermore, these enzymes are known to contribute the formation of biofilms, the bacterial communities inherently resilient to antimicrobials and host immune attack. In this review, we summarize the role of these enzymes in host immune evasion.
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Affiliation(s)
- Bijina J. Mathew
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Priyal Gupta
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
| | - Tabassum Naaz
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
| | - Rupal Rai
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Sudheer Gupta
- Research and Development, 3B Blackbio Biotech India Ltd., Bhopal, India
| | - Sudipti Gupta
- Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Shivendra K. Chaurasiya
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Shashank Purwar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
| | - Debasis Biswas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
| | - Ashish Kumar Vyas
- John C Martin Centre for Liver Research and Innovation, Liver Foundation Sonarpur, Kolkata, India
| | - Anirudh K. Singh
- School of Sciences, SAM Global University, Raisen, India,*Correspondence: Anirudh K. Singh,
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Loop 422–437 in NanA from Streptococcus pneumoniae plays the role of an active site lid and is associated with allosteric regulation. Comput Biol Med 2022; 144:105290. [DOI: 10.1016/j.compbiomed.2022.105290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 11/03/2022]
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Timonina D, Sharapova Y, Švedas V, Suplatov D. Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Comput Struct Biotechnol J 2021; 19:1302-1311. [PMID: 33738079 PMCID: PMC7933735 DOI: 10.1016/j.csbj.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Local 3D-structural differences in homologous proteins contribute to functional diversity observed in a superfamily, but so far received little attention as bioinformatic analysis was usually carried out at the level of amino acid sequences. We have developed Zebra3D - the first-of-its-kind bioinformatic software for systematic analysis of 3D-alignments of protein families using machine learning. The new tool identifies subfamily-specific regions (SSRs) - patterns of local 3D-structure (i.e. single residues, loops, or secondary structure fragments) that are spatially equivalent within families/subfamilies, but are different among them, and thus can be associated with functional diversity and function-related conformational plasticity. Bioinformatic analysis of protein superfamilies by Zebra3D can be used to study 3D-determinants of catalytic activity and specific accommodation of ligands, help to prepare focused libraries for directed evolution or assist development of chimeric enzymes with novel properties by exchange of equivalent regions between homologs, and to characterize plasticity in binding sites. A companion Mustguseal web-server is available to automatically construct a 3D-alignment of functionally diverse proteins, thus reducing the minimal input required to operate Zebra3D to a single PDB code. The Zebra3D + Mustguseal combined approach provides the opportunity to systematically explore the value of SSRs in superfamilies and to use this information for protein design and drug discovery. The software is available open-access at https://biokinet.belozersky.msu.ru/Zebra3D.
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Affiliation(s)
- Daria Timonina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
- Corresponding author.
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