Molecular characterization of myb-homologous transcriptional factors of the flavonoid pathway in Zea mays

Structural genes encoding enzymes that catalyze each step of flavonoid synthesis are temporally and spatially regulated. It has been shown that specific anthocyanin pigmentation patterns in maize are achieved by the tissue-specific expression of regulatory genes. Moreover, this tissue-specific regulation is a consequence of the generation of different alleles or duplicated copies of regulatory genes during evolution;In contrast, the myb-homologous P1 gene was the only known regulatory gene required for phlobaphene biosynthesis. The isolation and characterization of the P2 gene, reported here, provides direct molecular evidence that the P region contains duplicated genes. Furthermore, the duplicated P1 (herein, P1-rr ) and P2 genes have distinct tissue-specific expression patterns. The diverged 5\u27 regulatory sequences of each gene are proposed to confer their different tissue-specificities. The isolation and characterization of a single copy P-homologous gene (P2-t) from teosinte, and comparison of gene structure and sequences among the P1, P2, and P2-t genes predict a model for generation of the P1/P2 gene complex by gene duplication and subsequent retroelement insertion. The P2 and P1 genes were originally duplicated from an ancestral P gene (closely resembling the teosinte P2-t gene). The duplication generated a tandem repeat of the P gene coding region and 3\u27 flanking region, and thereby placed a P gene coding sequence immediately after a P gene 3 \u27 flanking sequence in a head-to-tail arrangement. In this unique way, the P1 gene acquired new 5\u27 regulatory sequences. Following the gene duplication, retroelement insertions separated the two genes. The site of retroelement insertions was such as to separate the P2 gene from its 3\u27 flanking region. The displaced 3\u27 flanking region is retained as the 5 \u27 flanking region of the P1 gene. This additionally explains the origin of the duplicated flanking sequences at the 5\u27 and 3\u27 ends of the P1 gene. The P2 gene function was investigated by screening maize populations for P2 deletion mutants. It was found that complete loss of silk browning is coincident with the deletion of both P1 and P2 genes. These results suggest that the P2 gene is another contributor to maysin synthesis, a flavonoid compound that inhibits corn earworm feeding. The regulatory function of the P2 gene was further characterized by analysis of maize cell cultures which ectopically express the P2 gene. Northern blot analysis indicates that the ectopically expressed P2 gene can activate expression of the target structural genes C2 and A1. The results support a regulatory role for the P2 gene in flavonoid (maysin) biosynthesis. Additionally, cellular distribution of P transcripts and phlobaphene pigments in developing pericarp were investigated in this thesis

Gut microbial biomarkers for the treatment response in first-episode, drug-naive schizophrenia: a 24-week follow-up study

Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis. However, its role in the antipsychotic treatment response is unclear. Here, we present a 24-week follow-up study to identify gut microbial biomarkers for SCH diagnosis and treatment response, using a sample of 107 first-episode, drug-naive SCH patients, and 107 healthy controls (HCs). We collected biological samples at baseline (all participants) and follow-up time points after risperidone treatment (SCH patients). Treatment response was assessed using the Positive and Negative Symptoms Scale total (PANSS-T) score. False discovery rate was used to correct for multiple testing. We found that SCH patients showed lower alpha-diversity (the Shannon and Simpson\u27s indices) compared to HCs at baseline (p = 1.21 x 10(-9), 1.23 x 10(-8), respectively). We also found a significant difference in beta-diversity between SCH patients and HCs (p = 0.001). At baseline, using microbes that showed different abundance between patients and controls as predictors, a prediction model can distinguish patients from HCs with an area under the curve (AUC) of 0.867. In SCH patients, after 24 weeks of risperidone treatment, we observed an increase of alpha-diversity toward the basal level of HCs. At the genus level, we observed decreased abundance of Lachnoclostridium (p = 0.019) and increased abundance Romboutsia (p = 0.067). Moreover, the treatment response in SCH patients was significantly associated with the basal levels of Lachnoclostridium and Romboutsia (p = 0.005 and 0.006, respectively). Our results suggest that SCH patients may present characteristic microbiota, and certain microbiota biomarkers may predict treatment response in this patient population

MetaCyc: a multiorganism database of metabolic pathways and enzymes

MetaCyc is a database of metabolic pathways and enzymes located at . Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the website. These PGDBs also include predicted operons and pathway hole fillers

Molecular characterization of myb-homologous transcriptional factors of the flavonoid pathway in Zea mays

Structural genes encoding enzymes that catalyze each step of flavonoid synthesis are temporally and spatially regulated. It has been shown that specific anthocyanin pigmentation patterns in maize are achieved by the tissue-specific expression of regulatory genes. Moreover, this tissue-specific regulation is a consequence of the generation of different alleles or duplicated copies of regulatory genes during evolution;In contrast, the myb-homologous P1 gene was the only known regulatory gene required for phlobaphene biosynthesis. The isolation and characterization of the P2 gene, reported here, provides direct molecular evidence that the P region contains duplicated genes. Furthermore, the duplicated P1 (herein, P1-rr ) and P2 genes have distinct tissue-specific expression patterns. The diverged 5' regulatory sequences of each gene are proposed to confer their different tissue-specificities. The isolation and characterization of a single copy P-homologous gene (P2-t) from teosinte, and comparison of gene structure and sequences among the P1, P2, and P2-t genes predict a model for generation of the P1/P2 gene complex by gene duplication and subsequent retroelement insertion. The P2 and P1 genes were originally duplicated from an ancestral P gene (closely resembling the teosinte P2-t gene). The duplication generated a tandem repeat of the P gene coding region and 3' flanking region, and thereby placed a P gene coding sequence immediately after a P gene 3 ' flanking sequence in a head-to-tail arrangement. In this unique way, the P1 gene acquired new 5' regulatory sequences. Following the gene duplication, retroelement insertions separated the two genes. The site of retroelement insertions was such as to separate the P2 gene from its 3' flanking region. The displaced 3' flanking region is retained as the 5 ' flanking region of the P1 gene. This additionally explains the origin of the duplicated flanking sequences at the 5' and 3' ends of the P1 gene. The P2 gene function was investigated by screening maize populations for P2 deletion mutants. It was found that complete loss of silk browning is coincident with the deletion of both P1 and P2 genes. These results suggest that the P2 gene is another contributor to maysin synthesis, a flavonoid compound that inhibits corn earworm feeding. The regulatory function of the P2 gene was further characterized by analysis of maize cell cultures which ectopically express the P2 gene. Northern blot analysis indicates that the ectopically expressed P2 gene can activate expression of the target structural genes C2 and A1. The results support a regulatory role for the P2 gene in flavonoid (maysin) biosynthesis. Additionally, cellular distribution of P transcripts and phlobaphene pigments in developing pericarp were investigated in this thesis.</p

ELISA source data for figshare.xlsx

source data of ELISA test from three cohorts</p