Temporal expression of polysaccharide biosynthesis genes in the leaves of Cyclocarya paliurus at different developmental stages

2019 ◽  
Author(s):  
Weida Lin ◽  
Huanwei Chen ◽  
Jianmei Wang ◽  
Yongli Zhen ◽  
Qiuwei Lu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Developmental Stages ◽  
Temporal Expression ◽  
Active Components ◽  
Cyclocarya Paliurus ◽  
Polysaccharide Biosynthesis ◽  
Gras Family ◽  
Polysaccharide Content ◽  
Polysaccharide Synthesis ◽  
Erf Family

Abstract Background: Cyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species. The leaves of C. paliurus are used as a Chinese medicine and the main active components are polysaccharides. However, the temporal pattern of polysaccharide synthesis at different leaf developmental stages has not been reported to date. Results: With the development of leaves, the content of polysaccharides increased first and the highest content was found at the F3 stage (the third larger full expanded leaf). A total of 499710194 clean reads were obtained using C. paliurus genomic data and were assembled into 296593 unigenes. Among 4708 identified DEGs, 429 DEGs were up-regulated and 451 DEGs were down-regulated from F1 stage (the smallest full expanded leaf) to F2 stage (the second larger full expanded leaf), 630 DEGs were up-regulated and 60 DEGs were down-regulated from F2 stage to F3 stage, and 1833 up-regulated and 1816 down-regulated DEGs from F3 stage to F4 stage. Forty DEGs associated with GT belong to 13 GT families. Among them, only one gene was down-regulated from F1 stage to F2 stage, two genes were down-regulated from F2 to F3 stages, and 23 genes were down-regulated and 15 genes were up-regulated from F3 stage to F4 stage, respectively. A significant correlation exists between the five unigenes and the polysaccharide content. UDP-glucose 4-epimerase gene was significantly positively correlated with the polysaccharide content. A pathway map for the biosynthesis of C. paliurus polysaccharide was proposed. Among 150 transcription factors identified from DEGs, the majority was members of the AP2/ERF family (21, 14%), followed by the C2H2 family (14, 9.33%), the MYB family (12, 8%), the C2C2-GATA family (10, 6.67%), the GRAS family (9, 6%), and the zf-HD family (7, 4.67%). Conclusions: These results identified genes involved in the biosynthesis of Cyclocarya paliurus polysaccharides during different leaf developmental stages and provided evidence for the change of polysaccharide content during the development of C. paliurus leaves. Possible synthetic pathways and related transcription factors were suggested. This study provides information for the screening of polysaccharide biosynthesis related genes and elucidates the mechanism underlying polysaccharide biosynthesis in C. paliurus.

scholarly journals Transcriptome analysis associated with polysaccharide synthesis and their antioxidant activity in Cyclocarya paliurus leaves of different developmental stages

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11615
Author(s):  
Weida Lin ◽  
Huanwei Chen ◽  
Jianmei Wang ◽  
Yongli Zheng ◽  
Qiuwei Lu ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Antioxidant Activities ◽  
Reducing Power ◽  
Rna Seq ◽  
Active Components ◽  
Cyclocarya Paliurus ◽  
Polysaccharide Content ◽  
Dependent Relationship ◽  
Polysaccharide Synthesis ◽  
Dose Dependent

Background Cyclocarya paliurus (Batal.) Iljinskaja is a common endemic tree species and used as a Chinese medicine. The main active components in the leaves of this plant are polysaccharides. However, the temporal patterns of gene expression underlying the synthesis of polysaccharides in C. paliurus at different leaf developmental stages and its relationship with the polysaccharide content and antioxidant activities has not been reported to date. Methods RNA-seq was used to investigate the biosynthesis pathway of polysaccharides at the four developmental stages of C. paliurus leaves. The content and the antioxidant activities of polysaccharides were measured with typical biochemical methods and the identified correlations were statistically evaluated. Results Sixty-nine differentially expressed genes were found in the leaves during different developmental stages of C. paliurus. These are associated with glycosyltransferases and belong to 18 families. During different developmental stages of C. paliurus, the polysaccharide content first increased and then decreased, and the UDP-glucose 4-epimerase gene was found to be significantly positively correlated with the polysaccharide content. The clearance rates of DPPH radicals, superoxide anion radicals, hydroxyl radicals, and the reducing power of polysaccharides in the leaves of C. paliurus at different developmental stages showed a dose-dependent relationship with the concentration of polysaccharides. Conclusions The smallest fully expanded leaves are suitable for high-quality tea, and leaves with sizes below the largest fully expanded leaves are suitable for industrial production of polysaccharides.

scholarly journals Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus

2020 ◽  
Vol 21 (4) ◽  
pp. 1337 ◽  
Author(s):  
Weida Lin ◽  
Yueling Li ◽  
Qiuwei Lu ◽  
Hongfei Lu ◽  
Junmin Li
Keyword(s):  
Transcription Factors ◽  
Candidate Genes ◽  
Phenolic Acid ◽  
Developmental Stages ◽  
Ultra Performance Liquid Chromatography ◽  
Differentially Expressed ◽  
Regulation Mechanism ◽  
Acid Biosynthesis ◽  
Cyclocarya Paliurus ◽  
Helix Loop Helix

To assess changes of metabolite content and regulation mechanism of the phenolic acid biosynthesis pathway at different developmental stages of leaves, this study performed a combined metabolome and transcriptome analysis of Cyclocarya paliurus leaves at different developmental stages. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. Transcriptome identification showed that 58 genes were involved in the biosynthesis of phenolic acid. Among them, 10 differentially expressed genes were detected between every two developmental stages. Identification and quantification of metabolites indicated that 14 metabolites were located in the phenolic acid biosynthetic pathway. Among them, eight differentially accumulated metabolites were detected between every two developmental stages. Association analysis between metabolome and transcriptome showed that six differentially expressed structural genes were significantly positively correlated with metabolite accumulation and showed similar expression trends. A total of 128 transcription factors were identified that may be involved in the regulation of phenolic acid biosynthesis; these include 12 MYBs and 10 basic helix–loop–helix (bHLH) transcription factors. A regulatory network of the phenolic acid biosynthesis was established to visualize differentially expressed candidate genes that are involved in the accumulation of metabolites with significant differences. The results of this study contribute to the further understanding of phenolic acid biosynthesis during the development of leaves of C. paliurus.

Temporal expression of pluripotency-associated transcription factors in sheep and cattle preimplantation embryos

Zygote ◽  
2018 ◽  
Vol 26 (4) ◽  
pp. 270-278 ◽  
Author(s):  
P.G.C. Silva ◽  
M.T. Moura ◽  
R.L.O. Silva ◽  
P.S. Nascimento ◽  
J.B. Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Developmental Stages ◽  
Quantitative Polymerase Chain Reaction ◽  
Mammalian Species ◽  
Preimplantation Development ◽  
Preimplantation Embryos ◽  
Temporal Expression ◽  
Cleavage Stage ◽  
Specific Regulation ◽  
Cattle And Sheep

SummaryPluripotency-associated transcription factors (PATFs) modulate gene expression during early mammalian embryogenesis. Despite a strong understanding of PATFs during mouse embryogenesis, limited progress has been made in ruminants. This work aimed to describe the temporal expression of eight PATFs during both sheep and cattle preimplantation development. Transcript availability of PATFs was evaluated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in eggs, cleavage-stage embryos, morulae, and blastocysts. Transcripts of five genes were detected in all developmental stages of both species (KLF5, OCT4, RONIN, ZFP281, and ZFX). Furthermore, CMYC was detected in all cattle samples but was found from cleavage-stage onwards in sheep. In contrast, NR0B1 was detected in all sheep samples but was not detected in cattle morulae. GLIS1 displayed the most significant variation in temporal expression between species, as this PATF was only detected in cattle eggs and sheep cleavage-stage embryos and blastocysts. In silico analysis suggested that cattle and sheep PATFs share similar size, isometric point and molecular weight. A phenetic analysis showed two patterns of PATF clustering between cattle and sheep, among several mammalian species. In conclusion, the temporal expression of pluripotency-associated transcription factors differs between sheep and cattle, suggesting species-specific regulation during preimplantation development.

scholarly journals A candidate gene identified in converting platycoside E to platycodin D from Platycodon grandiflorus by transcriptome and main metabolites analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinglong Su ◽  
Yingying Liu ◽  
Lu Han ◽  
Zhaojian Wang ◽  
Mengyang Cao ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Orthogonal Experiment ◽  
Triterpenoid Saponin ◽  
Gene Encoding ◽  
Triterpenoid Saponins ◽  
Platycodin D ◽  
Polysaccharide Content ◽  
Saponin Biosynthesis ◽  
Polysaccharide Synthesis ◽  
Experimental Use

AbstractPlatycodin D and platycoside E are two triterpenoid saponins in Platycodon grandiflorus, differing only by two glycosyl groups structurally. Studies have shown β-Glucosidase from bacteria can convert platycoside E to platycodin D, indicating the potential existence of similar enzymes in P. grandiflorus. An L9(34) orthogonal experiment was performed to establish a protocol for calli induction as follows: the optimal explant is stems with nodes and the optimum medium formula is MS + NAA 1.0 mg/L + 6-BA 0.5 mg/L to obtain callus for experimental use. The platycodin D, platycoside E and total polysaccharides content between callus and plant organs varied wildly. Platycodin D and total polysaccharide content of calli was found higher than that of leaves. While, platycoside E and total polysaccharide content of calli was found lower than that of leaves. Associating platycodin D and platycoside E content with the expression level of genes involved in triterpenoid saponin biosynthesis between calli and leaves, three contigs were screened as putative sequences of β-Glucosidase gene converting platycoside E to platycodin D. Besides, we inferred that some transcription factors can regulate the expression of key enzymes involved in triterpernoid saponins and polysaccharides biosynthesis pathway of P. grandiflorus. Totally, a candidate gene encoding enzyme involved in converting platycoside E to platycodin D, and putative genes involved in polysaccharide synthesis in P. grandiflorus had been identified. This study will help uncover the molecular mechanism of triterpenoid saponins biosynthesis in P. grandiflorus.

scholarly journals UDP-glucose dehydrogenases of maize: a role in cell wall pentose biosynthesis

2005 ◽  
Vol 391 (2) ◽  
pp. 409-415 ◽  
Author(s):  
Anna Kärkönen ◽  
Alain Murigneux ◽  
Jean-Pierre Martinant ◽  
Elodie Pepey ◽  
Christophe Tatout ◽  
...  
Keyword(s):  
Cell Wall ◽  
Sequence Similarity ◽  
Glucose Dehydrogenase ◽  
Soya Bean ◽  
Amino Acid Sequences ◽  
Cell Wall Polysaccharide ◽  
Polysaccharide Biosynthesis ◽  
Polysaccharide Synthesis ◽  
Ethanol Dehydrogenase ◽  
Adh Activity

UDPGDH (UDP-D-glucose dehydrogenase) oxidizes UDP-Glc (UDP-D-glucose) to UDP-GlcA (UDP-D-glucuronate), the precursor of UDP-D-xylose and UDP-L-arabinose, major cell wall polysaccharide precursors. Maize (Zea mays L.) has at least two putative UDPGDH genes (A and B), according to sequence similarity to a soya bean UDPGDH gene. The predicted maize amino acid sequences have 95% similarity to that of soya bean. Maize mutants with a Mu-element insertion in UDPGDH-A or UDPGDH-B were isolated (udpgdh-A1 and udpgdh-B1 respectively) and studied for changes in wall polysaccharide biosynthesis. The udpgdh-A1 and udpgdh-B1 homozygotes showed no visible phenotype but exhibited 90 and 60–70% less UDPGDH activity respectively than wild-types in a radiochemical assay with 30 μM UDP-glucose. Ethanol dehydrogenase (ADH) activity varied independently of UDPGDH activity, supporting the hypothesis that ADH and UDPGDH activities are due to different enzymes in maize. When extracts from wild-types and udpgdh-A1 homozygotes were assayed with increasing concentrations of UDP-Glc, at least two isoforms of UDPGDH were detected, having Km values of approx. 380 and 950 μM for UDP-Glc. Leaf and stem non-cellulosic polysaccharides had lower Ara/Gal and Xyl/Gal ratios in udpgdh-A1 homozygotes than in wild-types, whereas udpgdh-B1 homozygotes exhibited more variability among individual plants, suggesting that UDPGDH-A activity has a more important role than UDPGDH-B in UDP-GlcA synthesis. The fact that mutation of a UDPGDH gene interferes with polysaccharide synthesis suggests a greater importance for the sugar nucleotide oxidation pathway than for the myo-inositol pathway in UDP-GlcA biosynthesis during post-germinative growth of maize.

MULTIPLE PAR AND E4BP4 bZIP TRANSCRIPTION FACTORS IN ZEBRAFISH: DIVERSE SPATIAL AND TEMPORAL EXPRESSION PATTERNS

2010 ◽  
Vol 27 (8) ◽  
pp. 1509-1531 ◽  
Author(s):  
Zohar Ben-Moshe ◽  
Gad Vatine ◽  
Shahar Alon ◽  
Adi Tovin ◽  
Philipp Mracek ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Temporal Expression ◽  
Bzip Transcription Factors

scholarly journals Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative Upland Cotton line (Gossypium hirsutum L.)

2020 ◽  
Author(s):  
Li Wen ◽  
Wei Li ◽  
Stephen Parris ◽  
Matthew West ◽  
John Lawson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Transcription Factors ◽  
Gossypium Hirsutum ◽  
Embryogenic Callus ◽  
Developmental Stages ◽  
Baby Boom ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Study Gene Expression

Abstract • Background • Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. • Results • In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5,333 differentially expressed genes (DEG) with 2,534 upregulated and 2,799 downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias. • Conclusions • This comparative analysis of NEC and EC transcriptomes gives new insights into the genetic underpinnings of somatic embryogenesis in cotton.

Differential expression sites of TGF-β isoforms in chicken limb buds during morphogenesis

2005 ◽  
Vol 83 (4) ◽  
pp. 620-625 ◽  
Author(s):  
Shinya Aramaki ◽  
Fuminori Sato ◽  
Tomoki Soh ◽  
Nobuhiko Yamauchi ◽  
Masa-aki Hattori
Keyword(s):  
Limb Development ◽  
Developmental Stages ◽  
Polymerase Chain Reaction Analysis ◽  
Weak Signal ◽  
Temporal Expression ◽  
Chain Reaction ◽  
White Leghorn Chicken ◽  
Whole Mount ◽  
Polymerase Chain

TGF-β gene is expressed at various developmental stages and its principle role may be an involvement in organogenesis. The present study was performed to investigate the temporal expression of these TGF-β isoforms in the developing limb of White Leghorn Chicken, Gallus gallus (L., 1758). TGF-β isoforms were expressed in the developing limb as revealed by whole-mount in situ hybridization, but each showed a different pattern of expression. TGF-β2 was the dominant isoform compared with the other two isoforms. TGF-β2 first appeared along the proximodistal axis of the limb at stage 24 and condensed at the tip at stage 26. At stages 29–31, expression appeared in digits and then was extended to the interdigital spaces. A weak signal for TGF-β3 was first shown in the developing limb at stage 26, but there was no interdigital expression, unlike for TGF-β2. TGF-β4 was expressed in the developing limb at stage 26 and only in the interdigital spaces at stage 29. Reverse transcription – polymerase chain reaction analysis also showed that the transcript levels of TGF-β isoforms, especially TGF-β2, drastically increased at stage 29. These results suggest that TGF-β isoforms, with their patterns of expression, are specific regulatory factors that participate in limb development and digit morphogenesis.

Functional equivalence of the transcription factors Pax2 and Pax5 in mouse development

Development ◽  
2000 ◽  
Vol 127 (17) ◽  
pp. 3703-3713 ◽  
Author(s):  
M. Bouchard ◽  
P. Pfeffer ◽  
M. Busslinger
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Brain Regions ◽  
Vertebrate Evolution ◽  
Developmental Expression ◽  
Temporal Expression ◽  
Mouse Development ◽  
Highly Sensitive ◽  
Organizing Center ◽  
Cerebellum Development

Pax2 and Pax5 arose by gene duplication at the onset of vertebrate evolution and have since diverged in their developmental expression patterns. They are expressed in different organs of the mouse embryo except for their coexpression at the midbrain-hindbrain boundary (MHB), which functions as an organizing center to control midbrain and cerebellum development. During MHB development, Pax2 expression is initiated prior to Pax5 transcription, and Pax2(−/−) embryos fail to generate the posterior midbrain and cerebellum, whereas Pax5(−/−) mice exhibit only minor patterning defects in the same brain regions. To investigate whether these contrasting phenotypes are caused by differences in the temporal expression or biochemical activity of these two transcription factors, we have generated a knock-in (ki) mouse, which expresses a Pax5 minigene under the control of the Pax2 locus. Midbrain and cerebellum development was entirely rescued in Pax2(5ki/5ki) embryos. Pax5 could furthermore completely substitute for the Pax2 function during morphogenesis of the inner ear and genital tracts, despite the fact that the Pax5 transcript of the Pax2(5ki)allele was expressed only at a fivefold lower level than the wild-type Pax2 mRNA. As a consequence, the Pax2(5ki)allele was able to rescue most but not all Pax2 mutant defects in the developing eye and kidney, both of which are known to be highly sensitive to Pax2 protein dosage. Together these data demonstrate that the transcription factors Pax2 and Pax5 have maintained equivalent biochemical functions since their divergence early in vertebrate evolution.

scholarly journals Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Li Wen ◽  
Wei Li ◽  
Stephen Parris ◽  
Matthew West ◽  
John Lawson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Transcription Factors ◽  
Gossypium Hirsutum ◽  
Embryogenic Callus ◽  
Developmental Stages ◽  
Baby Boom ◽  
Expression Profiles ◽  
Study Gene Expression ◽  
Ec Cells

Abstract Background Genotype independent transformation and whole plant regeneration through somatic embryogenesis relies heavily on the intrinsic ability of a genotype to regenerate. The critical genetic architecture of non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells in a highly regenerable cotton genotype is unknown. Results In this study, gene expression profiles of a highly regenerable Gossypium hirsutum L. cultivar, Jin668, were analyzed at two critical developmental stages during somatic embryogenesis, non-embryogenic callus (NEC) cells and embryogenic callus (EC) cells. The rate of EC formation in Jin668 is 96%. Differential gene expression analysis revealed a total of 5333 differentially expressed genes (DEG) with 2534 genes upregulated and 2799 genes downregulated in EC. A total of 144 genes were unique to NEC cells and 174 genes were unique to EC. Clustering and enrichment analysis identified genes upregulated in EC that function as transcription factors/DNA binding, phytohormone response, oxidative reduction, and regulators of transcription; while genes categorized in methylation pathways were downregulated. Four key transcription factors were identified based on their sharp upregulation in EC tissue; LEAFY COTYLEDON 1 (LEC1), BABY BOOM (BBM), FUSCA (FUS3) and AGAMOUS-LIKE15 with distinguishable subgenome expression bias. Conclusions This comparative analysis of NEC and EC transcriptomes gives new insights into the genes involved in somatic embryogenesis in cotton.

Sign in / Sign up

Export Citation Format

Share Document