In silico comparative analysis of Aeromonas Type VI Secretion System

Moriel, Bárbara; Prediger, Karoline de Campos; Souza, Emanuel Maltempi de; Pedrosa, Fábio O.; Picheth, Geraldo; Cruz, Leonardo M.

doi:10.1007/s42770-020-00405-y

Cited by 5 publications

(5 citation statements)

References 71 publications

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“…A phylogenetic analysis performed with SweeP software showed that two strains identified as A. hydrophila (4AK4 and YL17) were misidentified at species level. These findings are in agreement with the studies by Beaz-Hidalgo et al (2015) and Moriel et al (2021) which indicated several problems with the taxonomic affiliation of Aeromonas genomes deposited at the NCBI database. These findings show the relevance of using complete genomes for taxonomy of Aeromonas.…”

Section: Discussionsupporting

confidence: 93%

“…They are components of the T6SS which in addition to virulence plays roles in inter-bacterial competition. T6SS is encoded within gene clusters containing the core genes of the secretion machinery, however, additional copies of hcp and vgrG can be found outside the main cluster ( Cianfanelli et al, 2016 ; Moriel et al, 2021 ), which explains the presence of these genes in two distinct predicted GIs in certain strains ( Supplementary Table 3 ). However, a search in the genome showed that strain AL06-06 does not have the complete T6SS cluster, differently from strains AH10 and KN-Mc-1R2.…”

Section: Discussionmentioning

confidence: 99%

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Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

et al. 2021

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Aeromonas are Gram-negative rods widely distributed in the environment. They can cause severe infections in fish related to financial losses in the fish industry, and are considered opportunistic pathogens of humans causing infections ranging from diarrhea to septicemia. The objective of this study was to determine in silico the contribution of genomic islands to A. hydrophila. The complete genomes of 17 A. hydrophila isolates, which were separated into two phylogenetic groups, were analyzed using a genomic island (GI) predictor. The number of predicted GIs and their characteristics varied among strains. Strains from group 1, which contains mainly fish pathogens, generally have a higher number of predicted GIs, and with larger size, than strains from group 2 constituted by strains recovered from distinct sources. Only a few predicted GIs were shared among them and contained mostly genes from the core genome. Features related to virulence, metabolism, and resistance were found in the predicted GIs, but strains varied in relation to their gene content. In strains from group 1, O Ag biosynthesis clusters OX1 and OX6 were identified, while strains from group 2 each had unique clusters. Metabolic pathways for myo-inositol, L-fucose, sialic acid, and a cluster encoding QueDEC, tgtA5, and proteins related to DNA metabolism were identified in strains of group 1, which share a high number of predicted GIs. No distinctive features of group 2 strains were identified in their predicted GIs, which are more diverse and possibly better represent GIs in this species. However, some strains have several resistance attributes encoded by their predicted GIs. Several predicted GIs encode hypothetical proteins and phage proteins whose functions have not been identified but may contribute to Aeromonas fitness. In summary, features with functions identified on predicted GIs may confer advantages to host colonization and competitiveness in the environment.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

et al. 2021

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“…8B ), which has approximately 120 residues and four conserved motifs. Genes encoding proteins containing the DUF4123 motif are commonly found downstream of vgrG or putative effector-encoding genes ( Moriel et al, 2021 ; Unterweger et al, 2015 ). This domain has been shown to be present in T6SS effector chaperones (TECs) in several bacterial species.…”

Section: Resultsmentioning

confidence: 99%

A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026

Casiano González,

Pacheco Villanueva,

Castro-Alarcón

et al. 2024

PeerJ

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Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75–95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN−) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system. Conclusions The ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026.

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“…Aeromonas septicemia is a bacterial disease that generally occurs in freshwater fish species in tropical waters by an anaerobic, Gram-negative, facultative bacterium called Aeromonas hydrophila. Septicemia, infections, and intra-abdominal or respiratory infections are the other main common symptoms in amphibians and humans [ 2 , 3 , 4 ]. A. hydrophila pathogenicity is multifactorial because the disease is caused by a variety of virulence factors, such as biofilm, various types of secretion systems (II, III, and VI) [ 2 ], cytotoxins, adhesions, hemolysins, proteases, lipases, etc.…”

Section: Introductionmentioning

confidence: 99%

“…Septicemia, infections, and intra-abdominal or respiratory infections are the other main common symptoms in amphibians and humans [ 2 , 3 , 4 ]. A. hydrophila pathogenicity is multifactorial because the disease is caused by a variety of virulence factors, such as biofilm, various types of secretion systems (II, III, and VI) [ 2 ], cytotoxins, adhesions, hemolysins, proteases, lipases, etc. [ 5 , 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Klebsiella pneumoniae Volatile Organic Compounds (VOCs) Protect Artemia salina from Fish Pathogen Aeromonas sp.: A Combined In Vitro, In Vivo, and In Silico Approach

et al. 2023

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Antibiotic resistance is an alarming threat all over the world, and the biofilm formation efficacy of bacteria is making the situation worse. The antagonistic efficacy of Klebsiella pneumoniae against one of the known fish pathogens, Aeromonas sp., is examined in this study. Moreover, Aeromonas sp.’s biofilm formation ability and in vivo pathogenicity on Artemia salina are also justified here. Firstly, six selected bacterial strains were used to obtain antimicrobial compounds against this pathogenic strain. Among those, Klebsiella pneumoniae, another pathogenic bacterium, surprisingly demonstrated remarkable antagonistic activity against Aeromonas sp. in both in vitro and in vivo assays. The biofilm distrusting potentiality of Klebsiella pneumoniae’s cell-free supernatants (CFSs) was likewise found to be around 56%. Furthermore, the volatile compounds of Klebsiella pneumoniae were identified by GC-MS in order to explore compounds with antibacterial efficacy against Aeromonas sp. through an in silico study, where 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) (PDB: 5B7P) was chosen as a target protein for its unique characteristics and pathogenicity. Several volatile compounds, such as oxime- methoxy-phenyl-, fluoren-9-ol, 3,6-dimethoxy-9-(2-phenylethynyl)-, and 2H-indol-2-one, 1,3-dihydro- showed a strong binding affinity, with free energy of −6.7, −7.1, and −6.4 Kcal/mol, respectively, in complexes with the protein MTAN. Moreover, the root-mean-square deviation, solvent-accessible surface area, radius of gyration, root-mean-square fluctuations, and hydrogen bonds were used to ensure the binding stability of the docked complexes in the atomistic simulation. Thus, Klebsiella pneumoniae and its potential compounds can be employed as an alternative to antibiotics for aquaculture, demonstrating their effectiveness in suppressing Aeromonas sp.

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In silico comparative analysis of Aeromonas Type VI Secretion System

Cited by 5 publications

References 71 publications

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026

Klebsiella pneumoniae Volatile Organic Compounds (VOCs) Protect Artemia salina from Fish Pathogen Aeromonas sp.: A Combined In Vitro, In Vivo, and In Silico Approach

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