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1.
PLoS Comput Biol ; 16(4): e1007197, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32275650

RESUMO

Accurate manipulation of metabolites in monolignol biosynthesis is a key step for controlling lignin content, structure, and other wood properties important to the bioenergy and biomaterial industries. A crucial component of this strategy is predicting how single and combinatorial knockdowns of monolignol specific gene transcripts influence the abundance of monolignol proteins, which are the driving mechanisms of monolignol biosynthesis. Computational models have been developed to estimate protein abundances from transcript perturbations of monolignol specific genes. The accuracy of these models, however, is hindered by their inability to capture indirect regulatory influences on other pathway genes. Here, we examine the manifestation of these indirect influences on transgenic transcript and protein abundances, identifying putative indirect regulatory influences that occur when one or more specific monolignol pathway genes are perturbed. We created a computational model using sparse maximum likelihood to estimate the resulting monolignol transcript and protein abundances in transgenic Populus trichocarpa based on targeted knockdowns of specific monolignol genes. Using in-silico simulations of this model and root mean square error, we showed that our model more accurately estimated transcript and protein abundances, in comparison to previous models, when individual and families of monolignol genes were perturbed. We leveraged insight from the inferred network structure obtained from our model to identify potential genes, including PtrHCT, PtrCAD, and Ptr4CL, involved in post-transcriptional and/or post-translational regulation. Our model provides a useful computational tool for exploring the cascaded impact of single and combinatorial modifications of monolignol specific genes on lignin and other wood properties.


Assuntos
Biologia Computacional/métodos , Lignina/genética , Lignina/metabolismo , Regulação da Expressão Gênica de Plantas/genética , Técnicas de Silenciamento de Genes/métodos , Lignina/biossíntese , Modelos Teóricos , Populus/genética , Madeira/genética
2.
Mol Genet Genomics ; 295(3): 717-739, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32124034

RESUMO

The phenylpropanoid pathway is an important route of secondary metabolism involved in the synthesis of different phenolic compounds such as phenylpropenes, anthocyanins, stilbenoids, flavonoids, and monolignols. The flux toward monolignol biosynthesis through the phenylpropanoid pathway is controlled by specific genes from at least ten families. Lignin polymer is one of the major components of the plant cell wall and is mainly responsible for recalcitrance to saccharification in ethanol production from lignocellulosic biomass. Here, we identified and characterized sugarcane candidate genes from the general phenylpropanoid and monolignol-specific metabolism through a search of the sugarcane EST databases, phylogenetic analysis, a search for conserved amino acid residues important for enzymatic function, and analysis of expression patterns during culm development in two lignin-contrasting genotypes. Of these genes, 15 were cloned and, when available, their loci were identified using the recently released sugarcane genomes from Saccharum hybrid R570 and Saccharum spontaneum cultivars. Our analysis points out that ShPAL1, ShPAL2, ShC4H4, Sh4CL1, ShHCT1, ShC3H1, ShC3H2, ShCCoAOMT1, ShCOMT1, ShF5H1, ShCCR1, ShCAD2, and ShCAD7 are strong candidates to be bona fide lignin biosynthesis genes. Together, the results provide information about the candidate genes involved in monolignol biosynthesis in sugarcane and may provide useful information for further molecular genetic studies in sugarcane.


Assuntos
Vias Biossintéticas/genética , Lignina/biossíntese , Proteínas de Plantas/genética , Propanóis/metabolismo , Saccharum/genética , Saccharum/metabolismo , Regulação da Expressão Gênica de Plantas , Genótipo , Lignina/genética , Propanóis/química , Saccharum/classificação , Saccharum/crescimento & desenvolvimento
3.
Artigo em Inglês | MEDLINE | ID: mdl-32005395

RESUMO

MicroRNA (miRNA)-mediated post-transcriptional regulation plays a vital role in the response of plants to pathogens. Although the microRNA397 family has been implicated in physiological processes as an important regulator, little is known about its function in the resistance of plants to pathogens. Here, Malus hupehensis miR397, which was induced by Botryosphaeria dothidea infection, was identified to directly target M. hupehensis Laccase7 (MhLAC7). The expression analysis of mature Mh-miR397 and MhLAC7 revealed their partly opposite expression patterns. The coexpression of Mh-miR397b in MhLAC7 overexpressing Nicotiana benthamiana suppressed the accumulation of exogenous MhLAC7 and endogenous NbLAC7, which led to decreased lignin content and reduced plant resistance to Botrytis cinerea. As reflected by increasing disease severity and pathogen growth, overexpression of miR397b in both the resistant M. hupehensis and susceptible M. domestica 'Gala' resulted in an increased sensitivity to B. dothidea infection, owing to reduced LAC7 expression and lignin content; however, the inhibition of miR397 had opposite effects. MicroRNA397 functions as a negative regulator in the resistance of Malus to B. dothidea by modulating the LAC7 expression and lignin biosynthesis.


Assuntos
Ascomicetos/fisiologia , Malus/genética , MicroRNAs/genética , Doenças das Plantas/genética , Proteínas de Plantas/genética , RNA de Plantas/genética , Resistência à Doença , Regulação da Expressão Gênica de Plantas , Lignina/biossíntese , Lignina/genética , Malus/metabolismo , Malus/microbiologia , MicroRNAs/metabolismo , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Plantas Geneticamente Modificadas/microbiologia , RNA de Plantas/metabolismo , Tabaco/genética , Tabaco/metabolismo , Tabaco/microbiologia
4.
Plant Cell Rep ; 39(4): 445-455, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31912218

RESUMO

KEY MESSAGE: An AP2 family gene CBX1 is involved in mycorrhizal symbiosis and growth of Lotus japonicus. APETALA 2 (AP2) transcriptional regulator is highly conserved in plants. CBX1 from Lotus japonicus is a member of AP2 family. AMF (Arbuscular mycorrhizal fungi) inoculation experiment demonstrated that expression of CBX1 was significantly induced by AMF. Further promoter analysis showed that the - 764 to - 498 bp region of the CBX1 promoter containing CTTC motif is the AMF responsive region. Functional analysis of cbx1 mutant suggested CBX1 is critical for mycorrhizal symbiosis, especially for arbuscule formation. Moreover, under noncolonized condition, overexpression of CBX1 reduced the root length of L. japonicus but increased the size of root system and shoot length, whereas cbx1 mutant reduced the root size and shoot length, but not effect on root length. In addition, cbx1 altered activity of monolignol biosynthetic gene and increased lignin levels. Collectively, these data indicated that CBX1 is a positive regulator of symbiotic activity and plays roles in the growth of L. japonicus.


Assuntos
Lotus/microbiologia , Micorrizas/metabolismo , Proteínas de Plantas/metabolismo , Simbiose/genética , Fatores de Transcrição/metabolismo , Regulação da Expressão Gênica de Plantas/genética , Lignina/biossíntese , Lignina/genética , Lignina/metabolismo , Lotus/genética , Lotus/crescimento & desenvolvimento , Lotus/metabolismo , Mutação , Micorrizas/genética , Micorrizas/crescimento & desenvolvimento , Proteínas de Plantas/genética , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/metabolismo , Plantas Geneticamente Modificadas , Regiões Promotoras Genéticas , RNA-Seq , Simbiose/fisiologia , Fatores de Transcrição/genética , Transcriptoma/genética , Regulação para Cima
5.
Artigo em Inglês | MEDLINE | ID: mdl-31884241

RESUMO

Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.


Assuntos
Fibra de Algodão , Genes de Plantas , Gossypium , Lignina , Celulose/química , Fibra de Algodão/normas , Genes de Plantas/genética , Gossypium/química , Gossypium/genética , Lignina/biossíntese , Lignina/genética , Pesquisa/tendências , Transcriptoma
6.
Int J Mol Sci ; 20(23)2019 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-31810184

RESUMO

Caffeoyl shikimate esterase (CSE) has been reported to be involved in lignin biosynthesis; however, studies of CSE in gymnosperms are lacking. In this study, CSE was successfully cloned from Larix kaempferi (LkCSE) based on Larix laricina transcriptome screening. LkCSE was likely to have catalytic activity based on homologous sequence alignment and phylogenetic analyses of CSEs from different species. In vitro assays with the recombinant enzyme validated the catalytic activity of LkCSE, indicating its function in converting caffeoyl shikimate into caffeate and shikimate. Additionally, the optimum reaction pH and temperature of LkCSE were determined to be 6.0 and 30 °C, respectively. The values of Km and Vmax of CSE for caffeoyl shikimate were 98.11 µM and 14.44 nM min-1, respectively. Moreover, LkCSE was observed to have tissue expression specificity and was abundantly expressed in stems and leaves, especially stems, which was 50 times higher than the expression levels of roots. Lastly, translational fusion assays using LkCSE fused with green fluorescent proteins (GFP) in tobacco leaves indicated that LkCSE was localized in the plasma membrane and endoplasmic reticulum (ER). These results revealed that CSE clearly functions in gymnosperms and it is possible for LkCSE to interact with other ER-resident proteins and regulate mass flux in the monolignol biosynthesis pathway.


Assuntos
Proteínas de Arabidopsis/química , Hidrolases de Éster Carboxílico/química , Larix/enzimologia , Lignina/biossíntese , Arabidopsis/enzimologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Hidrolases de Éster Carboxílico/genética , Cycadopsida/enzimologia , Cycadopsida/genética , Regulação da Expressão Gênica de Plantas , Larix/genética , Lignina/genética , Filogenia , Plantas Geneticamente Modificadas/enzimologia , Plantas Geneticamente Modificadas/genética , Ácido Chiquímico/química
7.
Molecules ; 24(23)2019 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-31783586

RESUMO

A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.


Assuntos
Frutas/metabolismo , Lignina/biossíntese , Doenças das Plantas , Proteínas de Plantas/metabolismo , Pyrus/genética , Fatores de Transcrição/metabolismo , Aldeído Oxirredutases/genética , Aldeído Oxirredutases/metabolismo , Frutas/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Dureza/fisiologia , Filogenia , Doenças das Plantas/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Caules de Planta/metabolismo , Plantas Geneticamente Modificadas/citologia , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Pyrus/metabolismo , RNA-Seq , Metabolismo Secundário , Tabaco/genética , Tabaco/metabolismo , Transativadores/genética , Transativadores/metabolismo , Fatores de Transcrição/genética
8.
Sci Rep ; 9(1): 20117, 2019 12 27.
Artigo em Inglês | MEDLINE | ID: mdl-31882839

RESUMO

Transgenic switchgrass overexpressing Lolium perenne L. delta1-pyrroline 5-carboxylate synthase (LpP5CS) in group I (TG4 and TG6 line) and group II (TG1 and TG2 line) had significant P5CS and ProDH enzyme activities, with group I plants (TG4 and TG6) having higher P5CS and lower ProDH enzyme activity, while group II plants had higher ProDH and lower P5CS enzyme activity. We found group II transgenic plants showed stunted growth, and the changed proline content in overexpressing transgenic plants may influence the growth and development in switchgrass. RNA-seq analysis showed that KEGG enrichment included phenylpropanoid biosynthesis pathway among group I, group II and WT plants, and the expression levels of genes related to lignin biosynthesis were significantly up-regulated in group II. We also found that lignin content in group II transgenic plants was higher than that in group I and WT plants, suggesting that increased lignin content may suppress switchgrass growth and development. This study uncover that proline can appropriately reduce lignin biosynthesis to improve switchgrass growth and development. Therefore, appropriate reduction in lignin content and increase in biomass are important for bioenergy crop to lower processing costs for biomass fermentation-derived fuels.


Assuntos
Lignina/biossíntese , Panicum/crescimento & desenvolvimento , Panicum/metabolismo , Desenvolvimento Vegetal , Prolina/metabolismo , Regulação da Expressão Gênica de Plantas , Redes e Vias Metabólicas , NADP/genética , NADP/metabolismo , Panicum/genética , Fenótipo , Desenvolvimento Vegetal/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas
9.
BMC Genomics ; 20(1): 875, 2019 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-31747881

RESUMO

BACKGROUND: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation. RESULTS: We identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others. CONCLUSIONS: SNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.


Assuntos
Genoma de Planta , Redes e Vias Metabólicas/genética , Populus/genética , Característica Quantitativa Herdável , Madeira/genética , California , Carbono/metabolismo , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Lignina/biossíntese , Metaboloma , Nitrogênio/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Polimorfismo de Nucleotídeo Único , Populus/metabolismo , Sequenciamento Completo do Exoma , Madeira/metabolismo
10.
BMC Plant Biol ; 19(1): 486, 2019 Nov 11.
Artigo em Inglês | MEDLINE | ID: mdl-31711424

RESUMO

BACKGROUND: Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species. RESULTS: Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERULATE 5-HYDROXYLASE1 (F5H1), encoding an enzyme involved in the biosynthesis of sinapyl alcohol (S unit monolignol), was elevated in OXPdWND3A transgenic plants. Saccharification analysis indicated that the rate of sugar release was reduced in the transgenic plants. In addition, OXPdWND3A transgenic plants produced lower amounts of biomass than wild-type plants. CONCLUSIONS: PdWND3A affects lignin biosynthesis and composition and negatively impacts sugar release and biomass production.


Assuntos
Lignina/biossíntese , Proteínas de Plantas/genética , Populus/genética , Fatores de Transcrição/genética , Perfilação da Expressão Gênica , Lignina/química , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Populus/química , Populus/metabolismo , Fatores de Transcrição/metabolismo
11.
BMC Plant Biol ; 19(1): 432, 2019 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-31623554

RESUMO

BACKGROUND: Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.). RESULTS: In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers. CONCLUSION: We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.


Assuntos
Proteínas de Arabidopsis/metabolismo , Gossypium/genética , Lignina/biossíntese , Proteínas Repressoras/metabolismo , Fatores de Transcrição/metabolismo , Proteínas de Arabidopsis/genética , Sítios de Ligação , Parede Celular/metabolismo , Fibra de Algodão , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Gossypium/metabolismo , Família Multigênica , Fenótipo , Filogenia , Reguladores de Crescimento de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas/genética , Proteínas Repressoras/genética , Fatores de Transcrição/genética , Técnicas do Sistema de Duplo-Híbrido
12.
Genes (Basel) ; 10(11)2019 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-31653111

RESUMO

Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie.


Assuntos
Boehmeria/genética , Lignina/biossíntese , Locos de Características Quantitativas , Transcriptoma , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla , Lignina/genética
13.
BMC Genomics ; 20(1): 785, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31664907

RESUMO

BACKGROUND: The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. RESULTS: High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. CONCLUSIONS: Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.


Assuntos
Parede Celular/genética , Caules de Planta/genética , Transcriptoma , Zea mays/genética , Arabidopsis/genética , Parede Celular/metabolismo , Parede Celular/ultraestrutura , Celulose/biossíntese , Lignina/biossíntese , Família Multigênica , Melhoramento Vegetal , Caules de Planta/crescimento & desenvolvimento , Caules de Planta/metabolismo , Regiões Promotoras Genéticas , Xilanos/biossíntese , Zea mays/crescimento & desenvolvimento , Zea mays/metabolismo , Zea mays/ultraestrutura
14.
BMC Plant Biol ; 19(1): 417, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31604417

RESUMO

BACKGROUND: The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. RESULTS: In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. CONCLUSIONS: Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.


Assuntos
Aldeído Oxirredutases/genética , Frutas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Pyrus/genética , Transcriptoma , Aldeído Oxirredutases/metabolismo , Frutas/genética , Perfilação da Expressão Gênica , Lignina/biossíntese , Proteínas de Plantas/metabolismo , Pyrus/crescimento & desenvolvimento
15.
Genes (Basel) ; 10(9)2019 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-31500311

RESUMO

Wood, the most abundant biomass on Earth, is composed of secondary xylem differentiated from vascular cambium. However, the underlying molecular mechanisms of wood formation remain largely unclear. To gain insight into wood formation, we performed a series of wood-forming tissue-specific transcriptome analyses from a hybrid poplar (Populus alba × P. glandulosa, clone BH) using RNA-seq. Together with shoot apex and leaf tissue, cambium and xylem tissues were isolated from vertical stem segments representing a gradient of secondary growth developmental stages (i.e., immature, intermediate, and mature stem). In a comparative transcriptome analysis of the 'developing xylem' and 'leaf' tissue, we could identify critical players catalyzing each biosynthetic step of secondary wall components (e.g., cellulose, xylan, and lignin). Several candidate genes involved in the initiation of vascular cambium formation were found via a co-expression network analysis using abundantly expressed genes in the 'intermediate stem-derived cambium' tissue. We found that transgenic Arabidopsis plants overexpressing the PtrHAM4-1, a GRAS family transcription factor, resulted in a significant increase of vascular cambium development. This phenotype was successfully reproduced in the transgenic poplars overexpressing the PtrHAM4-1. Taken together, our results may serve as a springboard for further research to unravel the molecular mechanism of wood formation, one of the most important biological processes on this planet.


Assuntos
Câmbio/genética , Parede Celular/genética , Populus/genética , Transcriptoma , Câmbio/crescimento & desenvolvimento , Parede Celular/metabolismo , Lignina/biossíntese , Lignina/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Caules de Planta/genética , Caules de Planta/crescimento & desenvolvimento , Populus/crescimento & desenvolvimento , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Xilanos/biossíntese , Xilanos/genética , Xilema/genética , Xilema/crescimento & desenvolvimento
16.
Int J Mol Sci ; 20(18)2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31510041

RESUMO

Apple skin russeting naturally occurs in many varieties, particularly in "Golden Delicious" and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of "Golden Delicious" apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.


Assuntos
Perfilação da Expressão Gênica/métodos , Malus/genética , Malus/metabolismo , Proteoma/metabolismo , Proteômica/métodos , Transcriptoma/genética , Vias Biossintéticas/genética , Frutas/genética , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Genes de Plantas/genética , Lignina/biossíntese , Malus/classificação , Filogenia , Epiderme Vegetal/genética , Epiderme Vegetal/metabolismo , Proteínas de Plantas/metabolismo
17.
Int J Mol Sci ; 20(17)2019 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-31450644

RESUMO

Auxin response factors (ARFs) are important regulators modulating the expression of auxin-responsive genes in various biological processes in plants. In the Populus genome, a total of 39 ARF members have been identified, but their detailed functions are still unclear. In this study, six poplar auxin response factor 2 (PtrARF2) members were isolated from P. trichocarpa. Expression pattern analysis showed that PtrARF2.1 is highly expressed in leaf tissues compared with other PtrARF2 genes and significantly repressed by exogenous auxin treatment. PtrARF2.1 is a nuclear-localized protein without transcriptional activation activity. Knockdown of PtrARF2.1 by RNA interference (RNAi) in poplars led to the dwarf plant, altered leaf shape, and reduced size of the leaf blade, while overexpression of PtrARF2.1 resulted in a slight reduction in plant height and the similar leaf phenotype in contrast to the wildtype. Furthermore, histological staining analysis revealed an ectopic deposition of lignin in leaf veins and petioles of PtrARF2.1-RNAi lines. RNA-Seq analysis showed that 74 differential expression genes (DEGs) belonging to 12 transcription factor families, such as NAM, ATAF and CUC (NAC), v-myb avian myeloblastosis viral oncogene homolog (MYB), ethylene response factors (ERF) and basic helix-loop-helix (bHLH), were identified in PtrARF2.1-RNAi leaves and other 24 DEGs were associated with the lignin biosynthetic pathway. Altogether, the data indicate that PtrARF2.1 plays an important role in regulating leaf development and influences the lignin biosynthesis in poplars.


Assuntos
Regulação da Expressão Gênica de Plantas , Lignina/biossíntese , Desenvolvimento Vegetal/genética , Folhas de Planta/fisiologia , Proteínas de Plantas/genética , Populus/fisiologia , Fatores de Transcrição/genética , Sequência de Aminoácidos , Vias Biossintéticas/genética , Clonagem Molecular , Especificidade de Órgãos , Fenótipo , Filogenia , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Populus/classificação , Análise de Sequência de DNA , Fatores de Transcrição/metabolismo , Transcriptoma
18.
Genes (Basel) ; 10(8)2019 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-31443318

RESUMO

Cryptomeria fortunei, also known as the Chinese cedar, is an important timber species in southern China. The primary component of its woody tissues is lignin, mainly present in secondary cell walls. Therefore, continuous lignin synthesis is crucial for wood formation. In this study, we aimed to discover key genes involved in lignin synthesis expressed in the vascular cambium of C. fortunei. Through transcriptome sequencing, we detected expression of two genes, 4CL and CCoAOMT, known to be homologous to enzymes involved in the lignin synthesis pathway. We studied the function of these genes through bioinformatics analysis, cloning, vascular cambium expression analysis, and transgenic cross-species functional validation studies. Our results show that Cf4CL and CfCCoAOMT do indeed function in the pathway of lignin synthesis and likely perform this function in C. fortunei. They are prime candidates for future (gene-editing) studies aimed at optimizing C. fortunei wood production.


Assuntos
Cryptomeria/genética , Lignina/biossíntese , Metiltransferases/genética , Proteínas de Plantas/genética , Transcinamato 4-Mono-Oxigenase/genética , Câmbio/genética , Câmbio/metabolismo , Cryptomeria/enzimologia , Cryptomeria/metabolismo , Lignina/genética , Metiltransferases/metabolismo , Proteínas de Plantas/metabolismo , Transcinamato 4-Mono-Oxigenase/metabolismo
19.
Plant Sci ; 286: 7-16, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31300144

RESUMO

Cotton fibers are developed epidermal cells of the seed coat and contain large amounts of cellulose and minor lignin-like components. Lignin in the cell walls of cotton fibers effectively provides mechanical strength and is also presumed to restrict fiber elongation and secondary cell wall synthesis. To analyze the effect of lignin and lignin-like phenolics on fiber quality and the transcriptional regulation of lignin synthesis in cotton fibers, we characterized the function of a bHLH transcription factor, GhbHLH18, during fiber elongation stage. GhbHLH18 knock-down plants have longer and stronger fibers, and accumulate less lignin-like phenolics in mature cotton fibers than control plants. By mining public transcriptomic data for developing fibers, we discovered that GhbHLH18 is coexpressed with most lignin synthesis pathway genes. Furthermore, we showed that GhbHLH18 strongly binds to the E-box in the promoter region of GhPER8 and activates its expression. Transient over expression of GhPER8 protein in tobacco leaves significantly decreased the content of coniferyl alcohol and sinapic alcohol-the substrate respectively for G-lignin and S-lignin biosynthesis. These results suggest that GhbHLH18 is negatively associated with fiber quality by activating peroxidase-mediated lignin metabolism, thus the paper represents an alternative strategy to improve fiber quality.


Assuntos
Fibra de Algodão/análise , Gossypium/genética , Lignina/biossíntese , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Gossypium/metabolismo , Proteínas de Plantas/metabolismo , Fatores de Transcrição/metabolismo
20.
Commun Biol ; 2: 238, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31263782

RESUMO

In the plant response to pathogen infection, many genes' expression is temporally induced, while few spatially induced expression genes have been reported. Here, we show that GhBOP1 can autonomously expand expression from restrained tissue when Gossypium hirsutum plants are attacked by Verticillium dahliae, which is considered to be spatially induced expression. Loss- and gain-of-function analyses show that GhBOP1 is a positive regulator in the modulation of plant resistance to V. dahliae. Yeast two-hybrid assays, luciferase complementation imaging and GUS reporting show that GhBOP1 interaction with GhTGA3 promotes its activation activity, regulating the expression of down-stream defence-related genes. Moreover, the induced spatial expression of GhBOP1 is accompanied by GhBP1 repression. Both antagonistically regulate the lignin biosynthesis, conferring cotton plants enhanced resistance to V. dahliae. Taken together, these results demonstrate that GhBOP1 is an economic positive regulator participating in plant defence through both the GhBOP1-GhTGA3 module and lignin accumulation.


Assuntos
Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Gossypium/microbiologia , Verticillium/patogenicidade , Proteínas de Arabidopsis/fisiologia , Fatores de Transcrição de Zíper de Leucina Básica/fisiologia , Resistência à Doença/genética , Gossypium/genética , Lignina/biossíntese , Técnicas do Sistema de Duplo-Híbrido
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