De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Gross, Stephen; Martin, Jeffrey A.; Simpson, June; Abraham-Juárez, María Jazmín; Wang, Zhong; Visel, Axel

doi:10.1186/1471-2164-14-563

Cited by 106 publications

(101 citation statements)

References 76 publications

(99 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Transcript abundance level was normalized using the fragments per kilobase per million mapped reads (FPKM) method, and FPKM values were computed as proposed by Mortazavi et al 56 . 57 and Allium cepa 58 were downloaded from Dryad (h5t68) and NCBI (PRJNA175446), respectively. We removed the redundant unigenes in A. cepa by CD-HIT-EST with 99% identity and used TransDecoder to predict proteins with default parameters.…”

mentioning

confidence: 99%

The Apostasia genome and the evolution of orchids

Zhang¹,

Liu²,

et al. 2017

Nature

290

347

View full text Add to dashboard Cite

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1-3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel thirdgeneration genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

show abstract

mentioning

confidence: 99%

The Apostasia genome and the evolution of orchids

Zhang¹,

Liu²,

et al. 2017

Nature

290

347

View full text Add to dashboard Cite

show abstract

“…In the absence of measurements of ATP citrate lyase and isocitrate lyase in CAM plants, it is not clear whether these two enzymes are involved in the catabolism of citrate in vivo. Transcripts for both enzymes were identified in a recent sequencing study of two agave species (Gross et al, 2013), but at present, there are no quantitative data on the expression or activity levels that could be used to discriminate between the possible routes. Ultimately, detailed metabolic flux analysis would be required to examine this issue.…”

Section: The Diel Metabolic Modeling Framework Allows Simulation and mentioning

confidence: 99%

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves

et al. 2014

View full text Add to dashboard Cite

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C 3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO 2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis.Photosynthetic metabolism continues to be studied intensively because of its importance for crop performance and the global carbon cycle in relation to climate change. The metabolic pathways and enzymes involved in carbon fixation and related metabolic processes, such as the synthesis of Suc and starch, have been wellcharacterized. However, it is apparent that full appreciation of leaf metabolism requires these metabolic processes to be placed in the context of the wider metabolic network (Szecowka et al., 2013). This is particularly important for predicting how strategies for engineering improved photosynthesis (Maurino and Weber, 2013) may affect network properties, such as redox and energy balancing (Kramer and Evans, 2011).Flux balance analysis (FBA) has emerged as the method of choice for predicting fluxes in large metabolic network models (Sweetlove and Ratcliffe, 2011), and several flux balance models have explicitly considered photosynthetic metabolism in a variety of plants species and microorganisms, including cyanobacteria (Synechocystis sp. PCC 6803; Knoop et al

show abstract

“…We therefore decided to test our hypothesis experimentally. We produced the agave (sequences mined from transcriptome data; Gross et al, 2013) and rice long (a) and short (b) Rca isoforms in Escherichia coli, followed by purification to homogeneity (Fig. 1A).…”

Section: Rubisco Activase From Agave Is Highly Functional At Activatimentioning

confidence: 99%

“…Nucleotide sequences encoding Rcaa and Rcab from rice (Oryza sativa; uniprot: P93431-1, residues 48-466; P93431-2, residues 48-433) and agave (Agave tequilana; locus 3705, residues 57-474; locus 27298, residues 58-435; Gross et al, 2013) were synthesized (GenScript) and cloned into the SacIIHindIII site of pHue (Catanzariti et al, 2004). The QuikChange protocol (Stratagene) was used to introduce desired point mutations.…”

Section: Molecular Biologymentioning

confidence: 99%

In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop

Shivhare

Mueller‐Cajar

2017

Plant Physiol.

View full text Add to dashboard Cite

To maintain metabolic flux through the Calvin-Benson-Bassham cycle in higher plants, dead-end inhibited complexes of Rubisco must constantly be engaged and remodeled by the molecular chaperone Rubisco activase (Rca). In C3 plants, the thermolability of Rca is responsible for the deactivation of Rubisco and reduction of photosynthesis at moderately elevated temperatures. We reasoned that crassulacean acid metabolism (CAM) plants must possess thermostable Rca to support Calvin-Benson-Bassham cycle flux during the day when stomata are closed. A comparative biochemical characterization of rice (Oryza sativa) and Agave tequilana Rca isoforms demonstrated that the CAM Rca isoforms are approximately10°C more thermostable than the C3 isoforms. Agave Rca also possessed a much higher in vitro biochemical activity, even at low assay temperatures. Mixtures of rice and agave Rca form functional hetero-oligomers in vitro, but only the rice isoforms denature at nonpermissive temperatures. The high thermostability and activity of agave Rca mapped to the N-terminal 244 residues. A Glu-217-Gln amino acid substitution was found to confer high Rca activity to rice Rca. Further mutational analysis suggested that Glu-217 restricts the flexibility of the a4-b4 surface loop that interacts with Rubisco via Lys-216. CAM plants thus promise to be a source of highly functional, thermostable Rca candidates for thermal fortification of crop photosynthesis. Careful characterization of their properties will likely reveal further protein-protein interaction motifs to enrich our mechanistic model of Rca function.

show abstract

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Cited by 106 publications

References 76 publications

The Apostasia genome and the evolution of orchids

The Apostasia genome and the evolution of orchids

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves

In Vitro Characterization of Thermostable CAM Rubisco Activase Reveals a Rubisco Interacting Surface Loop

Contact Info

Product

Resources

About