Occurrence, metabolism, transport and function of seven-carbon sugars

Cowan, A. Keith

doi:10.1007/s11101-016-9463-3

Cited by 16 publications

(17 citation statements)

References 124 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In 60‐day‐old leaf, more genes with a shortened 3′ UTR in indica were upregulated relative to 3′ UTR lengthening genes (Figure d). The 3′ UTR shortening genes were significantly enriched in GO terms and pathways related to photosynthesis and sugar metabolic processes (Figure S18a), which play key roles in controlling plant growth, development and crop yield (Yamori et al ., ; Cowan, ). In comparison to japonica varieties, genes involved in sucrose metabolic process have been found to be overexpressed in indica varieties (Nguyen et al ., ).…”

Section: Discussionmentioning

confidence: 98%

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Zhou

Yang

et al. 2019

The Plant Journal

View full text Add to dashboard Cite

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3 0 untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.

show abstract

Section: Discussionmentioning

confidence: 98%

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Zhou

Yang

et al. 2019

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…Monosaccharides play a key role in primary metabolism by linking energy derivation by photosynthesis to the demands of anabolic and catabolic processes. Monosaccharides are the substrates for sucrose biosynthesis, the major transportable sugar in most vascular plants (Cowan, 2017). However, avocado is quite unique, because C 7 sugars (mannoheptulose and perseitol) have been reported as the predominant transportable and storage sugars in leaves and fruit of avocado.…”

Section: Carbohydrate Metabolism During Avocado Fruit Development Andmentioning

confidence: 99%

“…However, avocado is quite unique, because C 7 sugars (mannoheptulose and perseitol) have been reported as the predominant transportable and storage sugars in leaves and fruit of avocado. Still, despite the importance of these C 7 sugars, there is only sparse information about the synthesis, metabolism, transport, and physiology of C 7 sugars not only in avocado but also in other species where they occur (Cowan, 2004, 2017). Roles of mannoheptulose and other C 7 sugars in the regulation of carbon flux and protection against oxidative damage are based on published studies (Cowan, 2004, 2017).…”

Section: Carbohydrate Metabolism During Avocado Fruit Development Andmentioning

confidence: 99%

“…Primary metabolism in avocado, even though an essential component of growth and major component of fruit quality, has been mainly focused on carbon and oil metabolism and to a much lesser extend to amino acids and organic acids. In the decades of the 1960s on, several studies on the role of C 7 sugars and starch during growth and development of avocado were reported (Bean et al, 1962; Liu et al, 1999a,b; Richings et al, 2000; Cowan, 2004, 2017; Tesfay et al, 2010). Unlike other fruit, avocado accumulates oil instead of sugars, thus oil metabolism during growth, development, and ripening has been of high interest (Salas et al, 2000; Ozdemir et al, 2004; Blakey et al, 2012; Ibarra-Laclette et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Primary Metabolism in Avocado Fruit

et al. 2019

View full text Add to dashboard Cite

Avocado ( Persea americana Mill) is rich in a variety of essential nutrients and phytochemicals; thus, consumption has drastically increased in the last 10 years. Avocado unlike other fruit is characterized by oil accumulation during growth and development and presents a unique carbohydrate pattern. There are few previous and current studies related to primary metabolism. The fruit is also quite unique since it contains large amounts of C 7 sugars (mannoheptulose and perseitol) acting as transportable and storage sugars and as potential regulators of fruit ripening. These C 7 sugars play a central role during fruit growth and development, but still confirmation is needed regarding the biosynthetic routes and the physiological function during growth and development of avocado fruit. Relatively recent transcriptome studies on avocado mesocarp during development and ripening have revealed that most of the oil is synthesized during early stages of development and that oil synthesis is halted when the fruit is harvested (pre-climacteric stage). Most of the oil is accumulated in the form of triacylglycerol (TAG) representing 60–70% in dry basis of the mesocarp tissue. During early stages of fruit development, high expression of transcripts related to fatty acid and TAG biosynthesis has been reported and downregulation of same genes in more advanced stages but without cessation of the process until harvest. The increased expression of fatty acid key genes and regulators such as PaWRI1 , PaACP4-2, and PapPK-β-1 has also been reported to be consistent with the total fatty acid increase and fatty acid composition during avocado fruit development. During postharvest, there is minimal change in the fatty acid composition of the fruit. Almost inexistent information regarding the role of organic acid and amino acid metabolism during growth, development, and ripening of avocado is available. Cell wall metabolism understanding in avocado, even though crucial in terms of fruit quality, still presents severe gaps regarding the interactions between cell wall remodeling, fruit development, and postharvest modifications.

show abstract

“…For example, the pink module is uniquely enriched in the biological process of embryo development; the red module is exclusively enriched in the biological process of anatomical structure morphogenesis. Green, brown and magenta modules are over-represented in processes such as carbohydrate metabolic process, biosynthetic process, photosynthesis, and lipid metabolic process, which play critical roles in controlling plant growth, development, and crop yield [40, 41]. We also performed KEGG pathway enrichment analysis for hub genes identified from each individual modules to investigate their functional importance.…”

Section: Resultsmentioning

confidence: 99%

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis

Fraser

Long

et al. 2019

BMC Genomics

View full text Add to dashboard Cite

BackgroundAlternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3′ end sequencing provides a valuable data source for the study of APA-related gene expression. Cluster analysis is a powerful technique for investigating the association structure among genes, however, conventional gene clustering methods are not suitable for APA-related data as they fail to consider the information of poly(A) sites (e.g., location, abundance, number, etc.) within each gene or measure the association among poly(A) sites between two genes.ResultsHere we proposed a computational framework, named PASCCA, for clustering genes from replicated or unreplicated poly(A) site data using canonical correlation analysis (CCA). PASCCA incorporates multiple layers of gene expression data from both the poly(A) site level and gene level and takes into account the number of replicates and the variability within each experimental group. Moreover, PASCCA characterizes poly(A) sites in various ways including the abundance and relative usage, which can exploit the advantages of 3′ end deep sequencing in quantifying APA sites. Using both real and synthetic poly(A) site data sets, the cluster analysis demonstrates that PASCCA outperforms other widely-used distance measures under five performance metrics including connectivity, the Dunn index, average distance, average distance between means, and the biological homogeneity index. We also used PASCCA to infer APA-specific gene modules from recently published poly(A) site data of rice and discovered some distinct functional gene modules. We have made PASCCA an easy-to-use R package for APA-related gene expression analyses, including the characterization of poly(A) sites, quantification of association between genes, and clustering of genes.ConclusionsBy providing a better treatment of the noise inherent in repeated measurements and taking into account multiple layers of poly(A) site data, PASCCA could be a general tool for clustering and analyzing APA-specific gene expression data. PASCCA could be used to elucidate the dynamic interplay of genes and their APA sites among various biological conditions from emerging 3′ end sequencing data to address the complex biological phenomenon.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5433-7) contains supplementary material, which is available to authorized users.

show abstract

Occurrence, metabolism, transport and function of seven-carbon sugars

Cited by 16 publications

References 124 publications

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

Primary Metabolism in Avocado Fruit

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis

Contact Info

Product

Resources

About