Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium

José D Antonino; Shalini Chaudhary; Mark Lubberts; Brendan J McConkey; Camilla A S Valença; Marcus V de Aragão Batista; Patricia Severino; Marcelo da Costa Mendonça; Eliana B Souto; Silvio S Dolabella; Sona Jain

doi:10.1016/j.jsb.2025.108167

Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium

J Struct Biol. 2025 Jan 5:108167. doi: 10.1016/j.jsb.2025.108167. Online ahead of print.

Affiliations

¹ Departament of Agronomy-Entomology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil.
² Department of Biology, University of Waterloo, Ontario, Canada.
³ Postgraduate Program in Industrial Biotechnology, Tiradentes University, Aracaju, Sergipe, Brazil.
⁴ Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil.
⁵ UCD School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland. Electronic address: eliana.souto@ucd.ie.
⁶ Department of Morphology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil.
⁷ Postgraduate Program in Industrial Biotechnology, Tiradentes University, Aracaju, Sergipe, Brazil; Department of Morphology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil. Electronic address: sonajain24@yahoo.com.

PMID: 39765318
DOI: 10.1016/j.jsb.2025.108167

Abstract

Cry proteins, commonly found in gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and as insect vectors. Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran Anthonomus grandis (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.

Keywords: Cry proteins; Cry8, Phylogenetic analysis; PCR identification; Protein modelling; Soil bacteria.