In silico comparative analysis of Aeromonas Type VI Secretion System

Abstract

Aeromonas are bacteria broadly spread in the environment, particularly in aquatic habitats and can induce human infections. Several virulence factors have been described associated with bacterial pathogenicity, such as the Type VI Secretion System (T6SS). This system translocates effector proteins into target cells through a bacteriophage-like contractile structure encoded by tss genes. Here, a total of 446 Aeromonas genome sequences were screened for T6SS and the proteins subjected to in silico analysis. The T6SS-encoding locus was detected in 243 genomes and its genes are encoded in a cluster containing 13 core and 5 accessory genes, in highly conserved synteny. The amino acid residues identity of T6SS proteins ranges from 78 to 98.8%. In most strains, a pair of tssD and tssI is located upstream the cluster (tssD-2, tssI-2) and another pair was detected distant from the cluster (tssD-1, tssI-1). Significant variability was seen in TssI (VgrG) C-terminal region, which was sorted in four groups based on its sequence length and protein domains. TssI containing ADP-ribosyltransferase domain are associated exclusively with TssI-1, while genes coding proteins carrying DUF4123 (a conserved domain of unknown function) were observed downstream tssI-1 or tssI-2 and escort of possible effector proteins. Genes coding proteins containing DUF1910 and DUF1911 domains were located only downstream tssI-2 and might represent a pair of toxin/immunity proteins. Nearly all strains display downstream tssI-3, that codes for a lysozyme family domain protein. These data reveal that Aeromonas T6SS cluster synteny is conserved and the low identity observed for some genes might be due to species heterogeneity or its niche/functionality.

Keywords: Aeromonas; Comparative genomic analysis; Type VI Secretion System; tss genes.

Fig. 1

T6SS gene cluster synteny in Aeromonas. On the left are indicated the names of strains analyzed; for draft genome sequences, the contig containing T6SS cluster is indicated within brackets; the T6SS gene names are shown at the top and homolog genes in Aeromonas genomes represented by squares at the correspondent column; the cluster structure is based on RAST annotation followed by manual curation of tssD, tssI, tssL, PAAR, and conserved hypothetical genes; only amino acid sequences containing phage late D protein (GPD) domain were considered TssI; T6SS-associated genes located outside the cluster were not considered. The number sign indicates gene coding for PAAR domain–containing protein

Fig. 2

Boxplot of identities (%) in the TSS6 proteins. The boxplot represents the identity percentage median of the amino acid sequences of the T6SS components. The number sign indicates gene coding for PAAR domain–containing protein

Fig. 3

Conservation in amino acid sequences of T6SS components. Numbers below gene boxes are amino acid identity percentages from a multiple sequence alignment including all homologs of each protein. hypot. = hypothetical protein. The number sign indicates gene coding for PAAR domain–containing protein

Fig. 4

Classification and distribution of T6SS structural protein TssI among Aeromonas strains. The VI_Rhs_Vgr domain includes the phage late gene D protein (GPD) domain; TssI was classified through group A to D according to amino acids sequence, length, and presence of protein family domains; the number of sequences of each TssI type according to tssI genomic location is also indicated. Seven draft genomes (A. bivalvium CECT 7113, A. caviae FDAARGOS_72, A. hydrophila 187, A. simiae CIP 107798, A. sobria CECT 4245, A. veronii AMC34, A. veronii Hm21) were not considered for the TssI distribution analysis since it was not possible to identify sequences of TssI-1 and TssI-2

Fig. 5

TssI paralog copies of coding sequences and its genomic neighborhood. The first column represents each TssI paralog–encoding gene, regarding its genomic position to the main cluster; the second column show protein-coding genes found upstream tssD; the third column indicates the TssI-coding gene group classification (from A to D) according to amino acids sequence, length, and presence of protein family domains; the fourth column represents the protein families codified downstream of tssI

Fig. 6

Aeromonas T6SS gene cluster and associated protein-coding genes. The protein-coding genes organization is shown in Aeromonas spp. genomes as columns; for tss genes, the number of copies are indicated and the tssI group classification is represented as the color code: type A, type B, type C, and type D; protein-coding genes upstream and downstream are also indicated, relative to tss cluster or tssDI copies. The number sign indicates gene coding for PAAR domain–containing protein