Biology subjects

Shi, J.-S.

Publications and source records attributed to Shi, J.-S..

4 recordsLinked to original sources

bioRxiv2024

Deep learning-based prediction of enzyme optimal pH and design of point mutations to improve acid resistance

An accurate deep learning predictor of enzyme optimal pH is essential to quantitatively describe how pH influences the enzyme catalytic activity. CatOpt, developed in this study, outperformed existing predictors of enzyme optimal pH (RMSE=0.833 and R2=0.479), and could provide good interpretability with informative residue attention weights. The classification of acidic and alkaline enzymes and prediction of enzyme optimal pH shifts caused by point mutations showcased the capability of CatOpt as an effective computational tool for identifying enzyme pH preferences. Furthermore, a single point mutation designed with the guidance of CatOpt successfully enhanced the activity of Pyrococcus horikoshii diacetylchitobiose deacetylase at low pH (pH=4.5/5.5) by approximately 7%, suggesting that CatOpt is a promising in-silico enzyme design tool for pH-dependent enzyme activities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/623957v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@ff8b46org.highwire.dtl.DTLVardef@110c721org.highwire.dtl.DTLVardef@817014org.highwire.dtl.DTLVardef@1e55d6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Restricted intake of sulfur-containing amino acids reversed the hepatic injury induced by excess Desulfovibrio through gut-liver axis

Gut-liver axis has been a study focus for liver diseases. Diet is a key player in influencing the gut microbiota. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used mouse standard chow and purified diet to mimic two common human dietary patterns: healthy grain and planted-based diet and Western style diet, respectively and explored their impacts on the gut microbiota and liver. Gut microbiota experienced a great shift with notable increase in Desulfovibrio, gut bile acid (BA) concentration elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation due to translocation of toxic lipopolysaccharides (LPS) and hydrophobic BAs from the damaged gut barrier was also observed in mice fed with the chow diet after receiving Desulfovibrio desulfuricans ATCC 29577 (DSV). Restricted intake of sulfur-containing amino acids reversed the liver injury due to excess Desulfovibrio through lowering the gut BA concentration and enhancing the hepatic antioxidant and detoxifying ability. Ex vivo fermentation of human fecal microbiota with primary BAs also demonstrated that DSV enhanced production of secondary BAs. Germ-free mice had higher concentration of both conjugated and unconjugated primary BAs in their gut after receiving DSV.

microbiology↗

bioRxiv2022

Novel insights into L-serine exporters in Corynebacterium glutamicum from gene mining and functional analysis

Amino acid exporters play an important role in regulating amino acid production by Corynebacterium glutamicum, and over 90% of amino acid export is attributed to exporters in this species. ThrE was reported to be an O_SCPLOWLC_SCPLOW-serine exporter, and SerE was identified as an O_SCPLOWLC_SCPLOW-serine exporter in our previous study. However, when both ThrE and SerE were deleted, the O_SCPLOWLC_SCPLOW-serine titer was decreased by 60%, suggesting other O_SCPLOWLC_SCPLOW-serine exporters may exist. In the present study, NCgl0254 and NCgl0255 were identified as novel O_SCPLOWLC_SCPLOW-serine exporters through comparative transcriptomics and gene functional analyses. The contributions of the four exporters (ThrE, SerE, NCgl0254 and NCgl0255) in O_SCPLOWLC_SCPLOW-serine export were studied by gene deletion, gene overexpression, amino acid export assay and real-time quantitative PCR (RT-qPCR). The results showed that SerE is the major O_SCPLOWLC_SCPLOW-serine exporter in C. glutamicum. Fermentation and amino acid export assays of SSAAI, SSAAI-serE-thrE-ncgl0254-ncgl0255 and SSAAI{Delta}serE{Delta}thrE{Delta}ncgl0254{Delta}ncgl0255 indicated that the four O_SCPLOWLC_SCPLOW-serine exporters undertake most of the O_SCPLOWLC_SCPLOW-serine export, and their overexpression enhanced export of O_SCPLOWLC_SCPLOW-serine in SSAAI. When one O_SCPLOWLC_SCPLOW-serine exporter was deleted, the transcription level of the other three exporters was upregulated. However, the decrease in O_SCPLOWLC_SCPLOW-serine titer caused by deletion of one exporter was not fully compensated by upregulation of the other three exporters at the transcription level, indicating that O_SCPLOWLC_SCPLOW-serine production by C. glutamicum may be determined by cooperative efficiency of all four O_SCPLOWLC_SCPLOW-serine exporters, with each being interdependent. IMPORTANCEThis work identified the novel O_SCPLOWLC_SCPLOW-serine exporters NCgl0254 and NCgl0255, and revealed their roles in O_SCPLOWLC_SCPLOW-serine export alongside the O_SCPLOWLC_SCPLOW-serine exporters. All four O_SCPLOWLC_SCPLOW-serine exporters are interdependent and undertake most of the O_SCPLOWLC_SCPLOW-serine export, but SerE is the major O_SCPLOWLC_SCPLOW-serine exporter. The findings expand our knowledge of amino acid exporters in C. glutamicum, and the approach can be employed for exploring of bacterial exporters of unknown function.

bioengineering↗

bioRxiv2019

A Novel L-Serine Exporter and Its Positive Regulator in Corynebacterium glutamicum

Exporters play an essential role in the fermentative production of amino acids. In Corynebacterium glutamicum, ThrE, which can export O_SCPCAPLC_SCPCAP-threonine and O_SCPCAPLC_SCPCAP-serine, is the only identified O_SCPCAPLC_SCPCAP-serine exporter so far. In this study, a novel O_SCPCAPLC_SCPCAP-serine exporter NCgl0580 was identified and characterized in C. glutamicum {Delta}SSAAI (SSAAI), and named as SerE (encoded by serE). Deletion of serE in SSAAI led to a 56.5% decrease in O_SCPCAPLC_SCPCAP-serine titer, whereas overexpression of serE compensated for the lack of serE with respect to O_SCPCAPLC_SCPCAP-serine titer. A fusion protein with SerE and enhanced green fluorescent protein (EGFP) was constructed to confirm that SerE localized at the plasma membrane. The function of SerE was studied by peptide feeding approaches, and the results showed that SerE is a novel exporter for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine in C. glutamicum. Subsequently, the interaction of a known O_SCPCAPLC_SCPCAP-serine exporter ThrE and SerE was studied, and the results suggested that SerE is more important than ThrE in O_SCPCAPLC_SCPCAP-serine export in SSAAI. Probe plasmid and electrophoretic mobility shift assays (EMSA) revealed NCgl0581 as the transcriptional regulator of SerE. Comparative transcriptomics between SSAAI and the NCgl0581 deletion strain showed that NCgl0581 regulated the transcription of 115 genes in C. glutamicum, among which the transcriptional level of NCgl0580 decreased 280-fold in a NCgl0581 deletion strain, indicating that NCgl0581 is a positive regulator of SerE. Thus, this study provides a novel target for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine export engineering as well as a novel global transcriptional regulator NCgl0581 in C. glutamicum.\n\nImportanceExporters are gaining increasing attention for improving industrial production of amino acids. This study identified a novel exporter NCgl0580 for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine in C. glutamicum, and its positive regulator (NCgl0581), which was shown to be a novel global transcriptional regulator in C. glutamicum. This study provides a new target for engineering efflux of O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine, expands the exporter and transcriptional regulator family, and enriches our understanding of amino acid transport system in C. glutamicum.

bioengineering↗