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Protein signatures to identify the different genera within the Xanthomonadaceae family

  • Bacterial Fungal and Virus Molecular Biology - Research Paper
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Abstract

The Xanthomonadaceae family comprises the genera Xanthomonas and Xylella, which include plant pathogenic species that affect economically important crops. The family also includes the plant growth-promoting bacteria Pseudomonas geniculata and Stenotrophomonas rhizophila, and some other species with biotechnological, medical, and environmental relevance. Previous work identified molecular signatures that helped to understand the evolutionary placement of this family within gamma-proteobacteria. In the present study, we investigated whether insertions identified in highly conserved proteins may also be used as molecular markers for taxonomic classification and identification of members within the Xanthomonadaceae family. Four housekeeping proteins (DNA repair and replication-related and protein translation enzymes) were selected. The insertions allowed discriminating phytopathogenic and plant growth-promoting groups within this family, and also amino acid sequences of these insertions allowed distinguishing different genera and, eventually, species as well as pathovars. Moreover, insertions in the proteins MutS and DNA polymerase III (subunit alpha) are conserved in Xylella fastidiosa, but signatures in DNA ligase NAD-dependent and Valyl tRNA synthetase distinguish particular subspecies within the genus. The genus Stenotrophomonas and Pseudomonas geniculata could be distinguishable based on the insertions in MutS, DNA polymerase III (subunit alpha), and Valyl tRNA synthetase, although insertion in DNA ligase NAD-dependent discriminates these bacteria at the species level. All these insertions differentiate species and pathovars within Xanthomonas. Thus, the insertions presented support evolutionary demarcation within Xanthomonadaceae and provide tools for the fast identification in the field of these bacteria with agricultural, environmental, and economic relevance.

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Funding

The work of CFMM is supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, Grant no. 2019/19435-3), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Ensino Superior, Funding Code 001), and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Grant no. 308868/2018-8), Brazil.

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Authors and Affiliations

  1. Centre of Studies for Industrial Biotechnology (CEBI), Faculty of Natural and Exact Sciences, University of Oriente, Ave. Patricio Lumumba s/n., Reparto Jiménez, CP 90500, Santiago de Cuba, Cuba

    Ania Margarita Cutiño-Jiménez

  2. Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, SP, 05508-000, Brazil

    Carlos Frederico Martins Menck

  3. Department of Biology and Geography, Faculty of Natural and Exact Sciences, University of Oriente, Ave. Patricio Lumumba s/n., Reparto Jiménez, CP 90500, Santiago de Cuba, Cuba

    Yusdiel Torres Cambas

  4. Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA

    Juan Carlos Díaz-Pérez

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  1. Ania Margarita Cutiño-Jiménez
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Correspondence to Ania Margarita Cutiño-Jiménez.

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Cutiño-Jiménez, A.M., Menck, C.F.M., Cambas, Y.T. et al. Protein signatures to identify the different genera within the Xanthomonadaceae family. Braz J Microbiol 51, 1515–1526 (2020). https://doi.org/10.1007/s42770-020-00304-2

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