Protein Model and Function Analysis in Quorum-Sensing Pathway of Vibrio qinghaiensis sp.-Q67

Abstract

Bioluminescent bacteria are mainly found in marine habitats. Vibrio qinghaiensis sp.-Q67 (Q67), a nonpathogenic freshwater bacterium, has been a focus due to its wide use in the monitoring of environmental pollution and the assessment of toxicity. However, the lack of available crystal structures limits the elucidation of the structures of the functional proteins of the quorum-sensing (QS) system that regulates bacterial luminescence in Q67. In this study, 19 functional proteins were built through monomer and oligomer modeling based on their coding proteins in the QS system of Q67 using MODELLER. Except for the failure to construct LuxM due to the lack of a suitable template, 18 functional proteins were successfully constructed. Furthermore, the relationships between the function and predicted structures of 19 functional proteins were explored one by one according to the three functional classifications: autoinducer synthases and receptors, signal transmission proteins (phosphotransferases, an RNA chaperone, and a transcriptional regulator), and enzymes involved in bacterial bioluminescence reactions. This is the first analysis of the whole process of bioluminescence regulation from the perspective of nonpathogenic freshwater bacteria at the molecular level. It provides a theoretical basis for the explanation of applications of Q67 in which luminescent inhibition is used as the endpoint.

BDE-99 Disrupts the Photoreceptor Patterning of Zebrafish Larvae via Transcription Factor six7

“…Molecular docking was then performed using AutoDock Vina to predict the binding modes and affinity of three components [BDE-99, T3, and all-trans retinoic acid (RA)] with THRβ with the settings as previously described. 38 Statistical Analysis. All the data were presented as the mean ± standard error of the mean (SEM).…”

“…Based on the NCBI reference sequence (NP_571415.1), homology modeling of THRβ [Danio rerio] was constructed and optimized using the online Swiss modeler server (). Molecular docking was then performed using AutoDock Vina to predict the binding modes and affinity of three components [BDE-99, T3, and all- trans retinoic acid (RA)] with THRβ with the settings as previously described …”

Application of Luminescent Bacteria Bioassay in the Detection of Pollutants in Soil

“…This standard is applicable to the detection of acute toxicity in industrial wastewater, wastewater receiving water bodies, and soluble chemicals under experimental conditions. There is no standard that uses Vibrio qinghaiensis, but Vibrio qinghaiensis shows a great advantage in testing as freshwater bacteria [38]. The three luminescent bacteria are applied in different conditions [39][40][41], as shown in Table 1.…”

Similarities and Differences in Quorum Sensing-Controlled Bioluminescence between Photobacterium phosphoreum T3 and Vibrio qinghaiensis sp.-Q67

“…Compared with the well-characterized QS systems in V. fischeri and V. harveyi, few studies have shown firm conclusions about whether the luminescence of T3 and Q67 are controlled by QS systems. Based on protein modeling and function analysis on the Q67 strain, Wang et al constructed 18 monomer models for functional proteins potentially involved in QS and bioluminescence to explore how the QS system controlled bioluminescence [12]. However, no clear evidence about the mechanism of bioluminescence in the T3 and Q67 strains has been determined experimentally.…”