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Background Noise has multiple negative effects on the organism, and gut microbes are influenced by the environment and are closely associated with the development of diseases. Currently, the effects of chronic noise exposure on intestinal microbiota are poorly understood. Objective To investigate the effects of noise exposure on the structure of rat gut microbiota and to make predictions of gut microbiota function. Methods Male Wistar rats (6 weeks old, 160-180 g) were randomly divided into control, NE_95dB, and NE_105dB groups, 10 rats in each group. Rats in the NE_95dB and the NE_105dB groups were exposed to noise at 95 dB sound pressure level (SPL) and 105 dB SPL, respectively, 4 h per day for consecutive 30 d, while the control group was exposed to background noise. Feces were collected after the last noise exposure for intestinal microbiota detection. Based on the 16S ribosomal RNA (rRNA) gene sequencing method, the diversity and structure of microbiota in rat intestinal contents were analyzed and compared. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to predict functions of the identified intestinal microbiota genes. Results Significant differences were found in the microbial structure of the rat gut after the designed noise exposure. In the α diversity results, there was a statistically significant difference in the Chao1 index between the NE_95dB group and the NE_105dB group (P=0.02), while there were no statistically significant differences in the Shannon and Simpson indexes between the noise exposure groups and the control group (P>0.05). The β diversity analysis results showed significant differences in species abundance between the control group and the noise exposure groups (P=0.001). Further species analysis results showed that the relative abundances of the Ruminococcaceae_NK4A214_group (P<0.05) and Peptococcaceae_unclassified (P<0.01) at the genus level were significantly higher in the NE_105dB group, and the relative abundance of Parasutterella (P<0.05) was significantly higher in the NE_95dB group compared to the control group. In addition, the Ruminococcaceae_NK4A214_group (P<0.05) was also significantly higher in the NE_105dB group compared to the NE_95dB group. The PICRUSt functional prediction analysis results showed that there were eight differential pathways between the control group and the NE_95dB group, in which D-arginine and D-ornithine metabolism, ascorbate and aldarate metabolism, carotenoid biosynthesis, glycerophospholipid metabolism, mineral absorption, NOD-like receptor signaling pathway and non-homologous end-joining were significantly down-regulated, and nucleotide metabolism was significantly up-regulated. There were 38 differential pathways between the control group and the NE_105dB group. Among them, D-arginine and D-ornithine metabolism, and mineral absorption were the differential metabolic pathways in both noise exposure groups, and both were down-regulated relative to the control group. Conclusion Chronic noise exposure could alter structure of rat gut microbiota and may affect metabolic functions of multiple microbiota genes.
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The plant growth, development, and secondary metabolism are regulated by R2 R3-MYB transcription factors. This study identified the R2 R3-MYB genes in the genome of Andrographis paniculata and analyzed the chromosomal localization, gene structure, and conserved domains, phylogenetic relationship, and promoter cis-acting elements of these R2 R3-MYB genes. Moreover, the gene expression profiles of R2 R3-MYB genes under abiotic stress and hormone treatments were generated by RNA-seq and validated by qRT-PCR. The results showed that A. paniculata contained 73 R2 R3-MYB genes on 21 chromosomes. These members belonged to 34 subfamilies, 19 of which could be classified into the known subfamilies in Arabidopsis thaliana. The 73 R2 R3-MYB members included 36 acidic proteins and 37 basic proteins, with the lengths of 148-887 aa. The domains, motifs, and gene structures of R2 R3-MYBs in A. paniculata were conserved. The promoter regions of these genes contains a variety of cis-acting elements related to the responses to environmental factors and plant hormones including light, ABA, MeJA, and drought. Based on the similarity of functions of R2 R3-MYBs in the same subfamily and the transcription profiles, ApMYB13/21/35/67/73(S22) may regulate drought stress through ABA pathway; ApMYB20(S11) and ApMYB55(S2) may play a role in the response of A. paniculata to high temperature and UV-C stress; ApMYB5(S7) and ApMYB33(S20) may affect the accumulation of andrographolide by regulating the expression of key enzymes in the MEP pathway. This study provides theoretical reference for further research on the functions of R2 R3-MYB genes in A. paniculata and breeding of A. paniculata varieties with high andrographolide content.
Subject(s)
Andrographis paniculata , Gene Expression Regulation, Plant , Genes, myb , Multigene Family , Phylogeny , Plant Proteins/metabolismABSTRACT
ObjectiveThe type 2C protein phosphatases （PP2C） are involved in numerous plant signal transduction pathways. They mainly participate in plant stress response and regulate second metabolites biosynthesis via negatively regulating MAPK signaling pathway. Herein，we were to identify and analyze PP2C （CsPP2C） gene family from hemp genome，in hope of providing comprehensive insights for studying CsPP2C function during the development of hemp. MethodMolecular Evolutionary Genetics Analysis （MAGA）-X was used to construct phylogenetic tree. Expert Protein Analysis System （ExPASy），WoLF PSORT，Multiple EM for Motif Elicitation （MEME），Batch Conserved Domain Search （Batch-CD-Search），PlantCare，and TBtools were used，respectively，to predict CsPP2C physicochemical properties，subcellular localization，conserved motifs，protein structure，cis-element in promoter and collinearity with Arabidopsis PP2C. Cannabis sativa transcriptome and Real-time polymerase chain reaction（Real-time PCR） were used to analyze and verify gene expressions，respectively. ResultFifty-two CsPP2C with conserved domains were identified from the entire genome of hemp，encoding proteins ranging from 244 to 1 089 aa in length and with molecular weights ranging from 26.76 to 122.53 kDa. Those genes were mainly distributed in the nucleus，cytoplasm and chloroplast. The 47 CsPP2C were divided into 10 subfamilies，and the remaining 5 were not clustered. Seven pairs of homologous genes between hemp and Arabidopsis thaliana were identified according to collinear analysis. The light-responsive elements and abscisic acid elements are most abundant in the prediction. The gene expression heat map showed varied expression pattern of CsPP2C in different tissues. Real-time PCR results of three CsPP2C were consistent with transcriptome data. Moreover，alternative splicing analysis showed that some CsPP2C had alternative-splicing genes during evolution. ConclusionWe predicted and analyzed CsPP2C gene family in genomic scale and showed that CsPP2C are involved in many biological processes，whereby provides foundation for CsPP2C functional study.
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ObjectiveThe type 2C protein phosphatases （PP2C） are involved in numerous plant signal transduction pathways. They mainly participate in plant stress response and regulate second metabolites biosynthesis via negatively regulating MAPK signaling pathway. Herein，we were to identify and analyze PP2C （CsPP2C） gene family from hemp genome，in hope of providing comprehensive insights for studying CsPP2C function during the development of hemp. MethodMolecular Evolutionary Genetics Analysis （MAGA）-X was used to construct phylogenetic tree. Expert Protein Analysis System （ExPASy），WoLF PSORT，Multiple EM for Motif Elicitation （MEME），Batch Conserved Domain Search （Batch-CD-Search），PlantCare，and TBtools were used，respectively，to predict CsPP2C physicochemical properties，subcellular localization，conserved motifs，protein structure，cis-element in promoter and collinearity with Arabidopsis PP2C. Cannabis sativa transcriptome and Real-time polymerase chain reaction（Real-time PCR） were used to analyze and verify gene expressions，respectively. ResultFifty-two CsPP2C with conserved domains were identified from the entire genome of hemp，encoding proteins ranging from 244 to 1 089 aa in length and with molecular weights ranging from 26.76 to 122.53 kDa. Those genes were mainly distributed in the nucleus，cytoplasm and chloroplast. The 47 CsPP2C were divided into 10 subfamilies，and the remaining 5 were not clustered. Seven pairs of homologous genes between hemp and Arabidopsis thaliana were identified according to collinear analysis. The light-responsive elements and abscisic acid elements are most abundant in the prediction. The gene expression heat map showed varied expression pattern of CsPP2C in different tissues. Real-time PCR results of three CsPP2C were consistent with transcriptome data. Moreover，alternative splicing analysis showed that some CsPP2C had alternative-splicing genes during evolution. ConclusionWe predicted and analyzed CsPP2C gene family in genomic scale and showed that CsPP2C are involved in many biological processes，whereby provides foundation for CsPP2C functional study.
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C2H2 transcription factors play an important role in plant growth, development and the regulation of secondary metabolism. This article identifies members of the C2H2 gene family in Cannabis sativa L. at the genome level. Chromosomal location and linkage, evolutionary relationships, and identification of conserved motifs was determined from the C. sativa genome and transcriptome data using bioinformatics tools and on-line websites such as TBtools, MEGA software, NCBI, PlantTFDB, ExPASy, HMMSCAN, MEME, WoLFPSORT and PlantCARE. The results show that C. sativa contains 30 members of the C2H2 gene family (named CsC2H2-1-CsC2H2-30) distributed on 9 chromosomes. The encoded proteins range in length from 138 to 635 amino acids, and the theoretical isoelectric points range from 5.85 to 9.52. Molecular weights range from 15 909.48 to 68 445.53 Da. Transcriptome analysis showed that CsC2H2 was differentially expressed in the female flowers, bracts, leaves, and stems of the Diku variety and female flowers of nine different varieties of C. sativa. Quantitative real-time PCR verified that CsC2H2-1, CsC2H2-5, and CsC2H2-19 were significantly expressed in the female flowers and bracts of the Diku variety. This provides a theoretical basis for in-depth study of the function of the C2H2 gene family and the breeding of high-quality C. sativa varieties.
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To obtain the microbial composition of traditional Chinese medicine of Faeces Trogopterori, ten samples were collected from the imitate wildness farmland in Shangluo City, Shaanxi Province. In this study, 16S rRNA gene was used as molecular marker to explore the microbiome and the sequences were analyzed by Usearch analysis platform. The COG and KEGG database is used to predict and analyze the function of the flora. A great number of 285 218 high quality clean reads with a length of 400-450 bp were obtained from 10 samples. Bacterial species detected in these samples covered 8 phyla, 25 families, 75 genera and 120 species. The dominant phylum microbial communities in these samples were Firmicutes (87.68% ± 2.68%) and the Bacteroidetes (7.62% ± 3.74%), all samples showed a high microbial diversity, the predicted functional metagenome was heavily involved in energy metabolism. This study provided that the beneficial bacteria in Faeces Trogopterori may be one of its active ingredients, and no pathogens are detected in the sample.
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Objective To provide a basis for further study and utilization of the functional gene family of Pht1 in Salviae miltiorrhizae, the Pht1 gene family members from S. miltiorrhizae genome should be explored, identified and functionally predicted. Methods By utilizing the bioinformatics methods, based on the genomic and NCBI database of S. miltiorrhiza, the sequences of Pht1 family candidate genes of S. miltiorrhiza were obtained firstly by screening, and then carried on the multiple sequence alignment, conserved structure lookup as well as phylogenetic tree construction. Finally, the characteristic analysis and biological function prediction were carried out. Results The results showed that 12 Pht1 candidate genes were extracted from the genome of Salvia miltiorrhiza, together with the reported Smpht1, there are 13 Pht1 members in total, their homology as high as 74.34%, and nine members of them could provide more reliable functional annotation. Among the gene family members, Smpht1 & Sm1, Sm4 & Sm6, Sm5 & Sm11, in which these three pairs may share similar function as well as coevolution relation between each other; Smpht1, Sm1, Sm3, Sm5, Sm7, and Sm11, all of the six members can be only expressed in the roots of S. miltiorrhiza. furthermore, except Sm7 induced by p-deficiency and Sm3 member unaffected by the phosphorus supply factor, the other four probably belong to the P-deficiency induced up-regulated expressive genotype, which play an important role in phosphorus absorption of S. miltiorrhiza; Moreover, both Sm7 and Sm16 are possible to expressed in the flower organs of S. miltiorrhiza and then participate in the regulation of phosphorus balance in the flowering stage of plants. In addition, Sm14 is likely to be a mycorrhizal-induced specific expressive gene with the function of phosphorus transfer in Pht1 family members. Conclusion The Pht1 gene family was screened and identified systematically from the genome of S. miltiorrhiza for the first time, in addition, the members with characteristic and biological function were found out, which will provide dependable background support and ideas reference for the further research on the role of Pht1 in the growth and development of S. miltiorrhiza.