Analysis of CRISPR-Cas loci distribution in Xanthomonas citri and its possible control by the quorum sensing system

Author(s)

Martins, Paula Maria Moreira ; Granato, Lais Moreira ; Morgan, Tulio ; Nalin, Julia Lopes ; Takita, Marco Aurelio ; Alfenas-Zerbini, Poliane ; de Souza, Alessandra Alves

• Document type: Journal article
• Source: FEMS Microbiology Letters; v. 371, p. 10-pg., 2024-02-14.

Abstract

Xanthomonas is an important genus of plant-associated bacteria that causes significant yield losses of economically important crops worldwide. Different approaches have assessed genetic diversity and evolutionary interrelationships among the Xanthomonas species. However, information from clustered regularly interspaced short palindromic repeats (CRISPRs) has yet to be explored. In this work, we analyzed the architecture of CRISPR-Cas loci and presented a sequence similarity-based clustering of conserved Cas proteins in different species of Xanthomonas. Although absent in many investigated genomes, Xanthomonas harbors subtype I-C and I-F CRISPR-Cas systems. The most represented species, Xanthomonas citri, presents a great diversity of genome sequences with an uneven distribution of the CRISPR-Cas systems among the subspecies/pathovars. Only X. citri subsp. citri and X. citri pv. punicae have these systems, exclusively of subtype I-C system. Moreover, the most likely targets of the X. citri CRISPR spacers are viruses (phages). At the same time, few are plasmids, indicating that CRISPR/Cas system is possibly a mechanism to control the invasion of foreign DNA. We also showed in X. citri susbp. citri that the cas genes are regulated by the diffusible signal factor, the quorum sensing (QS) signal molecule, according to cell density increases, and under environmental stress like starvation. These results suggest that the regulation of CRISPR-Cas by QS occurs to activate the gene expression only during phage infection or due to environmental stresses, avoiding a possible reduction in fitness. Although more studies are needed, CRISPR-Cas systems may have been selected in the Xanthomonas genus throughout evolution, according to the cost-benefit of protecting against biological threats and fitness maintenance in challenging conditions. The presence and distribution of clustered regularly interspaced short palindromic repeat-associated sequence loci in Xanthomonas, with potencial regulatation by the quorum sensing mechanism. (AU)

• FAPESP's process: 20/07045-3 - Biotechnological and genomic strategies for quality, productivity and sustainable management of citrus, coffee and sugar cane in the State of São Paulo
• Grantee: Mariângela Cristofani-Yaly
• Support Opportunities: Research Grants - Problem-Oriented Research Centers in São Paulo
• FAPESP's process: 16/01273-9 - Toxin-antitoxin systems in Xanthomonas citri subsp citri: function and strategy for programmed cell death induction
• Grantee: Paula Maria Moreira Martins
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 13/10957-0 - Xylella fastidiosa-vector-host plant interaction and approaches for citrus variegated chlorosis and citrus canker control
• Grantee: Alessandra Alves de Souza
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 14/50880-0 - INCT 2014: comparative and functional genomics and citrus-assisted breeding
• Grantee: Marcos Antonio Machado
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 19/01901-8 - Gene silecing of citrus floema: modulation of infection hypersensitivity by Candidatus liberibacter spp
• Grantee: Laís Moreira Granato
• Support Opportunities: Scholarships in Brazil - Post-Doctoral