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Shimokawa M, Ishiwata A, Kashima T, Nakashima C, Li J, Fukushima R, Sawai N, Nakamori M, Tanaka Y, Kudo A, Morikami S, Iwanaga N, Akai G, Shimizu N, Arakawa T, Yamada C, Kitahara K, Tanaka K, Ito Y, Fushinobu S, Fujita K. Identification and characterization of endo-α-, exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria. Nat Commun 2023; 14:5803. [PMID: 37726269 PMCID: PMC10509167 DOI: 10.1038/s41467-023-41431-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of D-arabinose, the enantiomer of the typical L-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-D-arabinanases, GH172 exo-α-D-arabinofuranosidase, and GH116 exo-β-D-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex D-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-D-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these D-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.
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Affiliation(s)
- Michiko Shimokawa
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Akihiro Ishiwata
- Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan
| | - Toma Kashima
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Nakashima
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jiaman Li
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Riku Fukushima
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naomi Sawai
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Miku Nakamori
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yuuki Tanaka
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Azusa Kudo
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Sae Morikami
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Nao Iwanaga
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Genki Akai
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Takatoshi Arakawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Chihaya Yamada
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan
- Graduate School of Science, Osaka University, Osaka, 560-0043, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- CRIIM, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. Mass Spectrom Rev 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Ganguly S. The pivotal role of Corynebacterium glutamicum in l-Glutamic acid fermentation: A concise review. Biocatalysis and Agricultural Biotechnology 2022. [DOI: 10.1016/j.bcab.2022.102578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Savková K, Huszár S, Baráth P, Pakanová Z, Kozmon S, Vancová M, Tesařová M, Blaško J, Kaliňák M, Singh V, Korduláková J, Mikušová K. An ABC transporter Wzm-Wzt catalyzes translocation of lipid-linked galactan across the plasma membrane in mycobacteria. Proc Natl Acad Sci U S A 2021; 118:e2023663118. [PMID: 33879617 DOI: 10.1073/pnas.2023663118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis, one of the deadliest pathogens in human history, is distinguished by a unique, multilayered cell wall, which offers the bacterium a high level of protection from the attacks of the host immune system. The primary structure of the cell wall core, composed of covalently linked peptidoglycan, branched heteropolysaccharide arabinogalactan, and mycolic acids, is well known, and numerous enzymes involved in the biosynthesis of its components are characterized. The cell wall biogenesis takes place at both cytoplasmic and periplasmic faces of the plasma membrane, and only recently some of the specific transport systems translocating the metabolic intermediates between these two compartments have been characterized [M. Jackson, C. M. Stevens, L. Zhang, H. I. Zgurskaya, M. Niederweis, Chem. Rev., 10.1021/acs.chemrev.0c00869 (2020)]. In this work, we use CRISPR interference methodology in Mycobacterium smegmatis to functionally characterize an ATP-binding cassette (ABC) transporter involved in the translocation of galactan precursors across the plasma membrane. We show that genetic knockdown of the transmembrane subunit of the transporter results in severe morphological changes and the accumulation of an aberrantly long galactan precursor. Based on similarities with structures and functions of specific O-antigen ABC transporters of gram-negative bacteria [C. Whitfield, D. M. Williams, S. D. Kelly, J. Biol. Chem. 295, 10593-10609 (2020)], we propose a model for coupled synthesis and export of the galactan polymer precursor in mycobacteria.
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Ghimire N, Han SR, Kim B, Jung SH, Park H, Lee JH, Oh TJ. Complete genome sequencing and comparative CAZyme analysis of Rhodococcus sp. PAMC28705 and PAMC28707 provide insight into their biotechnological and phytopathogenic potential. Arch Microbiol 2021; 203:1731-42. [PMID: 33459813 DOI: 10.1007/s00203-020-02177-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/27/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Study of carbohydrate-active enzymes (CAZymes) can reveal information about the lifestyle and behavior of an organism. Rhodococcus species is well known for xenobiotic metabolism; however, their carbohydrate utilization ability has been less discussed till date. This study aimed to present the CAZyme analysis of two Rhodococcus strains, PAMC28705 and PAMC28707, isolated from lichens in Antarctica, and compare them with other Rhodococcus, Mycobacterium, and Corynebacterium strains. Genome-wide computational analysis was performed using various tools. Results showed similarities in CAZymes across all the studied genera. All three genera showed potential for significant polysaccharide utilization, including starch, cellulose, and pectin referring their biotechnological potential. Keeping in mind the pathogenic strains listed across all three genera, CAZymes associated to pathogenicity were analyzed too. Cutinase enzyme, which has been associated with phytopathogenicity, was abundant in all the studied organisms. CAZyme gene cluster of Rhodococcus sp. PAMC28705 and Rhodococcus sp. PAMC28707 showed the insertion of cutinase in the cluster, further supporting their possible phytopathogenic properties.
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Ashokcoomar S, Reedoy KS, Senzani S, Loots DT, Beukes D, van Reenen M, Pillay B, Pillay M. Mycobacterium tuberculosis curli pili (MTP) deficiency is associated with alterations in cell wall biogenesis, fatty acid metabolism and amino acid synthesis. Metabolomics 2020; 16:97. [PMID: 32914199 DOI: 10.1007/s11306-020-01720-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION In an effort to find alternative therapeutic interventions to combat tuberculosis, a better understanding of the pathophysiology of Mycobacterium tuberculosis is required. The Mycobacterium tuberculosis curli pili (MTP) adhesin, present on the surface of this pathogen, has previously been shown using functional genomics and global transcriptomics, to play an important role in establishing infection, bacterial aggregation, and modulating host response in vitro and in vivo. OBJECTIVE This investigation aimed to determine the role of MTP in modulating the metabolism of M. tuberculosis, using mtp gene-knockout mutant and complemented strains. METHODS Untargeted two-dimensional gas chromatography time-of-flight mass spectrometry, and bioinformatic analyses, were used to identify significant differences in the metabolite profiles among the wild-type, ∆mtp mutant and mtp-complemented strains, and validated with results generated by real-time quantitative PCR. RESULTS A total of 28 metabolites were found to be significantly altered when comparing the ∆mtp mutant and the wild-type strains indicating a decreased utilisation of metabolites in cell wall biogenesis, a reduced efficiency in the breakdown of fatty acids, and decreased amino acid biosynthesis in the former strain. Comparison of the wild-type to mtp-complement, and ∆mtp to mtp-complemented strains revealed 10 and 16 metabolite differences, respectively. Real-time quantitative PCR results supported the metabolomics findings. Complementation of the ∆mtp mutant resulted in a partial restoration of MTP function. CONCLUSION The lack of the MTP adhesin resulted in various bacterial cell wall alterations and related metabolic changes. This study highlights the importance of MTP as a virulence factor and further substantiates its potential use as a suitable biomarker for the development of diagnostic tools and intervention therapeutics against TB.
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Affiliation(s)
- S Ashokcoomar
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - K S Reedoy
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - S Senzani
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - D T Loots
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - D Beukes
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - M van Reenen
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom, 2531, South Africa
| | - B Pillay
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - M Pillay
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa.
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Justen AM, Hodges HL, Kim LM, Sadecki PW, Porfirio S, Ultee E, Black I, Chung GS, Briegel A, Azadi P, Kiessling LL. Polysaccharide length affects mycobacterial cell shape and antibiotic susceptibility. Sci Adv 2020; 6:6/38/eaba4015. [PMID: 32938674 PMCID: PMC7494350 DOI: 10.1126/sciadv.aba4015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 08/05/2020] [Indexed: 05/04/2023]
Abstract
Bacteria control the length of their polysaccharides, which can control cell viability, physiology, virulence, and immune evasion. Polysaccharide chain length affects immunomodulation, but its impact on bacterial physiology and antibiotic susceptibility was unclear. We probed the consequences of truncating the mycobacterial galactan, an essential linear polysaccharide of about 30 residues. Galactan covalently bridges cell envelope layers, with the outermost cell wall linkage point occurring at residue 12. Reducing galactan chain length by approximately half compromises fitness, alters cell morphology, and increases the potency of hydrophobic antibiotics. Systematic variation of the galactan chain length revealed that it determines periplasm size. Thus, glycan chain length can directly affect cellular physiology and antibiotic activity, and mycobacterial glycans, not proteins, regulate periplasm size.
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Affiliation(s)
- Alexander M Justen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
| | - Heather L Hodges
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
| | - Lili M Kim
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
| | - Patric W Sadecki
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
| | - Sara Porfirio
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Eveline Ultee
- Institute of Biology, University of Leiden, 2333 BE Leiden, Netherlands
| | - Ian Black
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Grace S Chung
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
| | - Ariane Briegel
- Institute of Biology, University of Leiden, 2333 BE Leiden, Netherlands
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Konyariková Z, Savková K, Kozmon S, Mikušová K. Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target? Antibiotics (Basel) 2020; 9:E20. [PMID: 31935842 DOI: 10.3390/antibiotics9010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
While target-based drug design has proved successful in several therapeutic areas, this approach has not yet provided compelling outcomes in the field of antibacterial agents. This statement remains especially true for the development of novel therapeutic interventions against tuberculosis, an infectious disease that is among the top ten leading causes of death globally. Mycobacterial galactan is an important component of the protective cell wall core of the tuberculosis pathogen and it could provide a promising target for the design of new drugs. In this review, we summarize the current knowledge on galactan biosynthesis in Mycobacterium tuberculosis, including landmark findings that led to the discovery and understanding of three key enzymes in this pathway: UDP-galactose mutase, and galactofuranosyl transferases GlfT1 and GlfT2. Moreover, we recapitulate the efforts aimed at their inhibition. The predicted common transition states of the three enzymes provide the lucrative possibility of multitargeting in pharmaceutical development, a favourable property in the mitigation of drug resistance. We believe that a tight interplay between target-based computational approaches and experimental methods will result in the development of original inhibitors that could serve as the basis of a new generation of drugs against tuberculosis.
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Abstract
Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.
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Affiliation(s)
- Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Ian L Sparks
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, 639 North Pleasant Street, Amherst, MA, 01003, USA.
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Alderwick LJ, Birch HL, Krumbach K, Bott M, Eggeling L, Besra GS. AftD functions as an α1 → 5 arabinofuranosyltransferase involved in the biosynthesis of the mycobacterial cell wall core. ACTA ACUST UNITED AC 2018; 1:2-14. [PMID: 29998212 DOI: 10.1016/j.tcsw.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022]
Abstract
Generation of a single aftD and double aftB/aftD mutants in C. glutamicum. Phenotypic analysis of purified cell wall material indicates a cell wall lesion. Cell free biochemical assays indicate AftD functions as an α(1 → 5) AraT.
Arabinogalactan (AG) is an essential structural macromolecule present in the cell wall of Mycobacterium tuberculosis, serving to connect peptidoglycan with the outer mycolic acid layer. The D-arabinan segment is a highly branched component of AG and is assembled in a step-wise fashion by a variety of arabinofuranosyltransferases (AraT). We have previously used Corynebacterium glutamicum as a model organism to study these complex processes which are otherwise essential in mycobacteria. In order to further our understanding of the molecular basis of AG assembly, we investigated the role of a fourth AraT, now termed AftD by generating single (ΔaftD) and double deletion (ΔaftB ΔaftD) mutants of C. glutamicum. We demonstrate that AftD functions as an α(1 → 5) AraT and reveal the point at which it exerts its activity in the AG biosynthetic pathway.
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Abstract
UDP-galactopyranose mutase (Glf or UGM) catalyzes the formation of uridine 5'-diphosphate-α-d-galactofuranose (UDP-Galf) from UDP-galactopyranose (UDP-Galp). The enzyme is required for the production of Galf-containing glycans. UGM is absent in mammals, but members of the Corynebacterineae suborder require UGM for cell envelope biosynthesis. The need for UGM in some pathogens has prompted the search for inhibitors that could serve as antibiotic leads. Optimizing inhibitor potency, however, has been challenging. The UGM from Klebsiella pneumoniae (KpUGM), which is not required for viability, is more effectively impeded by small-molecule inhibitors than are essential UGMs from species such as Mycobacterium tuberculosis or Corynebacterium diphtheriae. Why KpUGM is more susceptible to inhibition than other orthologs is not clear. One potential source of difference is UGM ortholog conformation. We previously determined a structure of CdUGM bound to a triazolothiadiazine inhibitor in the open form, but it was unclear whether the small-molecule inhibitor bound this form or to the closed form. By varying the terminal tag (CdUGM-His6 and GSG-CdUGM), we crystallized CdUGM to capture the enzyme in different conformations. These structures reveal a pocket in the active site that can be exploited to augment inhibitor affinity. Moreover, they suggest the inhibitor binds the open form of most prokaryotic UGMs but can bind the closed form of KpUGM. This model and the structures suggest strategies for optimizing inhibitor potency by exploiting UGM conformational flexibility.
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Affiliation(s)
- Kittikhun Wangkanont
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Valerie J. Winton
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katrina T. Forest
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Department of Bacteriology University of Wisconsin-Madison, Madison, WI, 53706, USA,Corresponding authors: Katrina T. Forest (Tel. 608-265-3566, ) and Laura L. Kiessling (Tel. 608-262-0541, )
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA,Corresponding authors: Katrina T. Forest (Tel. 608-265-3566, ) and Laura L. Kiessling (Tel. 608-262-0541, )
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