Antequera-Zambrano Laura, Parra-Sánchez Ángel, González-Paz Lenin, Fernandez Eduardo, Martinez-Navarrete Gema
Genetics and Molecular Biology Laboratory, Biology Department, Universidad of Zulia, Maracaibo 4001, Venezuela.
Bioengineering Institute, University Miguel Hernández of Elche, 03202 Elche, Spain.
Microorganisms. 2025 Jun 6;13(6):1321. doi: 10.3390/microorganisms13061321.
The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material-reflected in the higher complexity and diversity of CRISPR loci in Archaea-and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures.
CRISPR-Cas系统是一种在多种古菌和细菌中发现的适应性免疫机制，使它们能够抵御病毒和质粒等入侵的遗传元件。尽管其分布广泛，但CRISPR-Cas系统在这些领域中的流行程度和复杂性存在显著差异。本研究旨在表征和比较30个古菌基因组和30个细菌基因组中CRISPR-Cas系统以及相关抗生素抗性基因的基因组分布、结构特征和功能意义。通过对CRISPR阵列、基因结构、直接重复序列（DR）和热力学性质的生物信息学分析，我们观察到古菌中CRISPR位点的数量更多且复杂性更高，具有更多仅属于1类的不同cas基因亚型。相比之下，细菌中的CRISPR位点较少，包括1类和2类系统的混合，其中1类占检测到的系统的大多数（约75%）。值得注意的是，缺乏CRISPR-Cas系统的细菌中抗生素抗性基因的流行率更高，这表明这些免疫系统的存在与此类基因的获得之间可能存在负相关。系统发育和热力学分析进一步突出了特定领域的适应性和保守模式。这些发现支持了CRISPR-Cas系统发挥双重作用的假设：第一，作为一种防御机制，防止外来遗传物质的整合——这体现在古菌中CRISPR位点的更高复杂性和多样性上；第二，作为水平基因转移的调节因子，这在具有活跃CRISPR-Cas系统的生物体中抗生素抗性基因的较低频率中得到证明。总之，这些结果强调了CRISPR-Cas系统在应对环境和选择压力时的进化和功能多样化。
