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Li N, Tan X, Yang Q. Recent Progress on Strategies and Applications of Imaging for Intestinal Microflora. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lin L, Du Y, Song J, Wang W, Yang C. Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut. Acc Chem Res 2021; 54:2076-2087. [PMID: 33856204 DOI: 10.1021/acs.accounts.1c00068] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As a newly discovered organ, gut microbiota has been extensively studied in the last two decades, with their highly diverse and fundamental roles in the physiology of many organs and systems of the host being gradually revealed. However, most of the current research heavily relies on DNA sequencing-based methodologies. To truly understand the complex physiological and pathological functions demonstrated by commensal and pathogenic gut bacteria, we need more powerful methods and tools, among which imaging strategies suitable for approaching this ecosystem in different settings are one of the most desirable. Although the phrase gut "dark matter" is often used in referring to the unculturability of many gut bacteria, it is also applicable to describing the formidable difficulties in visualizing these microbes in the intestines. To develop suitable and versatile chemical and biological tools for imaging bacteria in the gut, great efforts have been devoted in the past several years.In this Account, we highlight the recent progress made by our group and other laboratories in the development of visualization strategies for commensal microbiota and pathogenic bacteria in the gut. First, we summarize our efforts toward the development of derivatized antibiotic staining probes that directly bind to specific bacterial surface structures for selective labeling of different groups of gut bacteria. Next, metabolic labeling-based imaging strategies, using unnatural amino acids, unnatural sugars, and stable isotopes, for imaging gut bacteria on various scales and in different settings are discussed in detail. We then introduce nucleic acid staining-based bacterial imaging, using either general nucleic acid-binding reagents or selective-labeling techniques (e.g., fluorescence in situ hybridization) to meet the diverse needs in gut microbiota research. This classical imaging strategy has witnessed a renaissance owing to a series of new technical advancements. Furthermore, despite the notorious difficulties of performing genetic manipulations in many commensal gut bacteria, great effort has been made recently in engineering gut bacteria with reporters like fluorescent proteins and acoustic response proteins.Our perspectives on the current limitations of the chemical tools and strategies and the future directions for improvement are also presented. We hope that this Account can offer valuable references to spark new ideas and invite new efforts to help decipher the complex biological and chemical interactions between commensal microbiota and pathogenic bacteria and the hosts.
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Affiliation(s)
- Liyuan Lin
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yahui Du
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Ma J, Li Q, Tan H, Jiang H, Li K, Zhang L, Shi Q, Yin H. Unique N-glycosylation of a recombinant exo-inulinase from Kluyveromyces cicerisporus and its effect on enzymatic activity and thermostability. J Biol Eng 2019; 13:81. [PMID: 31737090 PMCID: PMC6844067 DOI: 10.1186/s13036-019-0215-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background Inulinase can hydrolyze polyfructan into high-fructose syrups and fructoligosaccharides, which are widely used in food, the medical industry and the biorefinery of Jerusalem artichoke. In the present study, a recombinant exo-inulinase (rKcINU1), derived from Kluyveromyces cicerisporus CBS4857, was proven as an N-linked glycoprotein, and the removal of N-linked glycan chains led to reduced activity. Results Five N-glycosylation sites with variable high mannose-type oligosaccharides (Man3–9GlcNAc2) were confirmed in the rKcINU1. The structural modeling showed that all five glycosylation sites (Asn-362, Asn-370, Asn-399, Asn-467 and Asn-526) were located at the C-terminus β-sandwich domain, which has been proven to be more conducive to the occurrence of glycosylation modification than the N-terminus domain. Single-site N-glycosylation mutants with Asn substituted by Gln were obtained, and the Mut with all five N-glycosylation sites removed was constructed, which resulted in the loss of all enzyme activity. Interestingly, the N362Q led to an 18% increase in the specific activity against inulin, while a significant decrease in thermostability (2.91 °C decrease in Tm) occurred, and other single mutations resulted in the decrease in the specific activity to various extents, among which N467Q demonstrated the lowest enzyme activity. Conclusion The increased enzyme activity in N362Q, combined with thermostability testing, 3D modeling, kinetics data and secondary structure analysis, implied that the N-linked glycan chains at the Asn-362 position functioned negatively, mainly as a type of steric hindrance toward its adjacent N-glycans to bring rigidity. Meanwhile, the N-glycosylation at the other four sites positively regulated enzyme activity caused by altered substrate affinity by means of fine-tuning the β-sandwich domain configuration. This may have facilitated the capture and transfer of substrates to the enzyme active cavity, in a manner quite similar to that of carbohydrate binding modules (CBMs), i.e. the chains endowed the β-sandwich domain with the functions of CBM. This study discovered a unique C-terminal sequence which is more favorable to glycosylation, thereby casting a novel view for glycoengineering of enzymes from fungi via redesigning the amino acid sequence at the C-terminal domain, so as to optimize the enzymatic properties.
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Affiliation(s)
- Junyan Ma
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China.,2Liaoning Province Key Laboratory of Bio-Organic Chemistry, Dalian University, Dalian, 116622 China
| | - Qian Li
- 2Liaoning Province Key Laboratory of Bio-Organic Chemistry, Dalian University, Dalian, 116622 China
| | - Haidong Tan
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Hao Jiang
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Kuikui Li
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Lihua Zhang
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Quan Shi
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Heng Yin
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
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de Graaff DR, Felz S, Neu TR, Pronk M, van Loosdrecht MCM, Lin Y. Sialic acids in the extracellular polymeric substances of seawater-adapted aerobic granular sludge. WATER RESEARCH 2019; 155:343-351. [PMID: 30852321 DOI: 10.1016/j.watres.2019.02.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Sialic acids have been discovered in the extracellular polymeric substances (EPS) of seawater-adapted aerobic granular sludge (AGS). Sialic acids are a group of monosaccharides with a nine-carbon backbone, commonly found in mammalian cells and pathogenic bacteria, and frequently described to protect EPS molecules and cells from attack by proteases or glycosidases. In order to further understand the role of these compounds in AGS, lectin staining, genome analysis of the dominant bacterial species, and shielding tests were done. Fluorescence lectin bar-coding (FLBC) analysis showed an overlap with protein staining, indicating presence of sialoglycoproteins in the EPS matrix. Genome analysis gives a positive indication for putative production of sialic acids by the dominant bacteria Candidatus Accumulibacter. FT-IR analysis shows upon selective removal of sialic acids a decrease in carbohydrates, extension of the protein side chain, and exposure of penultimate sugars. Enzymatic removal of sialic acids results in the removal of galactose residues from the EPS upon subsequent treatment with β-galactosidase, indicating a linkage between galactose and sialic acid at the terminus of glycan chains. This work indicates the importance of sialic acids in the protection of penultimate sugar residues of glycoproteins in EPS, and provides basis for future research in the composition of EPS from biofilms and granular sludge.
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Affiliation(s)
- Danny R de Graaff
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - Simon Felz
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre for Environmental Research - UFZ, Brueckstrasse 3A, 39114, Magdeburg, Germany
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
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A tridecaptin-based fluorescent probe for differential staining of Gram-negative bacteria. Anal Bioanal Chem 2018; 411:4017-4023. [PMID: 30415405 DOI: 10.1007/s00216-018-1465-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
Abstract
The traditional Gram-staining method, which was invented more than a century ago for differentiating bacteria as Gram positive or Gram negative, is still widely practiced in microbiology. However, Gram staining suffers from several problems which can affect the accuracy of the diagnosis. Here, we report a new Gram-negative-specific fluorescent probe, which is based on a narrow-spectrum antibiotic, tridecaptin A1, and allows selective staining of Gram-negative bacteria in different fixed bacterial samples. Solid-phase peptide synthesis was used to prepare the tridecaptin A1-fluorophore conjugate with a single structure. Labeling selectivity of the probe toward Gram-negative bacteria was confirmed by testing against a panel of bacterial species. By combining the use of a previously reported Gram-positive-specific fluorescent probe, we then further showed the capability of the new probe in differential labeling of a number of complex bacterial samples, which included a mouse gut microbiota cultured in vitro, as well as microbiotas collected from the human oral cavity, soil, and crude oil. High labeling selectivity and coverage were observed in most samples. This method offers a new Gram-negative-specific probe with a defined structure, which allows facile fluorescence-based differentiation of Gram-positive and Gram-negative bacteria for further microbial studies.
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Wang W, Chen X. Antibiotics-based fluorescent probes for selective labeling of Gram-negative and Gram-positive bacteria in living microbiotas. Sci China Chem 2018. [DOI: 10.1007/s11426-018-9236-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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A CMP-N-acetylneuraminic Acid Synthetase Purified from a Marine Bacterium,Photobacterium leiognathiJT-SHIZ-145. Biosci Biotechnol Biochem 2014; 75:47-53. [DOI: 10.1271/bbb.100506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Hussain MRM, Asfour H, Yasir M, Khan A, Mohamoud HSA, Al-Aama JY. The Microbial Pathology of Neu5Ac and Gal Epitopes. J Carbohydr Chem 2013. [DOI: 10.1080/07328303.2013.793773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Kajiwara H, Toda M, Mine T, Nakada H, Yamamoto T. Isolation of fucosyltransferase-producing bacteria from marine environments. Microbes Environ 2012; 27:515-8. [PMID: 23100020 PMCID: PMC4103564 DOI: 10.1264/jsme2.me12058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fucose-containing oligosaccharides on the cell surface of some pathogenic bacteria are thought to be important for host-microbe interactions and to play a major role in the pathogenicity of bacterial pathogens. Here, we screened marine bacteria for glycosyltransferases using two methods: a one-pot glycosyltransferase assay method and a lectin-staining method. Using this approach, we isolated marine bacteria with fucosyltransferase activity. There have been no previous reports of marine bacteria producing fucosyltransferase. This paper thus represents the first report of fucosyltransferase-producing marine bacteria.
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Affiliation(s)
- Hitomi Kajiwara
- Glycotechnology Business Unit, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438–0802, Japan
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Thompson FL, Neto AA, Santos EDO, Izutsu K, Iida T. Effect of N-acetyl-D-glucosamine on gene expression in Vibrio parahaemolyticus. Microbes Environ 2011; 26:61-6. [PMID: 21487204 DOI: 10.1264/jsme2.me10152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed the effect of N-acetyl-D-glucosamine (GlcNAc) on gene expression in the marine bacterium Vibrio parahaemolyticus. The total number of genes whose expression was induced and repressed genes in the presence of GlcNAc was 81 and 55, respectively. The induced genes encoded a variety of products, including proteins related to energy metabolism (e.g. GlcNAc and chitin utilization), transport, central metabolism and chemotaxis, hypothetical proteins, mannose-sensitive hemagglutinin pilus (MSHA), and a PilA protein, whereas the repressed genes encoded mainly hypothetical proteins. GlcNAc appears to influence directly or indirectly a variety of cellular processes, including energy metabolism, chitin utilization, competence, biofilm formation and pathogenicity. GlcNAc, one of the most abundant aminosugars in the oceans, is used by V. parahaemolyticus as an energy source and affects the cellular functioning of this marine bacterium.
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Affiliation(s)
- Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Brazil.
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Yamamoto T. Marine bacterial sialyltransferases. Mar Drugs 2010; 8:2781-94. [PMID: 21139844 PMCID: PMC2996176 DOI: 10.3390/md8112781] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/25/2010] [Accepted: 11/02/2010] [Indexed: 01/04/2023] Open
Abstract
Sialyltransferases transfer N-acetylneuraminic acid (Neu5Ac) from the common donor substrate of these enzymes, cytidine 5′-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac), to acceptor substrates. The enzymatic reaction products including sialyl-glycoproteins, sialyl-glycolipids and sialyl-oligosaccharides are important molecules in various biological and physiological processes, such as cell-cell recognition, cancer metastasis, and virus infection. Thus, sialyltransferases are thought to be important enzymes in the field of glycobiology. To date, many sialyltransferases and the genes encoding them have been obtained from various sources including mammalian, bacterial and viral sources. During the course of our research, we have detected over 20 bacteria that produce sialyltransferases. Many of the bacteria we isolated from marine environments are classified in the genus Photobacterium or the closely related genus Vibrio. The paper reviews the sialyltransferases obtained mainly from marine bacteria.
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Affiliation(s)
- Takeshi Yamamoto
- Glycotechnology Business Unit, Japan Tobacco Inc., 700 Higashibara, Iwata, Shizuoka 438-0802, Japan.
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