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Integrons are genetic elements able to incorporate, express, and exchange cassettes. Cassette exchanges are mediated by an integrase that excises and reinserts them via site-specific recombination between flanking att sequences. Cassettes lack for the most part a promoter, and their excision and reinsertion at the attI site, downstream a Pc promoter, render them transcriptionally active. This work documents the occurrence of complete integrons or parts of them in Aeromonas and examines the dynamics of these elements. Class 1 integrons linked to antibiotic-resistant cassettes were the most abundant in strains isolated from environmental and clinical samples. Detection of class 2 and 3 integrons was infrequent. Only one report of a class 4-like integron in Aeromonas sp. genomospecies paramedia was found, but a search of these integrons in Aeromonas genomes revealed that class 4-like integrons were the second most abundant after those belonging to class 1. In addition to complete integrons, clusters of attC sites lacking a neighboring integron-integrase (CALINs), single attC sites lacking integron-integrase (SALINs), and orphan integrase genes were found in chromosomes, and a low percentage in Aeromonas plasmids. Concerning the integron behavior, it is known to be regulated by SOS response and could be also controlled by host specific factors.
Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City, Mexico
Everardo Curiel-Quesada*
Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City, Mexico
Abigail Pérez-Valdespino*
Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City, Mexico
*Address all correspondence to: ecqmixcoacdf@gmail.com and valdespino_abigail@hotmail.com
1. Introduction
Integrons are genetic elements that contribute to the adaptability of the bacteria that contain them, since these elements allow bacteria to incorporate, store, express, and exchange gene cassettes through site-specific recombination. Integrons represent bacterial tools to overcome the evolutionary challenge represented by the antibiotic era [1, 2].
Integrons are stable genetic platforms that contain a conserved region composed of the intI gene encoding a site-specific recombinase transcribed from the Pint promoter, an attI recombination site and a divergent promoter(s) cassette (Pc) region adjacent to the integration site and required for the expression of cassettes. Next to this conserved portion, there is a variable region that contains cassette genes, whose expression depends on their proximity to Pc [3]. Cassettes are flanked by attC sites required for their excision and subsequent insertion at the attI site (Figure 1) [1]. Cassettes usually include a single open reading frame (orf); however, bicistronic cassettes (i.e., Bicistronic = having two cistrons, cistron is equivalent to orf) have been reported [4, 5]. The cassettes encode antibiotic resistances, virulence factors, and metabolic functions, and a great diversity of cassettes with unknown function have also been documented [2, 6, 7].
Figure 1.
Integron structure and function. Integron platform includes the intI (blue), the pc, and pint promoters (black thin arrows), as well an attI site (yellow). Cassettes (green and orange) are inserted in the variable region by the integrase through the attC site (gray). The direction of the arrows indicates the direction of the gene expression.
Integron-integrase is a member of the tyrosine recombinase family; it is a tetrameric protein that can recombine nucleotide sequences of low similarity and recognizes the att sites as a substrate. Three recombination reactions have been established: attI × attC, attC × attC, and attI × attI. The intI gene is under the control of the Pint promoter, which is subject to regulation and is independent of Pc [8]. The attI site is composed of two integrase binding sites, designated R and L; the recombination point is the GTT triplet located within the R box. It may also contain two imperfect direct repeats, DR1 and DR2, upstream of the L boxes and R, which improve but are not essential for recombination [1]. The attC sites are imperfect palindromic sequences of 55 to 141 bp, which contain two pairs of complementary motifs R´-L´ and R”-L” at the ends, that allow the formation of a hairpin structure, which is essential for recognition by the integrase [9].
Cassettes are reordering mobilizable elements by excision events via recombination between two consecutive attC sites, followed by integration in the attI site. However, the cassettes can also be integrated into attG sites (5’GWT3’), resulting in the clusters of attC sites lacking a neighboring integron-integrase (CALINs) and single attC site lacking integron-integrase (SALINs) [10].
Integrons are classified into classes 1 to 5 based on the sequences of their associated integrases; however, multiple unclassified integron-integrase have been described, questioning the initial classification system [11, 12]. Other classification schemes based on phylogeny analyses of the nucleotide sequenced intI genes complemented with genetic structure, environmental distribution, and taxonomic affiliation of the host exist: this is the marine γ-proteobacteria group, the soil/freshwater proteobacteria group, and the inverted integrase group [13, 14]. Nonetheless, integrons continue being grouped in classes 1 to 5 in the literature.
When integrons are associated with mobile genetic elements that guarantee their dissemination, such as transposons or plasmids, they are regarded as mobile integrons. If these elements are sedentary, they are chromosomal integrons. Integrons that contain a large number of cassettes in their variable region are called superintegrons [15].
2. Frequency and distribution of integrons in Aeromonas
The genus Aeromonas belongs to the Aeromonadaceae family, Aeromonadales order, and Gammaproteobacteria class. This genus comprises 36 species [16]. However, a new specie Aeromonas sp. genomoespecies paramedia have been suggested [4, 17]. Bacteria comprising the genus Aeromonas are non-spore-forming, Gram-negative bacilli, halophilic, facultative anaerobes, and they have a ubiquitous and cosmopolitan distribution since these bacteria have the ability to colonize different niches [18].
Aeromonas possess a complex mobilome including different genetic elements like plasmids, transposons, integrons, and phages, which probably resulted in the plasticity of their genomes [19, 20].
The presence of integrons has been well documented. Ninety-three complete reports of these elements in Aeromonas isolates from different regions and sources have been describe between 2001 and 2023 at National Center for Biotechnology Information (NCBI) [5, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111]. The detection of Aeromonas strains harboring integrons has been recorded in 34 countries on 5 continents (Figure 2); however, it is important to highlight that in some regions of Africa and Central America, there are no reports of the presence of integrons in these bacteria, despite the fact that both are indicators of fecal and anthropogenic contamination [112, 113, 114, 115]. In fact, these areas are low-income countries where very few resources are available for research [116].
Figure 2.
Distribution and frequency of integrons in Aeromonas genus. (A) Worldwide distribution of Aeromonas strains bearing integrons. (B) Source and type of sample collected for the isolation of Aeromonas spp. (C) Integrons class incidence. (D) Prevalence of cassettes and functions encoded in cassettes in the first position of integrons. Percentage in the graphs is the proportion of the literature reports [5, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111].
The search for integron-bearing Aeromonas strains includes samples from aquatic animals, water, sediments, sewage, food, clinics, livestock, and poultry. The reports that are used in this manuscript to estimate the distribution of integrons include studies that have determined the cassette array by PCR amplification of the integrase and gene cassettes with specific primers, nucleotide sequence, and restriction analysis with PCR amplicons. Only few reports involving whole genome sequencing to elucidate the presence of these elements have been issued. Class 1 integrons are described as the most prevalent and the most frequently linked to antibiotic resistance in Aeromonas species isolated from different samples and different countries. Class 2 integrons are second in abundance, and class 3 integrons have the lowest prevalence (Figure 2) [5, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111]. Only one report of a new class 4-like integron has been published [4].
The Aeromonas species linked to integrons are A. hydrophila, A. veronii, A. caviae, A. media, A. salmonicida, A. encheleia, A. bestiarum, A. sobria, A. eucrenophila, A. jandaei, A. bivalvium, A. saranelli, A. taiwanensis, A. enteropelogenes, A. dhakensis, A. fluvialis, Aeromonas sp. genomospecies paramedia, and Aeromonas sp. [5, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111]. In a wide number of reports, the species identification was not accurate, as they were identified by biochemical tests or only by 16S rRNA gene sequencing [16]. There are few reports in which a concatenated analysis of gyr and rpo gene sequences was carried out; however, a more accurate identification through a multilocus analysis of genes from 2 to 7 housekeeping genes has been suggested [117, 118].
Cassettes comprise the variable region of integrons and sometimes are absent from these structures (empty integron). Multiple cassettes may be inserted into the same integron to create a cassette array, and numerous combinations of gene cassettes have been reported. Although more than 300 cassette arrays have been described, less than 10 array compositions prevail in class 1 integrons [2, 119]. Aeromonas reports have shown cassette variants that mainly confer resistance to antibiotics as aminoglycosides, β-lactamics, chloramphenicol, trimethoprim, quaternary ammonium compounds, rifampicin, lincomycin, fosfomycin, and quinolones. In addition, gene cassettes with unknown function (gcu) and scarce reports of cassettes with other functions like lpt (lipoprotein) [4], dcyA (gene putatively involved in cell signaling) [71], and nitI (Txe/YoeB family addiction module toxin) (INTEGRALL database) have been described. The most abundant cassettes in the Aeromonas arrangements are variants of aacA (aminoglycoside 6′ acetyltransferases), bla (b-lactamases), aadA (aminoglycoside 3′ adenylyltransferases), and dfr (dihyrofolate reductases) (Figure 2, Table 1). It is fundamental to note that these genes and similar cassette arrangement have been described in other Gram-negative bacteria as Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Pseudomonas aeruginosa, Acinetobacter baumannii, Serratia marcescens, and others from diverse environments and geographical locations [120, 121, 122, 123, 124, 125].
Integrons are estimated to be present in at least 6% of the bacterial genomes [126, 127]. The INTEGRALL database (http://integrall.bio.ua.pt) was developed in order to provide an access to integron DNA sequences [128]; its database contains 277 descriptions of integrase 1, 2, 3 and cassettes in Aeromonas genus (Data extraction was performed on 2024-2102-20). To complete this analysis, integron finder v.2.0.2 (available at https://github.com/gem-pasteur/Integron_Finder), which is a bioinformatic tool to identify integrons and their most distinctive components—the integron-integrase, the attC sites, promoters, and attI site—was used [129]. A data set of 695 genomes of Aeromonas from NCBI (with high-quality chromosomal-level genome assembly) were analyzed through integron finder. This data set reflected the presence of integron components in 73% (N = 505) of the studied genomes, which corresponded to 234 complete integrons, 198 CALINs, 600 SALINs, and 53 orphan integrases. Remarkably, SALINs were more abundant than other components. The presence of CALINs and SALINs is the result of the integration of cassettes into bacterial genomes at specific attG recombination sites that are very abundant in the genomes [10].
Amino acid sequences of integrases were used for the phylogenetic analysis, which was performed using the Maximum Likelihood with MEGA 11.0.13 software [130]. The resulting phylogenetic tree was displayed with iTol V 6.8:1 [131]. Of the 287 integrases identified, 89.5% (N = 227) belong to class 1, 10% (N = 29) belong to class 4-like, and 0.5% (N = 1) belong to class 2. Class 3 integrases were not detected in the genome analysis (Figure 3). Interestingly, while the literature reports the presence of class 2 and 3 integrons in some Aeromonas isolates, in this analysis, class 2 and 3 were scarce, and class 4-like integrases were abundant. Also, the number of CALINs was surprisingly high, these arrangements of cassettes bear two to seven cassettes associated to antibiotic resistance, toxin-antitoxin systems, metabolic enzymes, antiphage genes, insertion sequences, and hypothetical proteins.
Figure 3.
Phylogenetic relationships among IntI integrases in Aeromonas. This tree was constructed using amino acid sequences recovered from annotated as integron-integrases in Aeromonas genomes in NCBI database and reference sequences (IntI1, IntI2, IntI3, IntI4 and IntI5 sequences). The colors indicate the sequence class.
Most integron reports attribute the dissemination of this element to horizontal genetic transfer (HGT) mediated by mobile elements like plasmids. However, Cury et al. [126] found that only 24 integrons were associated to plasmids among the 2006 plasmids of complete genomes of different bacterial taxa. Using integron finder, we analyzed the plasmidome of the Aeromonas strains at the PLSDB plasmid database v. 2023_11_03_v2 (Data extraction was performed on 2024-2102-20) [132]. Analysis of 462 Aeromonas plasmids revealed that 80% (N = 369) of plasmids did not carry integrons, 17% (N = 78) carried complete integrons, 4% (N = 20) had single orphan integron-integrase, 2.4% (N = 11) contained CALINs, and 5.4% (N = 25) showed SALINs. Plasmids bearing integrons were primarily distributed in A. caviae, A. hydrophila, and A. salmonicida.
Aeromonas conjugative plasmids like pAr32, pRAS1, pASOT, pFBATO6, pSN254, pASA8, and paASA5 bearing integrons enclosed in transposons to guarantee their propagation [54, 68, 89, 101]. However, clearly, the integron propagation depends not only on HGT but also on clonal or vertical dissemination [133, 134] since most conjugative or mobilizable plasmids of Aeromonas do not have integrons [41, 135].
Cassette rearrangements depend on the integrase activity; excised genes move to other positions in the variable region via covalently closed circular intermediaries [9]. The activity of integrases IntI1 e IntI4 (IntIA) is often regulated by the SOS response via the transcriptional regulator LexA. intI1 and intIA genes contain a lexA box adjacent to −10-promoter region. LexA binds to this box repressing the transcription. Different DNA damaging agents, including mutagens and different antibiotics, lead to the formation of single-stranded DNA, which in turn activates the RecA protein. RecA induces autoproteolysis of LexA, allowing expression of the integrase [14, 136]. However, the regulation of integrase by the SOS response is a highly conserved feature in integrons of class 1 and class 4 in Escherichia coli and Vibrio cholerae [137, 138, 139] but not in Aeromonas spp. A class 1 integron with the same cassette arrangement (dfrA12-orfF-aadA12) in a strain named A. dhakensis 3430-1 and another of A. hydrophila 6479 exhibited a different behavior in response to the presence of streptomycin. The intI1 and recA genes presented an increase in its expression induced by antibiotics in response to SOS in 6479 strains, but this did not occur in 3430-1; consequently, the host has factors that influence integrase expression differently [140].
Control of integron-integrase expression is host-dependent [3]. A recent description of a functional class 4-like integron in Aeromonas sp. genomospecies paramedia showed constitutive expression of the intI4-like gene, independent from SOS response in presence of streptomycin and mitomycin, despite containing a lexA box adjacent to the intI4-like promoter [4]. When this integron was mobilized to E. coli, it showed a clear dependence on SOS response (unpublished data).
cAMP-CRP complex is a global regulator, composed of the catabolite gene activator protein and cyclic adenosine monophosphate (cAMP). cAMP-CRP is involved in the regulation of integrases in Vibrio cholerae through glucose starvation, which depends on the intracellular concentration of cAMP [138]. A CRP box associated to catabolite repression was detected in a class 4-like integron, but no changes were detected in intI4-like expression in cells grown in the presence of arabinose or glucose [4], which indicates that integrase expression is not under catabolic repression in this strain. More work would be necessary to extend our understanding of the mechanisms controlling the dynamics of integrons in Aeromonas.
Most of the descriptive studies of integrons focus on the identification of the integrases involved and the arrangement of cassettes at the variable region; by this reason, we have a great deal of knowledge on the distribution of antibiotic-resistant genes in these genetic elements. Class 1 integrons linked to antibiotic resistance were the most abundant in Aeromonas species, and they are located mainly in the chromosome. In-depth understanding of the diversity of integron-integrase in Aeromonas by in-silico analysis and the distribution of integrases of class 2 and 3, as well as the description of new integrases in the Aeromonas genus will be necessary. CALINs and SALINs showed high incidence in Aeromonas genomes; therefore, it would be interesting to elucidate their function. Few studies exist where the functionalities of integrons and cassettes have been proved. A detailed investigation of integron behavior, including the regulation of integrase expression and the participation of host factors in different Aeromonas species, has to be undertaken in order to improve our comprehension of these elements.
R.R.R is a graduate CONACYT scholarship recipient. E.C.Q is a COFAA, EDI and SNI fellow. A.P.V is SNI and EDI fellow. This work was supported by Instituto Politécnico Nacional SIP grants 20231278, 20231290, 20241238 and 20241209.
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Written By
Rogelio Rojas-Rios, Everardo Curiel-Quesada and Abigail Pérez-Valdespino
Submitted: 23 February 2024Reviewed: 28 March 2024Published: 13 June 2024
Open access peer-reviewed chapter - ONLINE FIRST
