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Alekseeva et al. Microbiome Res Rep 2023;2:10 Microbiome Research
DOI: 10.20517/mrr.2023.06
Reports

Original Article Open Access

Study of the binding of ΔFN3.1 fragments of the
Bifidobacterium longum GT15 with TNF� and

prevalence of domain-containing proteins in groups
of bacteria of the human gut microbiota

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Maria G. Alekseeva , Ilya N. Dyakov , Kristina K. Bushkova , Dilara A. Mavletova , Roman A. Yunes 1,* ,
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Irina N. Chernyshova , Ilya A. Masalitin , Tatiana A. Koshenko , Venera Z. Nezametdinova , Valery N.
Danilenko 1,3
1
Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow
119991, Russia.
2
Laboratory of Immunoglobulin biosynthesis, Mechnikov Research Institute of Vaccines and Sera, Moscow 105064, Russia.
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Caspian International School of Medicine, Caspian University, Almaty 050000, Kazakhstan.
* Correspondence to: Dr. Roman A. Yunes, Laboratory of Genetics of Microorganisms, Vavilov Institute of Genetics of
Microorganisms, Gubkin Street, bd 3, Moscow 119991, Russia. E-mail: romanyunes@gmail.com
How to cite this article: Alekseeva MG, Dyakov IN, Bushkova KK, Mavletova DA, Yunes RA, Chernyshova IN, Masalitin IA,
Koshenko TA, Nezametdinova VZ, Danilenko VN. Study of the binding of ΔFN3.1 fragments of the Bifidobacterium longum GT15
with TNFα and prevalence of domain-containing proteins in groups of bacteria of the human gut microbiota. Microbiome Res Rep
2023;2:10. https://dx.doi.org/10.20517/mrr.2023.06
Received: 16 Jan 2023 Revised: 25 Mar 2023 Accepted: 31 Mar 2023 Published: 12 Apr 2023
Academic Editor: Francesca Turroni Copy Editor: Ke-Cui Yang Production Editor: Ke-Cui Yang

Abstract
Aim: This study is mainly devoted to determining the ability of FN3.1 protein fragments of Bifidobacterium (B.)
longum subsp. longum GT15, namely two FN3 domains (2D FN3) and a C-terminal domain (CD FN3), to bind to
tumor necrosis factor-alpha (TNF-α).

Methods: Fragments of the fn3 gene encoding the 2D FN3 and CD FN3 were cloned in Escherichia (E.) coli. In order
to assess the binding specificity between 2D FN3 and CD FN3 to TNFα, we employed the previously developed
sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied
cytokines. The trRosetta software was used to build 3D models of the FN3.1, 2D FN3, and CD FN3 proteins. The
detection of polymorphism in the amino acid sequences of the studied proteins and the analysis of human gut-
derived bacterial proteins carrying FN3 domains were performed in silico.

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
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