Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

Abstract

Background Vibrio parahaemolyticus causes serious seafood-borne gastroenteritis and death in humans. Raw seafood is often subjected to post-harvest processing and low-temperature storage. To date, very little information is available regarding the biological functions of cold shock proteins (CSPs) in the low-temperature survival of the bacterium. In this study, we determined the complete genome sequence of V. parahaemolyticus CHN25 (serotype: O5:KUT). The two main CSP-encoding genes (VpacspA and VpacspD) were deleted from the bacterial genome, and comparative transcriptomic analysis between the mutant and wild-type strains was performed to dissect the possible molecular mechanisms that underlie low-temperature adaptation by V. parahaemolyticus.ResultsThe 5,443,401-bp V. parahaemolyticus CHN25 genome (45.2% G + C) consisted of two circular chromosomes and three plasmids with 4,724 predicted protein-encoding genes. One dual-gene and two single-gene deletion mutants were generated for VpacspA and VpacspD by homologous recombination. The growth of the ΔVpacspA mutant was strongly inhibited at 10 °C, whereas the VpacspD gene deletion strongly stimulated bacterial growth at this low temperature compared with the wild-type strain. The complementary phenotypes were observed in the reverse mutants (ΔVpacspA-com, and ΔVpacspD-com). The transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 were significantly altered in the ΔVpacspA mutant when it was grown at 10 °C. These included genes that were involved in amino acid degradation, secretion systems, sulphur metabolism and glycerophospholipid metabolism along with ATP-binding cassette transporters. However, a low temperature elicited significant expression changes for 10.0% of the genes in the ΔVpacspD mutant, including those involved in the phosphotransferase system and in the metabolism of nitrogen and amino acids. The major metabolic pathways that were altered by the dual-gene deletion mutant (ΔVpacspAD) radically differed from those that were altered by single-gene mutants. Comparison of the transcriptome profiles further revealed numerous differentially expressed genes that were shared among the three mutants and regulators that were specifically, coordinately or antagonistically modulated by VpaCspA and VpaCspD. Our data also revealed several possible molecular coping strategies for low-temperature adaptation by the bacterium.ConclusionsThis study is the first to describe the complete genome sequence of V. parahaemolyticus (serotype: O5:KUT). The gene deletions, complementary insertions, and comparative transcriptomics demonstrate that VpaCspA is a primary CSP in the bacterium, while VpaCspD functions as a growth inhibitor at 10 °C. These results have improved our understanding of the genetic basis for low-temperature survival by the most common seafood-borne pathogen worldwide.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3784-5) contains supplementary material, which is available to a...

Cold Tolerance Regulated by the Pyruvate Metabolism in Vibrio parahaemolyticus

“…The ABC transporter proteins, also known as highly conserved in ATP-binding sites proteins (Higgins et al, 1986), are found in all domains of life, and are mainly involved in the uptake of nutrients and micronutrients, extrusion of building blocks, and drug resistance by exporting certain toxic substances outside of the cell (Cuthbertson et al, 2010; Locher, 2016). Similar to the present findings, ABC transporters were found to be significantly inhibited in V. parahaemolyticus isolates with a mutation in the CSP gene cspA to compensate for the deficiency and protect the bacterium from low temperature induced damage (Zhu et al, 2017). Another report showed that V. parahaemolyticus ABC transporters demonstrated notable variation in response to acid and toxicity stress (Nydam et al, 2014; Sun et al, 2014).…”

Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis

“…Selected salt resistance-associated genes were validated by qRT-PCR assay as described previously (Sun et al 2014;Zhu et al 2017). L. plantarum D31 and T9 strains were incubated in the MRS medium supplemented with 8% and 5% NaCl, respectively, and cell culture grown to logarithmic growth phase was harvested by centrifugation as described above.…”

“…A 20-μl reaction volume contained 10 μl TB Premix Ex TaqTM II, 0.4 μl of each of the oligonucleotide primers (10 μmol), 0.4 μl of ROX Reference DyeII, 2 μl of cDNA template, and appropriate volume of sterile DNase/RNase-Free deionized water. All RT-PCR reactions were performed in a 7500 Fast Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) under the following conditions: initial denaturation at 95°C for 10 min, followed by 40 cycles of denaturation at 95°C for 15 s, and primer annealing at 60°C for 60 s. The 16S rRNA gene was used as the reference gene, as previously described (Zhu et al 2017). The expression of the 16S rRNA gene in L. plantarum D31 and T9 strains grown to the logarithmic growth phase in MRS medium supplemented with no NaCl was used as a reference/baseline, respectively.…”

Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25

“…In our prior studies, V. parahaemolyticus CHN25 strain (serotype: O5:KUT) was isolated, identified, and characterized ( Song et al., 2013 ; Sun et al., 2014 ; He et al., 2015 ; Zhu et al., 2017 ). The complete genome sequence of V. parahaemolyticus CHN25 contains 5,443,401 bp with 45.2% G+C content ( Zhu et al., 2017 ). Comparative genomic analysis revealed five prophage gene clusters in V. parahaemolyticus CHN25.…”