Distinct C<sub>4</sub> Sub-Types and C<sub>3</sub> Bundle Sheath Isolation In The Paniceae Grasses

Washburn, Jacob D.; Kothapalli, Satya S.; Brose, Julia M.; Covshoff, Sarah; Hibberd, Julian M.; Conant, Gavin C.; Pires, J. Chris

doi:10.1101/162644

Cited by 4 publications

(3 citation statements)

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“…To further understand how the identified TFBS might regulate the expression pattern of CBB cycle enzymes, we obtained the transcriptomic data from a collection of RNA-seq experiments on C 4 species where samples were taken separately from mesophyll and bundle sheath cells (John et al, 2014;Rao et al, 2016;Washburn et al, 2017), and assessed the expression pattern of the trans-acting factors. Despite the complexities of using data from different experiments, and the limited validation of the interaction between trans-acting factors and the identified TFBS (i.e., only validated in the C 3 species A. thaliana), we identified ten trans-acting factors differentially enriched in M and BS cell types ( Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…Transcriptomic data from RNAseq experiments in which mesophyll and bundle sheath cells were separated in P. virgatum ( Rao et al, 2016 ), S. viridis ( John et al, 2014 ), Panicum hallii ( Washburn et al, 2017 ), and Setaria italica ( Washburn et al, 2017 ) were obtained from NCBI (BioProject accession numbers: PRJNA293441 , PRJEB5074 , PRJNA475365 ). A classification-based quantification was performed using kallisto ( Bray et al, 2016 ) with the transcriptomes and genome annotation obtained from Phytozome 12 ( Goodstein et al, 2011 ; Bennetzen et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

“…To construct Supplementary Table 1, we used the 57 A. thaliana transcription factors that have been shown to bind the identified transcription factor binding sites (TFBS, 50 shared by different orthologous genes, Figure 2; plus 7 absent from C 3 or C 4 species, Supplementary Figure S5). We identify the orthologous genes in grass species and evaluate their enrichment in M or BS cells using publicly available transcriptomic data for S. viridis (John et al, 2014), S. italica (Washburn et al, 2017), P. virgatum (Rao et al, 2016), P. halli (Washburn et al, 2017), Z. mays (Chang et al, 2012), and S. bicolor (Döring et al, 2016). All these databases separate M and BS cells from whole leaves.…”

Section: Transcriptomics Analysismentioning

confidence: 99%

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Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Afamefule

Raines

2020

Front. Plant Sci.

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C 4 photosynthesis is characterized by the compartmentalization of the processes of atmospheric uptake of CO 2 and its conversion into carbohydrate between mesophyll and bundle-sheath cells. As a result, most of the enzymes participating in the Calvin-Benson-Bassham (CBB) cycle, including RubisCO, are highly expressed in bundlesheath cells. There is evidence that changes in the regulatory sequences of RubisCO contribute to its bundle-sheath-specific expression, however, little is known about how the spatial-expression pattern of other CBB cycle enzymes is regulated. In this study, we use a computational approach to scan for transcription factor binding sites in the regulatory regions of the genes encoding CBB cycle enzymes, SBPase, FBPase, PRK, and GAPDH-B, of C 3 and C 4 grasses. We identified potential cis-regulatory elements present in each of the genes studied here, regardless of the photosynthetic path used by the plant. The transacting factors that bind these elements have been validated in A. thaliana and might regulate the expression of the genes encoding CBB cycle enzymes. In addition, we also found C 4-specific transcription factor binding sites in the genes encoding CBB cycle enzymes that could potentially contribute to the pathwayspecific regulation of gene expression. These results provide a foundation for the functional analysis of the differences in regulation of genes encoding CBB cycle enzymes between C 3 and C 4 grasses.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Transcriptomics Analysismentioning

confidence: 99%

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Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Afamefule

Raines

2020

Front. Plant Sci.

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Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes

et al. 2018

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Expanding knowledge of the C photosynthetic pathway can provide key information to aid biological improvements to crop photosynthesis and yield. While the C NADP-ME pathway is well characterised, there is increasing agricultural and bioengineering interest in the comparably understudied NAD-ME and PEPCK pathways. Within this study, a systematic identification of key differences across species has allowed us to investigate the evolution of C-recruited genes in one C and eleven C grasses (Poaceae) spanning two independent origins of C photosynthesis. We present evidence for C-specific paralogs of NAD-malic enzyme 2, MPC1 and MPC2 (mitochondrial pyruvate carriers) via increased transcript abundance and associated rates of evolution, implicating them as genes recruited to perform C photosynthesis within NAD-ME and PEPCK subtypes. We then investigate the localisation of AspAT across subtypes, using novel and published evidence to place AspAT3 in both the cytosol and peroxisome. Finally, these findings are integrated with transcript abundance of previously identified C genes to provide an updated model for C grass NAD-ME and PEPCK photosynthesis. This updated model allows us to develop on the current understanding of NAD-ME and PEPCK photosynthesis in grasses, bolstering our efforts to understand the evolutionary 'path to C' and improve C photosynthesis.

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Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

Washburn

Schnable

Conant

et al. 2017

Sci Rep

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The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends focus on the quantity of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inference. In this study, we combine de novo transcriptome data and sequenced genomes from an economically important group of grass species, the tribe Paniceae, to make phylogenomic inferences. This method, which we call “genome-guided phylo-transcriptomics”, is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses. These comparisons provide a framework for future researchers to evaluate the costs and benefits of adding sequenced genomes to transcriptome data sets.

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Distinct C₄ Sub-Types and C₃ Bundle Sheath Isolation In The Paniceae Grasses

Cited by 4 publications

References 84 publications

Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

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Distinct C4 Sub-Types and C3 Bundle Sheath Isolation In The Paniceae Grasses

Cited by 4 publications

References 84 publications

Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C3 and C4 Grasses

Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

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Distinct C₄ Sub-Types and C₃ Bundle Sheath Isolation In The Paniceae Grasses