Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification

Xie, Lulu; Liu, Pingli; Zhu, Zhi‐Xin; Zhang, Shifan; Zhang, Shujiang; Li, Fēi; Zhang, Hui; Li, Guoliang; Wei, Yunxiao; Sun, Rifei

doi:10.3389/fpls.2016.01312

Cited by 15 publications

(11 citation statements)

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“…More studies suggested that blue light should be recommended as a supplementary light source for accumulation of phenols and flavonoids [84, 85]. Moreover, the promotion of primary metabolism partly promoted contents of phenols and flavonoids in the LED-mix treatment (Table 3), since the products of primary metabolism are utilized to synthesize a wide range of secondary metabolites through the shikimate pathway, mevalonic acid pathway, and methylerythritol 4-phosphate (MEP) pathway in higher plants [86–89]. Results from Zhao et al [90] showed that enhanced accumulation of most secondary metabolites by elevated temperature is possibly due to increased contents of chlorophyll, sugar, and starch in Robinia pseudoacacia seedlings.…”

Section: Discussionmentioning

confidence: 99%

Supplementary Light Source Affects Growth, Metabolism, and Physiology ofAdenophora triphylla(Thunb.) A.DC. Seedlings

Liu

Ren

Jeong

2019

BioMed Research International

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Adenophora triphylla(Thunb.) A.DC., a well-known herbaceous medicinal species, has been reported to protect against human obesity, cancer, and inflammation. Supplementary lighting is a practical strategy to improve crop quality, especially at a propagation stage. However, there has been no study available on the optimal supplementary light source for the commercial production ofA. triphyllaseedlings. In this study, plug seedlings were cultivated in a greenhouse for four weeks under an average daily light intensity of 490μmol·m−2·s−1PPFD coming from the sun and a supplemental lighting (16 h per day) at 120μmol·m−2·s−1PPFD provided by high pressure sodium (HPS), metal halide (MH), far-red (FR) light, white LED (red: green: blue = 2:4:3, LED-w), or mixed (red: green: blue = 4:1:4) LED (LED-mix). The results showed that LED-mix, with a higher percentage of red and blue light, substantially promoted seedling growth compared to other treatments by increasing stem diameter, biomass, specific leaf weight, and root to shoot ratio. The LED-mix also promoted accumulation of soluble sugar, starch, and chlorophyll in the tissue and increased contents of total phenols and flavonoids. Moreover, stomata density and pore area per leaf area under the LED-mix were remarkably greater than those under other treatments. Furthermore, the Western blot analysis revealed that the expression of photosynthetic protein, D1, was notably enhanced by the LED-mix as compared with other light sources. In addition, the LED-mix alleviated the oxidative damage of seedlings by improving enzymatic and nonenzymatic antioxidant systems. Collectively, these results suggest that the LED-mix was the optimal supplementary light source for the production of highest qualityA. triphyllaseedlings.

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Section: Discussionmentioning

confidence: 99%

Supplementary Light Source Affects Growth, Metabolism, and Physiology ofAdenophora triphylla(Thunb.) A.DC. Seedlings

Liu

Ren

Jeong

2019

BioMed Research International

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“…To further evaluate these two hypotheses, we performed a phylogenetic analysis using PKS amino acid sequences to link their syntenic cluster membership with sequence divergence reflected in the phylogenetic tree. The analysis incorporated sequences from over 180 species thereby dramatically extending previous phylogenetic analyses on the type III PKS (41). Here, we included 1,607 different amino acid sequences and obtained detailed phylogenetic relationships using the Maximum likelihood method ( Figure 5), it seems likely that the 'R-4-C'-type genes in the syntenic clusters originated from the same evolutionary event by duplication/triplication events.…”

Section: Phylogenetic Analysis Indicates Timing Of the Appearance Of mentioning

confidence: 99%

Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

Naake

Maéda

Proost

et al. 2020

Preprint

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The emergence of type III polyketide synthases (PKSs) was a pre-requisite for the conquest of land by the green lineage. To study the deep evolutionary history of this key family, we used phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage. This study thereby combined study of genomic location and context with changes in gene sequences. We found that two major clades, CHS and LAP5/6 homologs, evolved early by a segmental duplication event prior to the divergence of Bryophytes and Tracheophytes. We propose that the macroevolution of the type III PKS superfamily is governed by whole-genome duplications and triplications. Intriguingly, the combined phylogenetic and synteny analyses in this study shed new insights into changes in the genomic location and context that are retained for a longer time scale with more recent functional divergence captured by gene sequence alterations.PKSs are present in all land plants albeit in varying copy numbers. However, PKS were not found, or only found in low copy numbers, in the Chlorophyta, and are absent in Chlorokybophyceae, Mesostigmaphyceae and Coleochaetaphyceae of the Charophyta (see Supplementary Text). By contrast, type III PKS were detected in Penium margaritaceum (36). Synteny network analysis detects clade-specific and reaction type-specific clustersTo study the diversification of the type III PKS superfamily we followed a synteny network approach (32). Whole genomes of 126 species were compared in a pairwise manner, followed by robust block detection of regions containing type III PKS genes and network analysis to detect syntenic clusters within the network. The resultant network contained 706 vertices corresponding to syntenic regions containing single or multiple type III PKS genes of which 166 vertices corresponded to regions with tandem-duplicated genes from a total of 105 species ( Supplementary Table S2).Tandem-duplicated genes may play important roles in providing genetic redundancy, gene dosage balance, genetic robustness, and to provide an additional means for divergence in transcriptional regulation and protein sequence (37-40). The highest number of tandem-duplicated PKS genes in one syntenic region was 23 (Arachis duranensis, containing mainly 'R-4-A'-type PKS sequences, Fig. 1 and Fig. 2).Arachis ipaensis (21 genes) and Vitis vinifera (20 genes) had the second-and thirdhighest numbers of tandem-duplicated genes (also containing mostly 'R-4-A'-type sequences), respectively.

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“…OsLAP6 , also called OsPKS1 (Wang et al 2013 ), encodes a plant PKS III superfamily protein, which catalyzes the synthesis of various plant secondary metabolites (Xie et al 2016 ). Secondary metabolites are involved in regulating a variety of developmental processes in plants, such as disease resistance, environmental stress response, and sexual reproduction (Wink 1988 ; Kliebenstein 2004 ; Gershenzon 1984 ; Galambosi et al 2009 ; Theis and Lerdau 2003 ).…”

Section: Discussionmentioning

confidence: 99%

OsLAP6/OsPKS1, an orthologue of Arabidopsis PKSA/LAP6, is critical for proper pollen exine formation

Zou

Xiao

et al. 2017

Rice

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BackgroundMale fertility is crucial for rice yield, and the improvement of rice yield requires hybrid production that depends on male sterile lines. Although recent studies have revealed several important genes in male reproductive development, our understanding of the mechanisms of rice pollen development remains unclear.ResultsWe identified a rice mutant oslap6 with complete male sterile phenotype caused by defects in pollen exine formation. By using the MutMap method, we found that a single nucleotide polymorphism (SNP) variation located in the second exon of OsLAP6/OsPKS1 was responsible for the mutant phenotype. OsLAP6/OsPKS1 is an orthologous gene of Arabidopsis PKSA/LAP6, which functions in sporopollenin metabolism. Several other loss-of-function mutants of OsLAP6/OsPKS1 generated by the CRISPR/Cas9 genomic editing tool also exhibited the same phenotype of male sterility. Our cellular analysis suggested that OsLAP6/OsPKS1 might regulate pollen exine formation by affecting bacula elongation. Expression examination indicated that OsLAP6/OsPKS1 is specifically expressed in tapetum, and its product is localized to the endoplasmic reticulum (ER). Protein sequence analysis indicated that OsLAP6/OsPKS1 is conserved in land plants.Conclusions OsLAP6/OsPKS1 is a critical molecular switch for rice male fertility by participating in a conserved sporopollenin precursor biosynthetic pathway in land plants. Manipulation of OsLAP6/OsPKS1 has potential for application in hybrid rice breeding.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12284-017-0191-0) contains supplementary material, which is available to authorized users.

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Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification

Cited by 15 publications

References 84 publications

Supplementary Light Source Affects Growth, Metabolism, and Physiology ofAdenophora triphylla(Thunb.) A.DC. Seedlings

Supplementary Light Source Affects Growth, Metabolism, and Physiology ofAdenophora triphylla(Thunb.) A.DC. Seedlings

Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

OsLAP6/OsPKS1, an orthologue of Arabidopsis PKSA/LAP6, is critical for proper pollen exine formation

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