Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria

Michiko Shimokawa, Akihiro Ishiwata, Toma Kashima, Chiho Nakashima, Jiaman Li, Riku Fukushima, Naomi Sawai, Miku Nakamori, Yuuki Tanaka, Azusa Kudo, Sae Morikami, Nao Iwanaga, Genki Akai, Nobutaka Shimizu, Takatoshi Arakawa, Chihaya Yamada, Kanefumi Kitahara, Katsunori Tanaka, Yukishige Ito, Shinya Fushinobu () and Kiyotaka Fujita ()
Additional contact information
Michiko Shimokawa: Kagoshima University
Akihiro Ishiwata: RIKEN
Toma Kashima: The University of Tokyo
Chiho Nakashima: The University of Tokyo
Jiaman Li: The University of Tokyo
Riku Fukushima: The University of Tokyo
Naomi Sawai: Kagoshima University
Miku Nakamori: Kagoshima University
Yuuki Tanaka: Kagoshima University
Azusa Kudo: Kagoshima University
Sae Morikami: Kagoshima University
Nao Iwanaga: Kagoshima University
Genki Akai: The University of Tokyo
Nobutaka Shimizu: High Energy Accelerator Research Organization (KEK)
Takatoshi Arakawa: Tokyo University of Science
Chihaya Yamada: Meiji University
Kanefumi Kitahara: Kagoshima University
Katsunori Tanaka: RIKEN
Yukishige Ito: RIKEN
Shinya Fushinobu: The University of Tokyo
Kiyotaka Fujita: Kagoshima University

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-41431-2

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