Additive efficacy and safety of probiotics in the treatment of ulcerative colitis: a systematic review and meta-analysis.

BACKGROUND: We aim to report the latest pooled analyses to evaluate the additive efficacy and safety of probiotics in the treatment of ulcerative colitis (UC). METHODS: We systematically searched the relevant literature investigating the efficacy and/or safety of probiotics in patients with UC from PubMed, Embase and Web of Science up to January 2023. Two researchers independently screened the literature, extracted data, and evaluated the quality of the included studies according to the inclusion and exclusion criteria. Any discrepancies throughout these processes were solved by consensus. All statistical analyses were performed by Review Manager version 5.4 and Stata version 15.0. RESULTS: A total of 13 articles were included in the pooled analyses, and the studies were all randomized controlled trials with a total of 930 patients. There were no significant differences between the probiotics and placebo groups concerning demographic and baseline characteristics. For patients with active UC, the probiotic group boosted the remission rate by 87% compared to the placebo group, but failed to reach a statistical difference (OR: 1.87; 95% CI 0.98, 3.57; P = 0.06, I2 = 67%); furthermore, there were no statistical differences in maintenance of clinical remission, clinical response, change in UCDAI scores, or mucosal healing outcomes in the probiotic group compared to the placebo group. For patients in clinical remission, the clinical relapse rates were significantly lower in the probiotic group than in the placebo group (OR: 0.34; 95% CI 0.14, 0.79; P = 0.01). Moreover, this study did not observe a significant difference between the two groups for general adverse events rate (OR: 1.98; 95% CI 0.69, 5.68; P = 0.20). CONCLUSION: Probiotic-assisted therapy may be effective in inhibiting UC recurrence in patients in clinical remission without increasing the risk of treatment-related adverse events; furthermore, probiotics may increase the rate of clinical remission in patients with active UC. However, caution is needed when interpreting the clinical efficacy of probiotics in improving the clinical outcome of patients with active UC.

Candidate Gene Identification and Transcriptome Analysis of Tomato male sterile-30 and Functional Marker Development for ms-30 and Its Alleles, ms-33, 7B-1, and stamenless-2.

Male sterility is a valuable trait for hybrid seed production in tomato (Solanum lycopersicum). The mutants male sterile-30 (ms-30) and ms-33 of tomato exhibit twisted stamens, exposed stigmas, and complete male sterility, thus holding potential for application in hybrid seed production. In this study, the ms-30 and ms-33 loci were fine-mapped to 53.3 kb and 111.2 kb intervals, respectively. Tomato PISTILLATA (TPI, syn. SlGLO2), a B-class MADS-box transcription factor gene, was identified as the most likely candidate gene for both loci. TPI is also the candidate gene of tomato male sterile mutant 7B-1 and sl-2. Allelism tests revealed that ms-30, ms-33, 7B-1, and sl-2 were allelic. Sequencing analysis showed sequence alterations in the TPI gene in all these mutants, with ms-30 exhibiting a transversion (G to T) that resulted in a missense mutation (S to I); ms-33 showing a transition (A to T) that led to alternative splicing, resulting in a loss of 46 amino acids in protein; and 7B-1 and sl-2 mutants showing the insertion of an approximately 4.8 kb retrotransposon. On the basis of these sequence alterations, a Kompetitive Allele Specific PCR marker, a sequencing marker, and an Insertion/Deletion marker were developed. Phenotypic analysis of the TPI gene-edited mutants and allelism tests indicated that the gene TPI is responsible for ms-30 and its alleles. Transcriptome analysis of ms-30 and quantitative RT-PCR revealed some differentially expressed genes associated with stamen and carpel development. These findings will aid in the marker-assisted selection for ms-30 and its alleles in tomato breeding and support the functional analysis of the TPI gene.

The safety and efficacy of sequential intramuscular/oral ziprasidone treatment of acute episode in patients with schizophrenia: a multicenter, open-labeled study.

BACKGROUND: Ziprasidone mesylate injection is an atypical antipsychotic drug which is recently approved in China. In combination with its oral formulation, sequential therapy with ziprasidone brings new interventions to patients with agitation in the acute phase of schizophrenia. The purpose of this 7-day multicenter study conducted in China was to evaluate the efficacy and safety of ziprasidone sequential treatment through intramuscular/oral routes in agitated patients with schizophrenia. METHODS: A total of 95 patients were enrolled from three centers in this study. The study duration was 7 days. In the first 3 days, subjects were administered an intramuscular injection of ziprasidone 10-40 mg daily and started sequentially with oral ziprasidone 40-80 mg at dinner (or lunch) from the day of the last intramuscular injection. In the following 4 days, according to the severity of the symptoms and the drug response, 120-160 mg of ziprasidone was orally administered daily. In total, six visits were scheduled to assess the Positive and Negative Syndrome Scale (PANSS), the Behavioral Activity Rating Scale (BARS), the Clinical Global Impression of Severity (CGI-S), and Improvement (CGI-I) scores throughout the procedure. Lastly, adverse events were recorded during treatment. RESULTS: Out of the 95 patients that were enrolled, 83 cases were effectively completed. Visits 3, 4, 6, PANSS, and PANSS-excited component (PANSS-EC) subscale points, and Visit 2-Visit 6 viewpoints, BARS scale points, and baseline scores denote a progressive downward trend (P < 0.001). In this study, 62 adverse events were reported. The most common adverse events were extrapyramidal symptoms (EPS) (23 cases) and excessive sedation(10 cases), and 13 cases of prolonged QTc interval were reported. CONCLUSIONS: Ziprasidone IM demonstrated significant and rapid reduction in agitation, and sequential oral formulation keep stability and continuation of the treatment can further ensure efficacy. Ziprasidone sequential therapy may provide a new approach to acute agitation in schizophrenic patients. TRIAL REGISTRATION: The Chinese Clinical Trials Registry; URL: https://www.chictr.org.cn : ChiCTR-OIC-16007970.

All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter.

The formation of locule gel is an important process in tomato and is a typical characteristic of berry fruit. In this study, we examined a natural tomato mutant that produces all-flesh fruit (AFF) in which the locule tissue remains in a solid state during fruit development. We constructed different genetic populations to fine-map the causal gene for this trait and identified SlMBP3 as the locus conferring the locule gel formation, which we rename as AFF. We determined the causal mutation as a 416-bp deletion in the promoter region of AFF, which reduces its expression dosage. Generally, this sequence is highly conserved among Solanaceae, as well as within the tomato germplasm. Using BC6 near-isogenic lines, we determined that the reduced expression dosage of AFF did not affect the normal development of seeds, whilst producing unique, non-liquefied locule tissue that was distinct from that of normal tomatoes in terms of metabolic components. Combined analysis using mRNA-seq and metabolomics indicated the importance of AFF in locule tissue liquefaction. Our findings provide insights into fruit-type differentiation in Solanaceae crops and also present the basis for future applications of AFF in tomato breeding programs.

Reconstruction and analysis of genome-scale metabolic model for thermophilic fungus Myceliophthora thermophila.

Myceliophthora thermophila, a thermophilic fungus that can degrade and utilize all major polysaccharides in plant biomass, has great potential in biotechnological industries. Here, the first manually curated genome-scale metabolic model iDL1450 for M. thermophila was reconstructed using an autogenerating pipeline with thorough manual curation. The model contains 1450 genes, 2592 reactions, and 1784 unique metabolites. High accuracy was shown in predictions related to carbon and nitrogen source utilization based on data obtained from Biolog experiments. Besides, metabolism profiles were analyzed using iDL1450 integrated with transcriptomics data of M. thermophila at various growth temperatures. The refined model provides new insights into thermophilic fungi metabolism and sheds light on model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus.

Preparation of Cellulose Nanocrystals from Jujube Cores by Fractional Purification.

Jujube cores are fiber-rich industrial waste. Dewaxing, alkali treatment, bleaching, and sulfuric acid hydrolysis were used to generate cellulose nanocrystals (CNCs) from the jujube cores in this study. The morphological, structural, crystallinity, and thermal properties of the fibers were investigated using FE-SEM, TEM, AFM, FT-IR, XRD, and TGA under various processes. CNCs' zeta (ζ) potential and water contact angle (WAC) were also investigated. The findings demonstrate that non-fibrous components were effectively removed, and the fiber particles shrunk over time because of many activities. CNCs had a rod-like shape, with a length of 205.7 ± 52.4 nm and a 20.5 aspect ratio. The crystal structure of cellulose Iß was preserved by the CNCs, and the crystallinity was 72.36%. The temperature of the fibers' thermal degradation lowered during the operations, although CNCs still had outstanding thermal stability (>200 °C). Aside from the CNCs, the aqueous suspension of CNCs was slightly agglomerated; thus, the zeta (ζ) potential of the CNCs' suspension was −23.72 ± 1.7 mV, and the powder had high hydrophilicity. This research will be valuable to individuals who want to explore the possibility for CNCs made of jujube cores.

Adjunctive vagus nerve stimulation for treatment-resistant depression: a preliminary study.

BACKGROUND: This study is the first to assess the safety and therapeutic efficacy of vagus nerve stimulation (VNS) as an adjunctive treatment for Chinese patients suffering from treatment-resistant depression (TRD). METHODS: A total of seven patients with TRD underwent surgical implantation of a VNS device were followed over a 9-month period. The 24-item Hamilton Rating Scale for Depression (HAMD-24) and the 14-item Hamilton Anxiety Scale (HAMA) were used to assess depressive and anxiety symptoms, respectively. Neurocognitive function was measured with the Wechsler Adult Intelligence Scale (WAIS) and the Wechsler Memory Scale (WMS). RESULTS: After 3 months of treatment with VNS, the antidepressant response and remission rates were 42.9% and 28.6%, respectively. After 9 months of treatment with VNS, the response and remission rates increased to 85.7% and 57.1%, respectively. Significant time main effects were identified for HAMD-24 scores, HAMA scores, the WMS memory quotient, and the full intelligence quotients measured with the WAIS (all ps < 0.05). The most frequent adverse effects of VNS treatment were voice alteration (100%) and cough frequency increase (71.4%). CONCLUSION: This preliminary study indicated that adjunctive VNS was effective and safe in treating Chinese patients who were suffering from TRD, and its efficacy increased with time.Key pointsThere is positive evidence to support the role of VNS as an adjunctive treatment in Chinese patients with TRD.The antidepressant efficacy of adjunctive VNS for Chinese patients with TRD increased with time.The most frequent adverse effects of VNS treatment were voice alteration and cough frequency increase.

Fine Mapping of the Ph-2 Gene Conferring Resistance to Late Blight (Phytophthora infestans) in Tomato.

Late blight is a devastating tomato disease. Breeding new varieties with multiple resistance (R) genes is highly effective for preventing late blight. The Ph-2 gene mediates resistance to Phytophthora infestans race T1 in tomato. In this study, we used an F2 population derived from a cross between Solanum lycopersicum Moboline (resistant) and LA3988 (susceptible) cultivars for the fine mapping of Ph-2. Two flanking markers, CAPS-1 and CC-Ase, mapped Ph-2 to a 141-kb genomic region containing 21 projected genes, 5 of which were identified as putative R genes. The Solyc10g085460 coding sequence varied significantly between the parents. The markers developed and candidate genes identified in this study shall be useful for the molecular breeding of tomato exhibiting increased late blight resistance and for the cloning of the Ph-2 gene.

Redescription and molecular characterization of sarcocysts of Sarcocystis cymruensis from Norway rats (Rattus norvegicus) and Sarcocystis ratti from black rats (R. rattus) in China.

In the present study, sarcocysts of Sarcocystis cymruensis were found in four of 42 (9.5%) Norway rats and those of S. ratti were observed in six of 60 (10%) black rats in China. With light microscopy, the sarcocysts of the two parasites were microscopic, and had smooth, thin cyst walls (≤ 1 µm). Ultrastructurally, the sarcocysts of S. cymruensis had small, osmiophilic, bleb-like protrusions, similar to type 1c; those of S. ratti had a cyst wall with regular, short, conical protrusions, similar to type 1 g. Three loci, i.e., 18S rDNA, the mitochondrial cox1 gene (Cox1), and the mitochondrial Cytb gene (Cytb), of the two parasites were sequenced and analyzed, and the Cytb sequences of the two parasites constituted the first records of this marker in GenBank. A comparison of the newly obtained sequences of the three loci between the two parasites revealed that the interspecific similarities of 18S rDNA, Cox1, and Cytb were 96.4-97.2%, 96.5%, and 93.7%, respectively. Therefore, the two species could be better discriminated with Cytb than with 18S rDNA and Cox1. Phylogenetic analysis based on 18S rDNA sequences and Cox1 sequences indicated that the two parasites had a close relationship with Sarcocystis in nonruminant animals, especially birds and canids.

Adjunctive Vagus Nerve Stimulation for Treatment-Resistant Depression: a Quantitative Analysis.

Vagus nerve stimulation (VNS) has been increasingly studied in treating treatment-resistant depression (TRD), but the findings have been mixed. This updated meta-analysis was conducted to examine the efficacy and safety of adjunctive VNS for TRD. Controlled studies reporting on the efficacy and safety of adjunctive VNS for TRD were screened, identified and analyzed. Standardized mean difference (SMD), risk ratio (RR) and their 95% confidence intervals (CIs) were analyzed using RevMan version 5.3. Three controlled studies with a total of 1048 patients with TRD compared VNS (n = 622) with control (n = 426) groups. Only one study was rated as 'high quality' using the Jadad scale. Adjunctive VNS was significantly superior to the control group regarding study-defined response [SMD:1.96 (95%CI:1.60, 2.40), P < 0.00001, I2 = 0%]. Patient-reported voice alteration occurred more frequently with adjunctive VNS for patients with TRD. No significant group differences were found regarding discontinuation due to any reason [RR:0.50 (95%CI:0.12, 2.09), P = 0.34, I2 = 85%]. Adjunctive VNS appeared to be effective and relatively safe treatment for TRD. Further randomized controlled trials are needed to confirm the efficacy and safety of VNS for TRD.

[Effect of vasoactive agents on the prognosis of children in the third stage of hand-foot-mouth disease].

OBJECTIVE: To study the effect of the application timing of vasoactive agents on the prognosis of children in the third stage of hand-foot-mouth disease (HFMD). METHODS: A retrospective analysis was performed on the medical data of children in the third stage of HFMD between April 2012 and September 2016. According to the application time of vasoactive agents (milrinone combined with phentolamine) after admission, the children were divided into an early stage (within 2 hours after admission) group with 32 children, a middle stage (within 2-6 hours after admission) group with 28 children, and a late stage (more than 6 hours after admission) group with 26 children. Venous blood samples were collected before vasoactive agent treatment and after 24 hours of vasoactive agent treatment to measure the levels of creatine kinase-MB (CK-MB), troponin (TnI), and brain natriuretic peptide (BNP). The recovery time of left ventricular ejection fraction (LVEF), respiratory rate, blood pressure, and heart rate were recorded. The response rate to the treatment within 72 hours of treatment was evaluated. RESULTS: The early stage group had a significantly higher overall response rate to the treatment than the middle stage and late stage groups (P<0.0167). After 24 hours of treatment, there were significant differences in heart rate, blood pressure, respiratory rate, and LVEF among the three groups (P<0.05). The early stage group showed the most significant improvement in these parameters (P<0.0167). Compared with the middle stage and late stage groups, the early stage group had significantly shorter recovery time of LVEF, respiratory rate, heart rate, and blood pressure (P<0.0167). After 24 hours of treatment, the early stage group had a significantly lower level of BNP than the middle stage and late stage groups (P<0.05). CONCLUSIONS: Vasoactive agents should be given to children with critical HFMD as early as possible to improve cardiovascular function, reduce the risk of disease progression, and improve prognosis.

Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato.

KEY MESSAGE: The tomato gray leaf spot resistance gene Sm was fine-mapped in a 185-kb region through a map-based cloning strategy and genome-wide association study; a candidate gene was proved to be involved in Sm-mediated resistance through transient gene silencing. Gray leaf spot, caused by Stemphylium spp., is a warm weather foliar disease in tomato (Solanum lycopersicum L). Resistance against gray leaf spot is conferred by a single incompletely dominant gene (Sm) located on chromosome 11. This study aimed to map and identify molecular marker tightly linked to the Sm gene for the use of marker-assisted selection in breeding. Using an F2 population derived from a cross between the resistant line '9706' and the susceptible line 'Heinz 1706', the Sm gene was mapped to a 185-kb interval between two markers, InDel343 and InDel-FT-32 on chromosome 11, which was consistent with the result of a genome-wide association study using 289 diverse accessions. An ORF predicted in this region was proved to be involved in Sm-mediated resistance through transient gene silencing and seems to be a good candidate of the Sm locus. To clone the Sm gene, a bacterial artificial chromosome (BAC) library was screened and one BAC clone B80B15 containing the predicted ORF was identified. The analysis of sequence and structure characteristics demonstrated that the candidate gene was not a typical type resistance gene. Additionally, a co-dominant marker Sm-InDel, which produced a 122-bp or 140-bp fragment for resistant or susceptible alleles, respectively, was developed. This marker was validated in 289 germplasm and could be used in marker-assisted selection for gray leaf spot resistance.

B-class MADS-box TM6 is a candidate gene for tomato male sterile-1526.

KEY MESSAGE: Tomato male sterile-1526 locus was fine-mapped to an interval of 44.6 kb, and a B-class MADS-box gene TM6 was identified as the candidate gene. Male sterile lines have been widely used for hybrid seed production in many crop plants. The tomato male sterile-1526 (ms-1526) mutant displays abnormal stamens and exerted stigmas and is suitable for practical use. In this study, the ms-1526 locus was fine-mapped to a 44.6 kb interval that contained four putative genes. Thereinto, Solyc02g084630 encodes tomato B-class MADS-box gene TM6 (syn. TDR6), which plays an important role in stamen development. Sequencing revealed that there was a 12.7 kb deletion in the ms-1526 region, where the promoter and first four exons of the TM6 gene were absent. ms-1547, an allele of ms-1526, also contained the same deletion in the TM6 gene. And the other allele ms-15 mutant contained a single-nucleotide polymorphism (SNP, C to A) in the coding region of the TM6 gene, which led to a missense mutation (G to W). The codominant insertion/deletion (InDel) marker MS26D and codominant derived cleaved amplified polymorphic sequence (dCAPS) marker MS15C were developed based on the deletion and SNP, respectively. A real-time quantitative reverse-transcription PCR showed that expression of the TM6 gene was barely detectable in the flowers of the ms-1526 and ms-1547 mutants. In addition, other floral organ identity genes, pollen development marker genes, and pistil marker genes were differentially expressed between wild type and mutant flowers. These findings may facilitate functional analysis of the TM6 gene and help in the marker-assisted selection of ms-15 and its alleles in tomato breeding.

Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum.

CRISPR/Cas9-guided cytidine deaminase enables C:G to T:A base editing in bacterial genome without introduction of lethal double-stranded DNA break, supplement of foreign DNA template, or dependence on inefficient homologous recombination. However, limited by genome-targeting scope, editing window, and base transition capability, the application of base editing in metabolic engineering has not been explored. Herein, four Cas9 variants accepting different protospacer adjacent motif (PAM) sequences were used to increase the genome-targeting scope of bacterial base editing. After a comprehensive evaluation, we demonstrated that PAM requirement of bacterial base editing can be relaxed from NGG to NG using the Cas9 variants, providing 3.9-fold more target loci for gene inactivation in Corynebacterium glutamicum. Truncated or extended guide RNAs were employed to expand the canonical 5-bp editing window to 7-bp. Bacterial adenine base editing was also achieved with Cas9 fused to adenosine deaminase. With these updates, base editing can serve as an enabling tool for fast metabolic engineering. To demonstrate its potential, base editing was used to deregulate feedback inhibition of aspartokinase via amino acid substitution for lysine overproduction. Finally, a user-friendly online tool named gBIG was provided for designing guide RNAs for base editing-mediated inactivation of given genes in any given sequenced genome (www.ibiodesign.net/gBIG).

Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume.

A Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001T, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001T represents a member of the genus Sphingomonas, with the highest sequence similarity (97.7 %) to the type strain of Sphingomonasginsengisoli. SYSUP0001T grew at 14-37 °C and pH 6-8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001T and closely related members of the genus Sphingomonas were below the cut-off level (95-96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001T (=KCTC 62179 T=CGMCC 1.16462T).

GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli.

BACKGROUND: Late-stage fermentation broth contains high concentrations of target chemicals. Additionally, it contains various cellular metabolites which have leaked from lysed cells, which would exert multifactorial stress to industrial hyperproducers and perturb both cellular metabolism and product formation. Although adaptive laboratory evolution (ALE) has been wildly used to improve stress tolerance of microbial cell factories, single-factor stress condition (i.e. target product or sodium chloride at a high concentration) is currently provided. In order to enhance bacterial stress tolerance to actual industrial production conditions, ALE in late-stage fermentation broth is desired. Genome replication engineering assisted continuous evolution (GREACE) employs mutants of the proofreading element of DNA polymerase complex (DnaQ) to facilitate mutagenesis. Application of GREACE coupled-with selection under stress conditions is expected to accelerate the ALE process. RESULTS: In this study, GREACE was first modified by expressing a DnaQ mutant KR5-2 using an arabinose inducible promoter on a temperature-sensitive plasmid, which resulted in timed mutagenesis introduction. Using this method, tolerance of a lysine hyperproducer E. coli MU-1 was improved by enriching mutants in a lysine endpoint fermentation broth. Afterwards, the KR5-2 expressing plasmid was cured to stabilize acquired genotypes. By subsequent fermentation evaluation, a mutant RS3 with significantly improved lysine production capacity was selected. The final titer, yield and total amount of lysine produced by RS3 in a 5-L batch fermentation reached 155.0 ± 1.4 g/L, 0.59 ± 0.02 g lysine/g glucose, and 605.6 ± 23.5 g, with improvements of 14.8%, 9.3%, and 16.7%, respectively. Further metabolomics and genomics analyses, coupled with molecular biology studies revealed that mutations SpeBA302V, AtpBS165N and SecYM145V mainly contributed both to improved cell integrity under stress conditions and enhanced metabolic flux into lysine synthesis. CONCLUSIONS: Our present study indicates that improving a lysine hyperproducer by GREACE-assisted ALE in its stressful living environment is efficient and effective. Accordingly, this is a promising method for improving other valuable chemical hyperproducers.

Metabolic engineering of Corynebacterium glutamicum by synthetic small regulatory RNAs.

Corynebacterium glutamicum is an important platform strain that is wildly used in industrial production of amino acids and various other biochemicals. However, due to good genomic stability, C. glutamicum is more difficult to engineer than genetically tractable hosts. Herein, a synthetic small regulatory RNA (sRNA)-based gene knockdown strategy was developed for C. glutamicum. The RNA chaperone Hfq from Escherichia coli and a rationally designed sRNA consisting of the E. coli MicC scaffold and a target binding site were proven to be indispensable for repressing green fluorescent protein expression in C. glutamicum. The synthetic sRNA system was applied to improve glutamate production through knockdown of pyk, ldhA, and odhA, resulting almost a threefold increase in glutamate titer and yield. Gene transcription and enzyme activity were down-regulated by up to 80%. The synthetic sRNA system developed holds promise to accelerate C. glutamicum metabolic engineering for producing valuable chemicals and fuels.

Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum).

Internode length is an important agronomic trait affecting plant architecture and crop yield. However, few genes for internode elongation have been identified in tomato. In this study, we characterized an elongated internode inbred line P502, which is a natural mutant of the tomato cultivar 05T606. The mutant P502 exhibits longer internode and higher bioactive GA concentration compared with wild-type 05T606. Genetic analysis suggested that the elongated internode trait is controlled by quantitative trait loci (QTL). Then, we identified a major QTL on chromosome 2 based on molecular markers and bulked segregant analysis (BSA). The locus was designated as EI (Elongated Internode), which explained 73.6% genetic variance. The EI was further mapped to a 75.8-kb region containing 10 genes in the reference Heinz 1706 genome. One single nucleotide polymorphism (SNP) in the coding region of solyc02g080120.1 was identified, which encodes gibberellin 2-beta-dioxygenase 7 (SlGA2ox7). SlGA2ox7, orthologous to AtGA2ox7 and AtGA2ox8, is involved in the regulation of GA degradation. Overexpression of the wild EI gene in mutant P502 caused a dwarf phenotype with a shortened internode. The difference of EI expression levels was not significant in the P502 and wild-type, but the expression levels of GA biosynthetic genes including CPS, KO, KAO, GA20ox1, GA20ox2, GA20ox4, GA3ox1, GA2ox1, GA2ox2, GA2ox4, and GA2ox5, were upregulated in mutant P502. Our results may provide a better understanding of the genetics underlying the internode elongation and valuable information to improve plant architecture of the tomato.

MACBETH: Multiplex automated Corynebacterium glutamicum base editing method.

CRISPR/Cas9 or Cpf1-introduced double strand break dramatically decreases bacterial cell survival rate, which hampers multiplex genome editing in bacteria. In addition, the requirement of a foreign DNA template for each target locus is labor demanding and may encounter more GMO related regulatory hurdle in industrial applications. Herein, we developed a multiplex automated Corynebacterium glutamicum base editing method (MACBETH) using CRISPR/Cas9 and activation-induced cytidine deaminase (AID), without foreign DNA templates, achieving single-, double-, and triple-locus editing with efficiencies up to 100%, 87.2% and 23.3%, respectively. In addition, MACBETH was applied to generate a combinatorial gene inactivation library for improving glutamate production, and pyk&ldhA double inactivation strain was found to improve glutamate production by 3-fold. Finally, MACBETH was automated with an integrated robotic system, which would enable us to generate thousands of rationally engineered strains per month for metabolic engineering of C. glutamicum. As a proof of concept demonstration, the automation platform was used to construct an arrayed genome-scale gene inactivation library of 94 transcription factors with 100% success rate. Therefore, MACBETH would be a powerful tool for multiplex and automated bacterial genome editing in future studies and industrial applications.

Enhancement of the thermal and alkaline pH stability of Escherichia coli lysine decarboxylase for efficient cadaverine production.

OBJECTIVE: To enhance the thermal and alkaline pH stability of the lysine decarboxylase from Escherichia coli (CadA) by engineering the decameric interface and explore its potential for industrial applications. RESULTS: The mutant T88S was designed for improved structural stability by computational analysis. The optimal pH and temperature of T88S were 7.0 and 55 °C (5.5 and 50 °C for wild-type). T88S showed higher thermostability with a 2.9-fold increase in the half-life at 70 °C (from 11 to 32 min) and increased melting temperature (from 76 to 78 °C). Additionally, the specific activity and pH stability (residual activity after 10 h incubation) of T88S at pH 8.0 were increased to 164 U/mg and 78% (58 U/mg and 57% for wild-type). The productivity of cadaverine with T88S (284 g L-lysine L-1 and 5 g DCW L-1) was 40 g L-1 h-1, in contrast to 28 g L-1 h-1 with wild-type. CONCLUSION: The mutant T88S showed high thermostability, pH stability, and activity at alkaline pH, indicating that this mutant is a promising biocatalyst for industrial production of cadaverine.