DUSP5 regulated by YTHDF1-mediated m6A modification promotes epithelial-mesenchymal transition and EGFR-TKI resistance via the TGF-ß/Smad signaling pathway in lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) patients have a dismal survival rate because of cancer metastasis and drug resistance. The study aims to identify the genes that concurrently modulate EMT, metastasis and EGFR-TKI resistance, and to investigate the underlying regulatory mechanisms. METHODS: Cox regression and Kaplan-Meier analyses were applied to identify prognostic oncogenes in LUAD. Gene set enrichment analysis (GSEA) was used to indicate the biological functions of the gene. Wound-healing and Transwell assays were used to detect migratory and invasive ability. EGFR-TKI sensitivity was evaluated by assessing the proliferation, clonogenic survival and metastatic capability of cancer cells with treatment with gefitinib. Methylated RNA immunoprecipitation (MeRIP) and RNA immunoprecipitation (RIP) analyses established the level of m6A modification present on the target gene and the protein's capability to interact with RNA, respectively. Single-sample gene set enrichment (ssGSEA) algorithm used to investigate levels of immune cell infiltration. RESULTS: Our study identified dual-specificity phosphatase 5 (DUSP5) as a novel and powerful predictor of adverse outcomes for LUAD by using public datasets. Functional enrichment analysis found that DUSP5 was positively enriched in EMT and transforming growth factor-beta (TGF-ß) signaling pathway, a prevailing pathway involved in the induction of EMT. As expected, DUSP5 knockdown suppressed EMT via inhibiting the canonical TGF-ß/Smad signaling pathway in in vitro experiments. Consistently, knockdown of DUSP5 was first found to inhibit migratory ability and invasiveness of LUAD cells in in vitro and prevent lung metastasis in in vivo. DUSP5 knockdown re-sensitized gefitinib-resistant LUAD cells to gefitinib, accompanying reversion of EMT progress. In LUAD tissue samples, we found 14 cytosine-phosphate-guanine (CpG) sites of DUSP5 that were negatively associated with DUSP5 gene expression. Importantly, 5'Azacytidine (AZA), an FDA-approved DNA methyltransferase inhibitor, restored DUSP5 expression. Moreover, RIP experiments confirmed that YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), a m6A reader protein, could bind DUSP5 mRNA. YTHDF1 promoted DUSP5 expression and the malignant phenotype of LUAD cells. In addition, the DUSP5-derived genomic model revealed the two clusters with distinguishable immune features and tumor mutational burden (TMB). CONCLUSIONS: Briefly, our study discovered DUSP5 which was regulated by epigenetic modification, might be a potential therapeutic target, especially in LUAD patients with acquired EGFR-TKI resistance.

The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa).

Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.

Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice.

Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01345-1.

Small Auxin Up RNA 56 (SAUR56) regulates heading date in rice.

Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01409-w.

Characterization of GshAB of Tetragenococcus halophilus: a two-domain glutathione synthetase.

The γ-glutamyl tripeptide glutathione (γ-Glu-Cys-Gly) is a low molecular thiol that acts as antioxidant in response to oxidative stress in eukaryotes and prokaryotes. γ-Glutamyl dipeptides including γ-Glu-Cys, γ-Glu-Glu, and γ-Glu-Gly also have kokumi activity. Glutathione is synthesized by first ligating Glu with Cys by γ-glutamylcysteine ligase (Gcl/GshA), and then the resulting dipeptide γ-glutamylcysteine is ligated with Gly by glutathione synthetase (Gs/GshB). GshAB/GshF enzymes that contain both Gcl and Gs domains are capable of catalyzing both reactions. The current study aimed to characterize GshAB from Tetragenococcus halophilus after heterologous expression in Escherichia coli. The optimal conditions for GshAB from T. halophilus were pH 8.0 and 25 °C. The substrate specificity of the Gcl reaction of GshAB was also determined. GshAB has a high affinity to Cys. γ-Glu-Cys was the only dipeptide generated when Glu, Cys, Gly, and other amino acids were present in the reaction system. This specificity differentiates GshAB from T. halophilus from Gcl of heterofermentative lactobacilli and GshAB of Streptococcus agalactiae, which also use amino acids other than Cys as glutamyl-acceptor. Quantification of gshAB in cDNA libraries from T. halophilus revealed that gshAB was overexpressed in response to oxidative stress but not in response to acid, osmotic, or cold stress. In conclusion, GshAB in T. halophilus served as part of the oxidative stress response but this study did not provide any evidence for a contribution to the resistance to other stressors.Key points Glutathione synthesis in Tetragenococcus halophilus is carried out by the two-domain enzyme GshAB. GshAB is inhibited by glutathione and is highly specific for Cys as acceptor. T. halophilus synthesizes glutathione in response to oxidative stress.

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-YafQ1tha was characterized in T. halophilus. The toxin protein YafQ1tha acts as a ribonuclease, and its overexpression severely inhibits Escherichia coli growth. These toxic effects can be eliminated by introducing DinJ1tha, indicating that YafQ1tha activity is blocked by the formed DinJ1-YafQ1tha complex. In vivo and in vitro assays showed that DinJ1tha alone or DinJ1-YafQ1tha complex can repress the transcription of dinJ1-yafQ1tha operon by binding directly to the promoter sequence. In addition, dinJ1-yafQ1tha 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-YafQ1tha system in the stress adaptation processes of T. halophilus during fermentation. A single antitoxin DinJ2tha without a cognate toxin protein was also found. Its sequence shows low similarity to that of DinJ1tha, indicating that this antitoxin may have evolved from a different ancestor. Moreover, DinJ2tha can cross-interact with noncognate toxin YafQ1tha and cross-regulate with dinJ1-yafQ1tha operon. In summary, DinJ-YafQtha 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-yafQ1tha is the first functional TA module characterized in T. halophilus and upregulated significantly upon osmotic and acidic stress. • DinJ2tha can exhibit physical and transcriptional interplay with DinJ1-YafQ1tha. • dinJ2tha may be acquired from bacteria in distant affiliation and inserted into the T. halophilus genome through horizontal gene transfer.

Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages.

BACKGROUND: Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. However, there are few studies on the metabolome or transcriptome of germination and young seedling growth in rice. RESULTS: Here, an indica rice and a japonica rice were used as materials, and the transcripts and metabolites were detected during the germination and young seedling growth periods on a large scale by using RNA sequencing and a widely targeted metabolomics method, respectively. Fourteen shared transcripts and 15 shared metabolites that were continuously differentially expressed in the two materials were identified and may be essential for seed germination and young seedling growth. Enrichment analysis of differentially expressed genes in transcriptome expression profiles at different stages indicated that cell wall metabolism, lipid metabolism, nucleotide degradation, amino acid, etc., were enriched at 0-2 days, and most of the results are consistent with those of previous reports. Specifically, phenylpropanoid biosynthesis and glutathione metabolism were continuously enriched during the seed germination and young seedling growth stages. Next, KO enrichment analysis was conducted by using the differentially expressed genes of the two materials at 2, 3 and 4 days. Fourteen pathways were enriched. Additionally, 44 differentially expressed metabolites at 2, 3 and 4 days were identified. These metabolites may be responsible for the differences in germination and young seedling growth between the two materials. Further attention was focused on the ascorbate-glutathione pathway, and it was found that differences in ROS-scavenging abilities mediated by some APX, GPX and GST genes may be directly involved in mediating differences in the germination and young seedling growth speed of the two materials. CONCLUSIONS: In summary, these results may enhance the understanding of the overall mechanism of seed germination and young seedling growth, and the outcome of this study is expected to facilitate rice breeding for direct seeding.

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.

Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq.

BACKGROUND: Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties. RESULTS: In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination. CONCLUSIONS: Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions.

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, busATha, which plays an important role in adapting to salinity condition. The expression of busATha enhanced the growth of the recombinant strain under high salinity. BusRTha, a transcription regulator that represses the expression of busATha, 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.

Mechanisms of Cr(VI) reduction by Bacillus sp. CRB-1, a novel Cr(VI)-reducing bacterium isolated from tannery activated sludge.

Cr(VI) reduction by microorganisms has been extensively reported, however, the mechanism of Cr(VI) reduction varies among different microorganisms. In this study, a Cr(VI)-reducing bacterium identified as Bacillus sp. was isolated from tannery activated sludge, strain CRB-1 was able to completely reduce 50 mg/L of Cr(VI) within 24 h under aerobic conditions and exhibited considerable Cr(VI) removal efficiency in the pH range from 7.0 to 9.0, temperature 24-42 °C. Cr(VI) reduction assays with resting cells, permeabilized cells, and subcellular fractions suggested that Cr(VI) reduction mainly occurred in the cytoplasm. According to qRT-PCR analysis, a chrA gene and a nitR2 gene were up-regulated under Cr(VI) stress. Heterologous expression of the chrA gene and the nitR2 gene indicated that ChrA was associated with Cr(VI) resistance, while NitR2 was responsible for Cr(VI) reduction. Furthermore, soluble end products were detected. On the basis of FTIR, it was speculated that the formation of soluble end products may be due to the complexation of EPS with Cr(III). Consequently, the Cr(VI)-reducing ability of strain CRB-1 and its chromate reductases enables CRB-1 a potential candidate for Cr(VI) bioremediation.

Daqu Fermentation Selects for Heat-Resistant Enterobacteriaceae and Bacilli.

Daqu is a spontaneous solid-state cereal fermentation used as saccharification and starter culture in Chinese vinegar and liquor production. The evolution of microbiota in this spontaneous fermentation is controlled by the temperature profile, which reaches temperatures from 50 to 65°C for several days. Despite these high temperatures, mesophilic Enterobacteriaceae (including Cronobacter) and bacilli are present throughout Daqu fermentation. This study aimed to determine whether Daqu spontaneous solid-state fermentation selects for heat-resistant variants of these organisms. Heat resistance in Enterobacteriaceae is mediated by the locus of heat resistance (LHR). One LHR-positive strain of Kosakonia cowanii was identified in Daqu, and it exhibited higher heat resistance than the LHR-negative K. cowanii isolated from malted oats. Heat resistance in Bacillus endospores is mediated by the spoVA2mob operon. Out of 10 Daqu isolates of the species Bacillus licheniformis, Brevibacillus parabrevis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus velezensis, 5 did not contain spoVA2mob, 3 contained one copy, and 2 contained two copies. The presence and copy number of the spoVA2mob operon increased the resistance of spores to treatment with 110°C. To confirm the selection of LHR- and spoVA2mob-positive strains during Daqu fermentation, the copy numbers of these genetic elements in Daqu samples were quantified by quantitative PCR (qPCR). The abundance of LHR and the spoVA2mob operon in community DNA relative to that of total bacterial 16S rRNA genes increased 3-fold and 5-fold, respectively, during processing. In conclusion, culture-dependent and culture-independent analyses suggest that Daqu fermentation selects for heat-resistant Enterobacteriaceae and bacilli.IMPORTANCE Daqu fermentations select for mobile genetic elements conferring heat resistance in Enterobacteriaceae and bacilli. The locus of heat resistance (LHR), a genomic island conferring heat resistance in Enterobacteriaceae, and the spoVA2mob operon, conferring heat resistance on bacterial endospores, were enriched 3- to 5-fold during Daqu fermentation and maturation. It is therefore remarkable that the LHR and the spoVA2mob operon are accumulated in the same food fermentation. The presence of heat-resistant Kosakonia spp. and Bacillus spp. in Daqu is not of concern for food safety; however, both genomic islands are mobile and transferable to pathogenic bacteria or toxin-producing bacteria by horizontal gene transfer. The identification of the LHR and the spoVA2mob operon as indicators of fitness of Enterobacteriaceae and bacilli in Daqu fermentation provides insights into environmental sources of heat-resistant organisms that may contaminate the food supply.

Effect of bioaugmented inoculation on microbiota dynamics during solid-state fermentation of Daqu starter using autochthonous of Bacillus, Pediococcus, Wickerhamomyces and Saccharomycopsis.

Daqu, a traditional fermentation starter that is used for Chinese liquor and vinegar production, is still manufactured through a traditional spontaneous solid-state fermentation process with no selected microorganisms are intentionally inoculated. The aim of this work was to analyze the microbiota dynamics during the solid-state fermentation process of Daqu using a traditional and bioaugmented inoculation with autochthonous of Bacillus, Pediococcus, Saccharomycopsis and Wickerhamomyces at an industrial scale. Highly similar dynamics of physicochemical parameters, enzymatic activities and microbial communities were observed during the traditional and bioaugmented solid-state fermentation processes. Both in the two cases, groups of Streptophyta, Rickettsiales and Xanthomonadales only dominated the first two days, but Bacillales and Eurotiales became predominant members after 2 and 10 days fermentation, respectively. Phylotypes of Enterobacteriales, Lactobacillales, Saccharomycetales and Mucorales dominated the whole fermentation process. No significant difference (P > 0.05) in microbial structure was observed between the traditional and bioaugmented fermentation processes. However, slightly higher microbial richness was found during the bioaugmented fermentation process after 10 days fermentation. Our results reinforced the microbiota dynamic stability during the solid-state fermentation process of Daqu, and might aid in controlling the traditional Daqu manufacturing process.

Chromosome mapping, molecular cloning and expression analysis of a novel gene response for leaf width in rice.

Genetic analysis revealed that narrow leaf, small panicle, thin and slender stems as well as low fertility rate of an Indica rice variety were recessive traits and controlled by a single gene. Applying map-based cloning strategy, a novel narrow leaf gene, which was named nal11 was delimited to an interval of 58.3 kb between the InDel markers N10 and InD5016. There are 9 genes in the mapping interval, and only a heat shock DNAJ protein encode gene (Os07g09450) has a specific G to T SNP, which was occurred at the last base of the second exon of Os07g09450 in ZYX. 5' and 3' RACE result shown that there were two transcripts in NAL11, and the SNP in nal11 leads to a variable shear of mRNA. In addition, this type of mRNA alternative splicing together with a stop codon closely followed the SNP which caused termination of translation destroyed the DNAJ domain of nal11's product. These results suggested that the heat shock DNAJ gene was most likely to be the candidate gene of nal11. The results of RT-PCR and real-time PCR further verified that the SNP in the ZYX-nal11 gene affects mRNA splicing pattern. Phenotype of ZYX may be caused by a statistically significant reduction in the total number of small veins in leaf, size and number of small vascular bundles and cells in stems, similar to several previous reported mutations. The basic molecular information we provide here will be useful for further investigations of the physiological function of the heat shock DNAJ gene, which will be helpful in better understanding the role of the DNAJ family in regulation of plant type traits such as leaf width of rice.

Paenibacillus aceti sp. nov., isolated from the traditional solid-state acetic acid fermentation culture of Chinese cereal vinegar.

A Gram-stain-negative, rod-shaped, motile, endospore-forming, facultatively anaerobic bacterium, designated strain L14T, was isolated from the traditional acetic acid fermentation culture of Chinese cereal vinegars. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain L14T was affiliated to the genus Paenibacillus, most closely related to Paenibacillus motobuensis MC10T with 97.8 % similarity. Chemotaxonomic characterization supported the allocation of the strain to the genus Paenibacillus. The polar lipid profile of strain L14T contained the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The predominant menaquinone was MK-7, and the major fatty acid components were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The DNA G+C content of strain L14T was 49.9 mol%. The DNA-DNA relatedness value between strain L14T and P. motobuensis MC10T was 51.2 %. The results of physiological and biochemical tests allowed phenotypic differentiation of strain L14T from closely related species. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic analysis and DNA-DNA relatedness values, strain L14T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus aceti sp. nov. is proposed. The type strain is L14T (=CGMCC 1.15420T=JCM 31170T).

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar.

Solid-state acetic acid fermentation (AAF), a natural or semi-controlled fermentation process driven by reproducible microbial communities, is an important technique to produce traditional Chinese cereal vinegars. Highly complex microbial communities and metabolites are involved in traditional Chinese solid-state AAF, but the association between microbiota and metabolites during this process are still poorly understood. In this study, we performed amplicon 16S rRNA gene sequencing on the Illumina MiSeq platform, PCR-denaturing gradient gel electrophoresis, and metabolite analysis to trace the bacterial dynamics and metabolite changes under AAF process. A succession of bacterial assemblages was observed during the AAF process. Lactobacillales dominated all the stages. However, Acetobacter species in Rhodospirillales were considerably accelerated during AAF until the end of fermentation. Quantitative PCR results indicated that the biomass of total bacteria showed a "system microbe self-domestication" process in the first 3 days, and then peaked at the seventh day before gradually decreasing until the end of AAF. Moreover, a total of 88 metabolites, including 8 organic acids, 16 free amino acids, and 66 aroma compounds were detected during AAF. Principal component analysis and cluster analyses revealed the high correlation between the dynamics of bacterial community and metabolites.

Chinese herb medicine against Sortase A catalyzed transformations, a key role in gram-positive bacterial infection progress.

Many Gram-positive bacteria can anchor their surface proteins to the cell wall peptidoglycan covalently by a common mechanism with Sortase A (SrtA), thus escaping from the host's identification of immune cells. SrtA can complete this anchoring process by cleaving LPXTG motif conserved among these surface proteins and thus these proteins anchor on the cell wall. Moreover, those SrtA mutants lose this capability to anchor these relative proteins, with these bacteria no longer infectious. Therefore, SrtA inhibitors can be promising anti-infective agents to cure bacterial infections. Chinese herb medicines (CHMs) (chosen from Science Citation Index) have exhibited inhibition on SrtA of Gram-positive pathogens irreversibly or reversibly. In general, CHMs are likely to have important long-term impact as new antibacterial compounds and sought after by academia and the pharmaceutical industry. This review mainly focuses on SrtA inhibitors from CHMs and the potential inhibiting mechanism related to chemical structures of compounds in CHMs.

Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation.

Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters. Lactobacillales and Saccharomycetales dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant Bacillales, Eurotiales, and Mucorales were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation. Enterobacteriales were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera Sanguibacter, Beutenbergia, Agrobacterium, and Erwinia dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of Bacillus, Aspergillus, and Mucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, ß-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters.

Hypoosmotic expression of Dunaliella bardawil ζ-carotene desaturase is attributed to a hypoosmolarity-responsive element different from other key carotenogenic genes.

Some key carotenogenic genes (crts) in Dunaliella bardawil are regulated in response to salt stress partly due to salt-inducible cis-acting elements in their promoters. Thus, we isolated and compared the ζ-carotene desaturase (Dbzds) promoter with other crts promoters including phytoene synthase (Dbpsy), phytoene desaturase (Dbpds), and lycopene ß-cyclase1 (DblycB1) to identify salt-inducible element(s) in the Dbzds promoter. In silico analysis of the Dbzds promoter found several potential cis-acting elements, such as abscisic acid response element-like sequence, myelocytomatosis oncogene1 recognition motif, AGC box, anaerobic motif2, and activation sequence factor1 binding site. Remarkably, instead of salt-inducible elements, we found a unique regulatory sequence architecture in the Dbzds promoter: a hypoosmolarity-responsive element (HRE) candidate followed by a potential hypoosmolarity-inducible factor GBF5 binding site. Deletion experiments demonstrated that only HRE, but not the GBF5 binding site, is responsible for hypoosmotic expression of the fusion of Zeocin resistance gene (ble) to the enhanced green fluorescent protein (egfp) chimeric gene under salt stress. Dbzds transcripts were in accordance with those of ble-egfp driven by the wild-type Dbzds promoter. Consequently, Dbzds is hypoosmotically regulated by its promoter, and HRE is responsible for this hypoosmotic response. Finally, the hypoosmolarity mechanism of Dbzds was studied by comparing transcript profiles and regulatory elements of Dbzds with those of Dbpsy, Dbpds, DblycB1, and DblycB2, revealing that different induction characteristics of crts may correlate with regulatory sequence architecture.

Microbial diversity and their roles in the vinegar fermentation process.

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.