Comparative transcriptomic analysis reveals novel genes and regulatory mechanisms of Tetragenococcus halophilus in response to salt stress

Insight into the mechanisms of combined toxicity of cadmium and flotation agents in luminescent bacteria: Role of micro/nano particles

Currently, risk assessment and pollution management in mines primarily focus on toxic metals, with the flotation agents being overlooked. However, the combined effects of metals and flotation agents in mines remain largely unknown. Therefore, this study aimed to evaluate the combined effects of Cd and two organic flotation agents (ethyl xanthate (EX) and diethyldithiocarbamate (DDTC)), and the associated mechanisms. The results showed that Cd + EX and Cd + DDTC exhibited synergistic toxicity. The EC50 values for luminescent bacteria were 1.6 mg/L and 1.0 mg/L at toxicity unit ratios of 0.3 and 1, respectively. The synergistic effects were closely related with the formation of Cd(EX)2 and Cd(DDTC)2 micro/nano particles, with nano-particles exhibiting higher toxicity. We observed severe cell membrane damage and cell shrinkage of the luminescent bacteria, which were probably caused by secondary harm to cells through the released CS2 during their decomposition inside cells. In addition, these particles induced toxicity by altering cellular levels of biochemical markers and the transcriptional levels of transport proteins and lipoproteins, leading to cell membrane impairment and DNA damage. This study has demonstrated that particulates formed by Cd and flotation agents contribute to the majority of the toxicity of the binary mixture. This study helps to better understand the complex ecological risk of inorganic metals and organic flotation agents in realistic mining environments.

Effect and potential mechanism of nitrite reductase B on nitrite degradation by Limosilactobacillus fermentum RC4

Nitrite has the potential risk of hypoxic poisoning or cancer in pickled food. In our previous study, Limosilactobacillus fermentum (L. fermentum) RC4 is effective in nitrite degradation by producing nitrite reductase B (NirB). To investigate the detailed mechanism from the genome, response, and regulation of NirB, the whole-genome sequence of L. fermentum RC4 was analyzed, the L. fermentum-EGFP-nirB with enhanced green fluorescent protein (EGFP) labeled the nitrite reductase large subunit nirB, and the recombined L. fermentum-NirB with overexpression NirB strain was conducted. The key genes within the dominant metabolism pathways may be involved in stress tolerance to regulate the degrading process. The green fluorescence density of EGFP indicated that NirB activity has a threshold and peaked under 300 mg/L nitrite concentration. NirB overexpressed in L. fermentum RC4 boosted the enzyme activity by 39.6% and the degradation rate by 10.5%, when fermented in 300 mg/L for 40 h, compared to the control group. RNA-seq detected 248 differential genes mainly enriched in carbohydrate, amino acid, and energy metabolism. The ackA gene for pyruvate metabolism and the mtnN gene for cysteine metabolism were up-regulated. NirB regulates these genes to produce acid and improve stress resistance for L. fermentum RC4 to accelerate nitrite degradation.

Genome-wide transcriptome profiling reveals molecular response pathways of Trichoderma harzianum in response to salt stress

Trichoderma harzianum exhibits a strong biological control effect on many important plant pathogens, such as Fusarium oxysporum, Botrytis cinerea, and Meloidogyne. However, its biocontrol effectiveness is weakened or reduced under salt stress. The aim of this study was to investigate the molecular response of T. harzianum to salt stress at the whole-genome level. Here, we present a 44.47 Mb near-complete genome assembly of the T. harzianum qt40003 strain for the first time, which was assembled de novo with 7.59 Gb Nanopore sequencing long reads (~170-fold) and 5.2 Gb Illumina short reads (~116-fold). The assembled qt40003 genome contains 12 contigs, with a contig N50 of 4.81 Mb, in which four of the 12 contigs were entirely reconstructed in a single chromosome from telomere to telomere. The qt40003 genome contains 4.27 Mb of repeat sequences and 12,238 protein-coding genes with a BUSCO completeness of 97.5%, indicating the high accuracy and completeness of our gene annotations. Genome-wide transcriptomic analysis was used to investigate gene expression changes related to salt stress in qt40003 at 0, 2% (T2), and 4% (T4) sodium chloride concentrations. A total of 2,937 and 3,527 differentially expressed genes (DEGs) were obtained under T2 and T4 conditions, respectively. GO enrichment analysis showed that the T2-treatment DEGs were highly enriched in detoxification (p < 0.001), while the T4 DEGs were mainly enriched in cell components, mostly in cellular detoxification, cell surface, and cell wall. KEGG metabolic pathway analysis showed that 91 and 173 DEGs were significantly enriched in the T2 and T4 treatments, respectively (p < 0.01), mainly in the glutathione metabolism pathway. We further experimentally analyzed the differentially expressed glutathione transferase genes in the glutathione metabolic pathway, most of which were downregulated (13/15). In addition, we screened 13 genes related to active oxygen clearance, including six upregulated and seven downregulated genes, alongside five fungal hydrophobic proteins, of which two genes were highly expressed. Our study provides high-quality genome information for the use of T. harzianum for biological control and offers significant insights into the molecular responses of T. harzianum under salt-stress conditions.

Examining the impact of Tetragenococcus halophilus, Zygosaccharomyces rouxii, and Starmerella etchellsii on the quality of soy sauce: a comprehensive review of microbial population dynamics in fermentation

Soy sauce is a popular fermented seasoning due to its distinct flavor and rich umami taste. Its traditional production involves two stages: solid-state fermentation and moromi (brine fermentation). During moromi, the dominant microbial population in the soy sauce mash changes, which is called microbial succession and is essential for the formation of soy sauce flavor compounds. Research has identified the sequence of succession, starting with Tetragenococcus halophilus, then Zygosaccharomyces rouxii, and lastly, Starmerella etchellsii. Factors such as the environment, microbial diversity, and interspecies relationships drive this process. Salt and ethanol tolerance influence microbial survival, while nutrients in the soy sauce mash support the cells in resisting external stress. Different microbial strains have varying abilities to survive and respond to external factors during fermentation, which impacts soy sauce quality. In this review, we would examine the factors behind the succession of common microbial populations in the soy sauce mash and explore how microbial succession affects soy sauce quality. The insights gained can help better manage the dynamic changes in microbes during fermentation, leading to improved production efficiency.

Monitoring the growth dynamics of Tetragenococcus halophilus strains in lupine moromi fermentation using a multiplex-PCR system

OBJECTIVE

The microbiota of a seasoning sauce fermentation process is usually complex and includes multiple species and even various strains of one species. Moreover, composition and cell numbers of individual strains vary over the course of the entire fermentation. This study demonstrates the applicability of a multiplex PCR system to monitor growth dynamics of Tetragenococcus (T.) halophilus strains in order to evaluate their performance and help to select the most competitive starter strain.

RESULTS

In a previous study we isolated T. halophilus strains from multiple lupine moromi fermentation processes and characterized them. In this study we wanted to monitor the growth dynamics of these strains in a competitive lupine moromi model fermentation process using a multiplex PCR system. Therefore, pasteurized lupine koji was inoculated with eight different T. halophilus strains, six from lupine moromi, one from an experimental buckwheat moromi fermentation process and the type strain DSM 20,339^T, to create the inoculated lupine moromi pilot scale fermentation process. With the multiplex PCR system, we could detect that all strains could grow in lupine moromi but, that TMW 2.2254 and TMW 2.2264 outperformed all other strains. Both strains dominated the fermentation after three weeks with cell counts between 4 × 10⁶ to 4 × 10⁷ CFU/mL for TMW 2.2254 and 1 × 10⁷ to 5 × 10⁷ CFU/mL for TMW 2.2264. The pH dropped to value below 5 within the first 7 days, the selection of these strains might be related to their acid tolerance.

SIRT1 activation attenuates microglia-mediated synaptic engulfment in postoperative cognitive dysfunction

BACKGROUND

Postoperative cognitive dysfunction (POCD) is a debilitating neurological complication in surgical patients. Current research has focused mainly on microglial activation, but less is known about the resultant neuronal synaptic changes. Recent studies have suggested that Sirtuin-1 (SIRT1) plays a critical role in several different neurological disorders via its involvement in microglial activation. In this study, we evaluate the effects of SIRT1 activation in a POCD mouse model.

MATERIALS AND METHODS

Exploratory laparotomy was performed in mice aged 12-14 months under sevoflurane anesthesia to establish our animal POCD model. Transcriptional changes in the hippocampus after anesthesia and surgery were evaluated by RNA sequencing. SIRT1 expression was verified by Western Blot. Mice were treated with SIRT1 agonist SRT1720 or vehicle after surgery. Changes in microglia morphology, microglial phagocytosis, presence of dystrophic neurites, and dendritic spine density were evaluated. Cognitive performance was evaluated using the Y maze and Morris water maze (MWM).

RESULTS

Sirtuin-1 expression levels were downregulated in POCD. Exposure to anesthesia and surgery lead to alteration in microglia morphology, increased synaptic engulfment, dendritic spine loss, and cognitive deficits. These effects were alleviated by SRT1720 administration.

CONCLUSION

This study suggests an important neuroprotective role for SIRT1 in POCD pathogenesis. Increasing SIRT1 function represents a promising therapeutic strategy for prevention and treatment of POCD.

Evaluating the effect of lactic acid bacterial fermentation on salted soy whey for development of a potential novel soy sauce-like condiment

There were two main objectives of this study: (1) to understand the effect of salt concentration on the growth of four lactic acid bacteria (LAB) in soy whey and determine the non-volatile and volatile profiles generated after fermentation; (2) to evaluate the potential of using salted soy whey to develop a sauce-like condiment through LAB fermentation. The four LAB included non-halophilic Lactiplantibacillus plantarum ML Prime, Limosilactobacillus fermentum PCC, Oenococcus oeni Enoferm Beta and halophilic Tetragenococcus halophilus DSM20337. At 2% salt, all LAB grew remarkably from day 0 to day 1, except for T. halophilus, while at 6% salt, the growth of L. plantarum, L. fermentum and O. oeni was suppressed. Conversely, the higher salt concentration enhanced the growth of T. halophilus in soy whey as the cell count only increased from 6.36 to 6.60 log CFU/mL at 2% salt but it elevated from 6.61 to 7.55 log CFU/mL at 6% salt. Similarly, the higher salt content negatively affected the sugar and amino acids metabolism and organic acids production by non-halophilic LAB. L. plantarum and O. oeni generated significantly (p < 0.05) more lactic acid (3.83 g/L and 4.17 g/L, respectively) than L. fermentum and T. halophilus (2.02 g/L and 0 g/L, respectively) at 2% salt. In contrast, a higher amount of acetic acid was generated by L. fermentum (0.72 g/L at 2% salt) and T. halophilus (0.51 g/L at 6% salt). LAB could remove the green and beany off-flavours in soy whey by metabolizing C6 and C7 aldehydes. However, to develop a novel soy sauce-like condiment, yeast fermentation and Maillard reaction may be required to generate more characteristic soy sauce-associated aroma compounds.

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Soy whey with 2% and 6% NaCl supported the growth of lactic acid bacteria (LAB).

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At 6% NaCl, T. halophilus grew better while the growth of other LAB was impeded.

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T. halophilus and L. fermentum produced significant amounts of acetic acid.

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Through LAB fermentation, green and beany off-odour of soy whey could be removed.

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Yeast fermentation and heating are required to produce key aroma soy sauce compounds.

The function of uridine diphosphate glucose pyrophosphorylase in the lyophilization-stress response of Lactobacillus acidophilus

Purpose

Uridine diphosphate glucose pyrophosphorylase (UGPase) plays an important role in glucose metabolism, catalyzing the reversible formation and decomposition of UDP-glucose (UDPG). In previous work, we found that UGPase is a key enzyme in lyophilization response for Lactobacillus acidophilus (L. acidophilus). However, its function and regulatory mechanism in the freeze-drying stress response are unknown. Herein, the effect of UGPase on freeze-drying survival rate of Staphylococcus carnosus (S. carnosus) was studied.

Methods

In this work, the genes LBA1719 encoding UGPase of L. acidophilus ATCC4356 were inserted into plasmid pMG-36e to construct the recombinant plasmid pMG-LBA1719 and then overexpressed in S. carnosus; the control group was S. carnosus transformed by pMG-36e. The lyophilization-survival rate of overexpressed S. carnosus was determined, and the differentially expressed genes (DEGs) were analyzed by transcriptome to disclose the mechanism of LBA1719 in regulating the lyophilization-survival rate.

Results

Compared with the control group, the UGPase activities of the overexpressed S. carnosus increased by 35.49%, while the lyophilization-survival rates decreased by 11.17% (p < 0.05). Overexpression of LBA1719 decreased the expression of genes gapA, gapB, and pgiA in carbohydrate metabolism and dapA, dapB, and dapE in amino acid metabolism, significantly changing the physiological characteristics of S. carnosus and decreasing its lyophilization-survival rate.

Conclusion

In summary, overexpression of UGPase accelerated the growth rate of S. carnosus and reduced its lyophilization-survival rates. GapA, gapB, pgiA, dapA, dapB, and dapE are vital to lyophilization protection in lactic acid bacteria (LAB). These findings provide new theoretical basis for analyzing the regulatory and molecular mechanisms of lyophilization resistance in LABs.

Effects of microbial community structure and its co-occurrence on the dynamic changes of physicochemical properties and free amino acids in the Cantonese soy sauce fermentation process

The soy sauce produced by Cantonese fermentation has a unique flavor, among which brine fermentation plays an important role. In this fermentation process, 61 volatile compounds, including 19 esters, 10 aldehydes, 9 alcohols, 5 phenols, and 18 others, were identified by headspace solid-phase microextraction-gas chromatography-mass spectrometry. Seventeen kinds of free amino acids were detected by high-performance liquid chromatography. Results showed that Touyou, which comprised 1.5 g/100 g total nitrogen, 1.0 g/100 mL amino acid nitrogen, 3.66 g/100 g reducing sugar, 1.44 g/100 mL total acid, 17.04 g/100 mL salt content, and 27.3% umami free amino acids, had excellent quality. High-throughput sequencing was used to identify microorganisms. The top 3 of bacteria were Weissella, Staphylococcus, and Lactobacillus, and the top 3 fungi were Aspergillus, Zygosaccharomyces, and Candida. The co-occurrence network analysis of microorganisms showed that the top-ranked microorganisms were Plectosphaerella, Aureobasidium, unidentified_Mortierellales_sp, Glutinomyces, Faecalibacterium, and Cladophialophora. Then, eight microorganisms (VIP_[pred] > 1) were obtained by two-way orthogonal partial least squares model, namely, Staphylococcus, Candida, Weissella, Aspergillus, Zygosaccharomyces, Lactobacillus, Monilinia, and Clavispora. Correlation analysis showed that these microorganisms were strongly related to flavor metabolites. This study explored the dynamics of traditional Cantonese fermentation, which has positive implications for optimizing this traditional fermentation process.

Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation

Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.

The diversity among the species Tetragenococcus halophilus including new isolates from a lupine seed fermentation

BACKGROUND

Tetragenococcus (T.) halophilus can be isolated from a variety of fermented foods, such as soy sauce, different soy pastes, salted fish sauce and from cheese brine or degraded sugar beet thick juice. This species contributes by the formation of short chain acids to the flavor of the product. Recently, T. halophilus has been identified as a dominant species in a seasoning sauce fermentation based on koji made with lupine seeds.

RESULTS

In this study we characterized six strains of T. halophilus isolated from lupine moromi fermentations in terms of their adaptation towards this fermentation environment, salt tolerance and production of biogenic amines. Phylogenic and genomic analysis revealed three distinctive lineages within the species T. halophilus with no relation to their isolation source, besides the lineage of T. halophilus subsp. flandriensis. All isolated strains from lupine moromi belong to one lineage in that any of the type strains are absent. The strains form lupine moromi could not convincingly be assigned to one of the current subspecies. Taken together with strain specific differences in the carbohydrate metabolism (arabinose, mannitol, melibiose, gluconate, galactonate) and amino acid degradation pathways such as arginine deiminase pathway (ADI) and the agmatine deiminase pathway (AgDI) the biodiversity in the species of T. halophilus is greater than expected. Among the new strains, some strains have a favorable combination of traits wanted in a starter culture.

CONCLUSIONS

Our study characterized T. halophilus strains that were isolated from lupine fermentation. The lupine moromi environment appears to select strains with specific traits as all of the strains are phylogenetically closely related, which potentially can be used as a starter culture for lupine moromi. We also found that the strains can be clearly distinguished phylogenetically and phenotypically from the type strains of both subspecies T. halophilus subsp. halophilus and T. halophilus subsp. flandriensis.

Incorporation of Exogenous Fatty Acids Enhances the Salt Tolerance of Food Yeast Zygosaccharomyces rouxii

Fatty acids have great effects on the maintenance of the cell membrane structure, cell viability, and cell metabolisms. In this study, we sought to elucidate the effects of exogenous fatty acids on the salt tolerance of food yeast Zygosaccharomyces rouxii. Results showed that Z. rouxii can grow by using exogenous fatty acids (C12:0, C14:0, C16:0, C16:1, C18:0, C18:1, and C18:2) as the sole carbon source. Four fatty acids (C12:0, C16:0, C16:1, and C18:1) can improve the salt tolerance of cells, enhance the formation of the cell biofilm, regulate the chemical compositions, restore growth in the presence of cerulenin, regulate the contents of membrane fatty acids, and control the expression of key genes in the fatty acid metabolism. Our results reveal that Z. rouxii can synthesize membrane fatty acids from exogenous fatty acids and the supplementation of these fatty acids can override the need for de novo fatty acid biosynthesis.

Comparative proteomic analysis of three Lactobacillus plantarum strains under salt stress by iTRAQ

BACKGROUND

Lactobacillus plantarum, a common species of lactic acid bacteria, is used to improve the flavor of traditional fermented food. Under salt stress, different strains of L. plantarum can respond differently. In this work, proteomics and bioinformatics analysis of L. plantarum strains (ATCC14917, FS5-5, and 208) grown under salt stress (240 g L^-1 sodium chloride (NaCl)) were investigated based on the isobaric tags for relative and absolute quantitation method.

RESULTS

Although 171 differentially expressed proteins (DEPs) were observed, only 44, 57, and 112 DEPs were identified in the strains ATCC14917, FS5-5, and 208 respectively. There were 33, 191, and 179 specific DEPs in ATCC14917 versus FS5-5, in 208 versus FS5-5, and in strain 208 versus ATCC14917 in 240 g L^-1 NaCl. These DEPs indicate that the three strains, from pickles, fermented soybean paste, and fermented milk, may have different salt stress responses. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis showed that most DEPs observed were involved in protein biosynthesis, nucleotide metabolism, and sugar metabolism. Twenty-six significantly different DEPs that were possibly associated with salt response were selected and further analyzed for gene expression level and pattern by quantitative reverse transcription polymerase chain reaction. Pyruvate kinase and cysteine desulfurase had similar expression patterns in all three strains; glutamate decarboxylase expression was upregulated in FS5-5 and significantly upregulated in strain 208; RNA polymerase subunit alpha was downregulated in FS5-5 but upregulated in strain 208.

CONCLUSIONS

These results also showed that the salt stress response of strain 208 may involve higher numbers of genes than the other strains. This research provides a theoretical basis for improvement of salt tolerance of L. plantarum in industrial production. © 2020 Society of Chemical Industry.

Characterization of DinJ-YafQ toxin-antitoxin module in Tetragenococcus halophilus: activity, interplay, and evolution

Tetragenococcus halophilus is a moderately halophilic lactic acid bacterium widely used in high-salt food fermentation because of its coping ability under various stress conditions. Bacterial toxin-antitoxin (TA) modules are widely distributed and play important roles in stress response, but those specific for genus Tetragenococcus have never been explored. Here, a bona fide TA module named DinJ₁-YafQ₁^tha was characterized in T. halophilus. The toxin protein YafQ₁^tha acts as a ribonuclease, and its overexpression severely inhibits Escherichia coli growth. These toxic effects can be eliminated by introducing DinJ₁^tha, indicating that YafQ₁^tha activity is blocked by the formed DinJ₁-YafQ₁^tha complex. In vivo and in vitro assays showed that DinJ₁^tha alone or DinJ₁-YafQ₁^tha complex can repress the transcription of dinJ₁-yafQ₁^tha operon by binding directly to the promoter sequence. In addition, dinJ₁-yafQ₁^tha is involved in plasmid maintenance and stress response, and its transcriptional level is regulated by various stresses. These findings reveal the possible roles of DinJ₁-YafQ₁^tha system in the stress adaptation processes of T. halophilus during fermentation. A single antitoxin DinJ₂^tha without a cognate toxin protein was also found. Its sequence shows low similarity to that of DinJ₁^tha, indicating that this antitoxin may have evolved from a different ancestor. Moreover, DinJ₂^tha can cross-interact with noncognate toxin YafQ₁^tha and cross-regulate with dinJ₁-yafQ₁^tha operon. In summary, DinJ-YafQ^tha characterization may be helpful in investigating the key roles of TA systems in T. halophilus and serves as a foundation for further research. KEY POINTS: • dinJ₁-yafQ₁^tha is the first functional TA module characterized in T. halophilus and upregulated significantly upon osmotic and acidic stress. • DinJ₂^tha can exhibit physical and transcriptional interplay with DinJ₁-YafQ₁^tha. • dinJ₂^tha may be acquired from bacteria in distant affiliation and inserted into the T. halophilus genome through horizontal gene transfer.

Effects of CcpA against salt stress in Lactiplantibacillus plantarum as assessed by comparative transcriptional analysis

Lactiplantibacillus plantarum is frequently exposed to salt stress during industrial applications. Catabolite control protein (CcpA) controls the transcription of many genes, but its role in the response to salt stress remains unclear. In this study, we used transcriptome analyses to investigate differences in the logarithmic growth phases of Lactiplantibacillus plantarum ST-III and its ccpA-knockout mutant when grown with or without salt and glycine betaine (GB). The deletion of ccpA significantly affected bacterial growth under different conditions. Among the comparisons, the highest proportion of differentially expressed genes (64%) was observed in the comparison between the wild-type and ccpA mutant grown with NaCl, whereas the lowest proportion (6%) was observed in the comparison between the ccpA mutant strain cultures grown with NaCl alone or with GB together. Transcriptomic analyses showed that CcpA could regulate GB uptake, activate iron uptake, produce acetyl-CoA, and affect fatty acid composition to maintain membrane lipid homeostasis in the adaptation of high-salinity conditions. Conclusively, these results demonstrate the importance of CcpA as a master regulator of these processes in response to salt stress, and provide new insights into the complex regulatory network of lactic acid bacteria. KEY POINTS: • The absence of CcpA significantly affected growth of L. plantarum and its response to salt stress. • CcpA regulates compatible solutes absorption and ions transport to resist salt stress. • CcpA alters fatty acids composition to maintain membrane lipid homeostasis towards salt stress.

Cell surface properties and transcriptomic analysis of cross protection provided between heat adaptation and acid stress in Tetragenococcus halophilus

Cross protection is a widely existed phenomenon in microorganisms which subjected to a mild stress develop tolerance to other stresses, yet the underlying mechanisms for this protection have not been fully elucidated. Here, we report that heat preadaptation induced cross protection against acid stress in Tetragenococcus halophilus, and the cross protective mechanisms were revealed based on cell surface characterizations and transcriptomic analysis. The results showed that heat preadaptation of T. halophilus at 45 °C for 1.5 h improved the acid tolerance of cells at pH 2.5, and the preadapted cells exhibited higher pH_i compared with the un-preadapted cells during acid stress. Analysis of the cell surface properties suggested that the heat-treated cells displayed smoother surface, lower roughness and higher integrity than those of untreated cells. Meanwhile, the distributions of membrane fatty acids also changed in response to acid stress, and the treated cells reveled lower ratio of unsaturated to saturated fatty acids. RNA-Sequencing was employed to further elucidate the cross protective mechanism induced by heat preadaptation, and the results showed that the differentially expressed genes (DGEs) were mainly involved in cellular metabolism and membrane transport during heat preadaptation. A detailed analysis of gene expression profile of cells between heat treated and untreated revealed that genes associated with energy metabolism, amino acid metabolism and genetic information processing were induced upon heat stress. Results presented in this study may broaden our understanding on cross protection and provide a potential strategy to enhance the performance of cells during industrial processes.

Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432T by physiological analysis and comparative transcriptomics

Egicoccus halophilus EGI 80432^T, a halotolerant bacterium isolated from a saline-alkaline soil, belongs to a member of the class Nitriliruptoria, which exhibits high adaptability to salt environments. At present, the detailed knowledge of the salinity adaptation strategies of Nitriliruptoria was limited except for one research by using comparative genomics analysis. Here, we investigated the salinity adaptation mechanism of E. halophilus EGI 80432^T by comparative physiological and transcriptomic analyses. The results of physiological analyses showed that trehalose and glutamate were accumulated by salt stress and showed the maximum at moderate salinity condition. Furthermore, the contents of histidine, threonine, proline, and ectoine were increased with increasing salt concentration. We found that both 0% and 9% NaCl conditions resulted in increased expressions of genes involved in carbohydrate and energy metabolisms, but negatively affected the Na⁺ efflux, iron, and molybdate transport. Moreover, the high salt condition led to enhancement of transcription of genes required for the synthesis of compatible solutes, e.g., glutamate, histidine, threonine, proline, and ectoine, which agree with the results of physiological analyses. The above results revealed that E. halophilus EGI 80432^T increased inorganic ions uptake and accumulated trehalose and glutamate in response to moderate salinity condition, while the salinity adaptation strategy was changed from a "salt-in-cytoplasm" strategy to a "compatible solute" strategy under high salinity condition. The findings in this study would promote further studies in salt tolerance molecular mechanism of Nitriliruptoria and provide a theoretical support for E. halophilus EGI 80432^T's application in ecological restoration.Key Points• Salt stress affected gene expressions responsible for carbohydrate and energy metabolisms of E. halophilus EGI 8042^T.• E. halophilus EGI 80432^T significantly accumulated compatible solutes under salt stress.• E. halophilus EGI 80432^T adopted a "compatible solute" strategy to withstand high salt stress.

Co-culture with Tetragenococcus halophilus improved the ethanol tolerance of Zygosaccharomyces rouxii by maintaining cell surface properties

The accumulation of ethanol has a negative effect on the viability and fermentation performance of microorganisms during the production of fermented foods because of its toxicity. In this study, we investigated the effect of co-culture with Tetragenococcus halophilus on ethanol stress resistance of Zygosaccharomyces rouxii. The result showed that co-culture with T. halophilus promoted cell survival of Z. rouxii under ethanol stress, and the tolerance improved with increasing co-culture time when ethanol content was 8%. Physiological analysis showed that the co-cultured Z. rouxii cells maintained higher intracellular content of trehalose and amino acids including tyrosine, tryptophan, arginine and proline after 8% ethanol stress for 90 min. The membrane integrity analysis and biophysical analysis of the cell surface indicated that the presence of ethanol resulted in cell membrane damage and changes of Young's modulus value and roughness of cell surface. While the co-cultured Z. rouxii cells exhibited better membrane integrity, stiffer and smoother cell surface than single-cultured cells under ethanol stress. As for transcriptomic analyses, the genes involved in unsaturated fatty acid biosynthesis, trehalose biosynthesis, various types of N-glycan biosynthesis, inositol phosphate metabolism, MAPK signaling pathway and tight junction had higher expression in co-cultured Z. rouxii cells with down-regulation of majority of gene expression after stress. And these genes may function in the improvement of ethanol tolerance of Z. rouxii in co-culture.

Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism

The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.

Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean

The special ecological environment of the Arctic has brought about a large number of salt-tolerant and psychrotolerant microorganisms. We isolated two culturable bacterial strains of the genus Mesonia; one from the Arctic ocean, Mesonia algae K4-1, and one from the tropical sea, Mesonia sp. HuA40. Our genome analysis and phenotypic experiments indicated that Mesonia algae K4-1 is a moderately halophilic and psychrophilic bacterium. Mesonia algae K4-1 can tolerate 3–14% NaCl and grow at a wide range of temperatures from 4 to 50°C. Mesonia sp. HuA40 is a mesophilic bacterium that can only grow with 3–9% NaCl. In addition, the salt adaptation strategy of Mesonia algae K4-1 accumulates organic osmolytes in the cell. RNA helicases, glutathione and organic compatible solutes may play important roles in maintaining the metabolism and physiological function of Mesonia algae K4-1 under cold stress. Moreover, the ability of Mesonia algae K4-1 to adapt to an oligotrophic marine environment is likely due to the synthesis of a large number of extracellular polysaccharides and the secretion of various families of extracellular proteases. This study systematically analyzed the relationship between genomic differentiation and environmental factors of the Mesonia genus and revealed the possible adaptation mechanism of Mesonia algae K4-1 in the extreme Arctic marine environment at the genomic level.

N6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis

Circular RNAs (circRNAs) have been implicated in cancer progression through largely unknown mechanisms. Herein, we identify an N⁶-methyladenosine (m⁶A) modified circRNA, circNSUN2, frequently upregulated in tumor tissues and serum samples from colorectal carcinoma (CRC) patients with liver metastasis (LM) and predicts poorer patient survival. The upregulated expression of circNSUN2 promotes LM in PDX metastasis models in vivo and accelerates cancer cells invasion in vitro. Importantly, N⁶-methyladenosine modification of circNSUN2 increases export to the cytoplasm. By forming a circNSUN2/IGF2BP2/HMGA2 RNA-protein ternary complex in the cytoplasm, circNSUN2 enhances the stability of HMGA2 mRNA to promote CRC metastasis progression. Clinically, the upregulated expressions of circNSUN2 and HMGA2 are more prevalent in LM tissues than in primary CRC tissues. These findings elucidate that N⁶-methyladenosine modification of circNSUN2 modulates cytoplasmic export and stabilizes HMGA2 to promote CRC LM, and suggest that circNSUN2 could represent a critical prognostic marker and/or therapeutic target for the disease.

Intra-tumor heterogeneity for endometrial cancer and its clinical significance

BACKGROUND

Management of tumors has become more complex owing to tumor heterogeneity. Fewer studies have been performed on intra-tumor heterogeneity of endometrial cancer (EC) until now. Therefore, it is of great clinical value to explore the intra-tumor heterogeneity of EC based on clinical features and gene expression profiles.

METHODS

A total of 1688 patients with EC were screened and 114 patients were finally selected, including specimens from 84 patients with primary EC without relapse (PE) and the paired metastases (P-M) specimens, as well as specimens from 30 patients with primary EC with relapse (RPE) and the paired relapsed EC (P-RE) specimens. Microarray and RNA-seq were used to detect gene expression of EC samples. Clinicopathological characteristics and molecular data were compared between PE and P-M groups and between RPE and P-RE groups to explore the intra-tumor heterogeneity of EC.

RESULTS

The clinical intra-tumor spatial heterogeneity of pathological type, grade, ER status, and PR status between PE and P-M were 17.9%, 13.1%, 28.6%, and 28.6%, respectively. The clinical intra-tumor spatiotemporal heterogeneity of pathological type, grade, ER status, and PR status between RPE and P-RE were 16.7%, 33.3%, 25.0%, and 37.5%, respectively. Cluster analysis sorts EC samples based on progression type of lesion and their pathological type. There were differentially expressed genes between PE and P-M and between RPE and P-RE, of which gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis were mainly enriched in cell proliferation, the p53 signaling pathway, etc. CONCLUSIONS:: Clinical and molecular data showed that there was spatiotemporal heterogeneity in intra-tumor of EC, which may add to the complexity of diagnosis and therapeutics for EC. Considering the intra-tumor heterogeneity, sequential chemotherapy and precision medicine may be a more suitable treatment plan for EC.

Identification of a GntR family regulator BusRTha and its regulatory mechanism in the glycine betaine ABC transport system of Tetragenococcus halophilus

Glycine betaine is one of the most effective compatible solutes of the halophilic lactic acid bacterium Tetragenococcus halophilus, the transportation of which is essential for its survival under salinity stress condition. In the current study, we attempted to define a glycine betaine ABC transporter system of T. halophilus, busA_Tha, which plays an important role in adapting to salinity condition. The expression of busA_Tha enhanced the growth of the recombinant strain under high salinity. BusR_Tha, a transcription regulator that represses the expression of busA_Tha, was characterized, and the repression was abrogated under high salinity. The binding of the regulator was demonstrated through electrophoretic mobility shift assays, and the binding sites were characterized as 5'-AAA(T/G)TGAC(C/A)(G/A)T(C/A)C-3'. This is the first studied transcription regulator of T. halophilus, and our findings provide insights into the molecular mechanism of halophilic life and tools for further application of halophiles as chassis in industrial biotechnology.

Identification of cucumber circular RNAs responsive to salt stress

BACKGROUND

Circular RNAs (circRNAs) are 3'-5' head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition.

RESULTS

In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Characteristics analysis of these circRNAs revealed following features: most of them are exon circRNAs (79.51%) and they prefer to arise from middle exon(s) of parent genes (2035/2516); moreover, most of circularization events (88.3%) use non-canonical-GT/AG splicing signals; last but not least, pairing-driven circularization is not the major way to generate cucumber circRNAs since very few circRNAs (18) contain sufficient flanking complementary sequences. Annotation and enrichment analysis of both parental genes and target mRNAs were launched to uncover the functions of differentially expressed circRNAs induced by salt stress. The results showed that circRNAs may be paly roles in salt stress response by mediating transcription, signal transcription, cell cycle, metabolism adaptation, and ion homeostasis related pathways. Moreover, circRNAs may function to regulate proline metabolisms through regulating associated biosynthesis and degradation genes.

CONCLUSIONS

The present study identified large number of cucumber circRNAs and function annotation revealed their possible biological roles in response to salt stress. Our findings will lay a solid foundation for further structure and function studies of cucumber circRNAs.

Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses

The genomic and metabolic diversity and features of Tetragenococcus halophilus, a moderately halophilic lactic acid bacterium, were investigated by pan-genome, transcriptome, and metabolite analyses. Phylogenetic analyses based on the 16S rRNA gene and genome sequences of 15 T. halophilus strains revealed their phylogenetic distinctness from other Tetragenococcus species. Pan-genome analysis of the T. halophilus strains showed that their carbohydrate metabolic capabilities were diverse and strain dependent. Aside from one histidine decarboxylase gene in one strain, no decarboxylase gene associated with biogenic amine production was identified from the genomes. However, T. halophilus DSM 20339^T produced tyramine without a biogenic amine-producing decarboxylase gene, suggesting the presence of an unidentified tyramine-producing gene. Our reconstruction of the metabolic pathways of these strains showed that T. halophilus harbors a facultative lactic acid fermentation pathway to produce l-lactate, ethanol, acetate, and CO₂ from various carbohydrates. The transcriptomic analysis of strain DSM 20339^T suggested that T. halophilus may produce more acetate via the heterolactic pathway (including d-ribose metabolism) at high salt conditions. Although genes associated with the metabolism of glycine betaine, proline, glutamate, glutamine, choline, and citrulline were identified from the T. halophilus genomes, the transcriptome and metabolite analyses suggested that glycine betaine was the main compatible solute responding to high salt concentration and that citrulline may play an important role in the coping mechanism against high salinity-induced osmotic stresses. Our results will provide a better understanding of the genome and metabolic features of T. halophilus, which has implications for the food fermentation industry.

Glycine betaine enhances biodegradation of phenol in high saline environments by the halophilic strainOceanobacillussp. PT-20

Glycine betaine enhanced the biodegradation of phenol by halophilic strain PT-20 in high salinity conditions.

Transcriptomic Analysis of Oenococcus oeni SD-2a Response to Acid Shock by RNA-Seq

Oenococcus oeni can be applied to conduct malolactic fermentation (MLF), but also is the main species growing naturally in wine. Due to the high stress tolerance, it is an interesting model for investigating acid response mechanisms. In this study, the changes in the transcriptome of O.oeni SD-2a during the adaptation period have been studied. RNA-seq was introduced for the transcriptomic analysis of O. oeni samples treated with pH 4.8 and pH 3.0 at 0 and 1 h, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) were performed to compare the transcriptome data between different treatments. From GO analysis, the majority of differentially expressed genes (DEGs) (pH 3.0_1 h-VS-pH 4.8_1 h, pH 3.0_1 h-VS-pH 4.8_0 h, and pH 4.8_1 h-VS-pH 4.8_0 h) were found to be involved in the metabolic process, catalytic activity, cellular process, and binding. KEGG analysis reveals that the most functional gene categories affected by acid are membrane transport, amino acid metabolism and carbohydrate metabolism. Some genes, like the heat shock protein Hsp20, malate transporter and malate permease, were also over-expressed in response to acid stress. In addition, a considerable proportion of gene indicate a significantly different expression in this study, are novel, which needs to be investigated further. These results provide a new viewpoint and crucial resource on the acid stress response in O. oeni.

A partial proteome reference map of Tetragenococcus halophilus and comparative proteomic and physiological analysis under salt stress

Tetragenococcus halophilus, a moderately halophilic Gram-positive lactic acid bacteria, was widely existed in many food fermentation systems, where salt stress is an environmental condition commonly encountered.

Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea

Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations. A total of 2149 genes were predicted to be up-regulated and 1638 genes were down-regulated in the presence of 5.5M NaCl. The salt tolerance of Halolamina sp. YKT1 involves the up-regulation of genes related with membrane transporters, CRISPR-Cas systems, osmoprotectant solutes, oxidative stress proteins, and iron metabolism. On the other hand, the genes encoding the proteins involved in DNA replication, transcription, translation, mismatch and nucleotide excision repair were down-regulated. The RNA-seq data were verified for seven up-regulated genes as well as six down-regulated genes via qRT-PCR analysis. This comprehensive transcriptome analysis showed that the halophilic archaeon canalizes its energy towards keeping the intracellular osmotic balance minimizing the production of nucleic acids and peptides.

Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli

We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli), Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification) approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology) and KEGG (Kyoto encyclopedia of genes and genomes) enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species) scavenging, membrane proteins and ABC (ATP binding cassette) transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame) of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.