Computational Biology - Publications

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Browsing Computational Biology - Publications by Author "Acebron, Kelvin"
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    A low CO < inf > 2 < /inf > -responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C < inf > 4 < /inf > photosynthesis
    ( 2021-04-02) Chatterjee, Jolly ; Coe, Robert A. ; Acebron, Kelvin ; Thakur, Vivek ; Yennamalli, Ragothaman M. ; Danila, Florence ; Lin, Hsiang Chun ; Balahadia, Christian Paolo ; Bagunu, Efren ; Padhma, Preiya P.O.S. ; Bala, Soumi ; Yin, Xiaojia ; Rizal, Govinda ; Dionora, Jacqueline ; Furbank, Robert T. ; Von Caemmerer, Susanne ; Quick, William Paul
    In C4 species, β-carbonic anhydrase (CA), localized to the cytosol of the mesophyll cells, accelerates the interconversion of CO2 to HCO3-, the substrate used by phosphoenolpyruvate carboxylase (PEPC) in the first step of C4 photosynthesis. Here we describe the identification and characterization of low CO2-responsive mutant 1 (lcr1) isolated from an N-nitroso-N-methylurea-(NMU) treated Setaria viridis mutant population. Forward genetic investigation revealed that the mutated gene Sevir.5G247800 of lcr1 possessed a single nucleotide transition from cytosine to thymine in a β-CA gene causing an amino acid change from leucine to phenylalanine. This resulted in severe reduction in growth and photosynthesis in the mutant. Both the CO2 compensation point and carbon isotope discrimination values of the mutant were significantly increased. Growth of the mutants was stunted when grown under ambient pCO2 but recovered at elevated pCO2. Further bioinformatics analyses revealed that the mutation has led to functional changes in one of the conserved residues of the protein, situated near the catalytic site. CA transcript accumulation in the mutant was 80% lower, CA protein accumulation 30% lower, and CA activity ∼98% lower compared with the wild type. Changes in the abundance of other primary C4 pathway enzymes were observed; accumulation of PEPC protein was significantly increased and accumulation of malate dehydrogenase and malic enzyme decreased. The reduction of CA protein activity and abundance in lcr1 restricts the supply of bicarbonate to PEPC, limiting C4 photosynthesis and growth. This study establishes Sevir.5G247800 as the major CA allele in Setaria for C4 photosynthesis and provides important insights into the function of CA in C4 photosynthesis that would be required to generate a rice plant with a functional C4 biochemical pathway.
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    Bundle sheath suberisation is required for C < inf > 4 < /inf > photosynthesis in a Setaria viridis mutant
    ( 2021-12-01) Danila, Florence R. ; Thakur, Vivek ; Chatterjee, Jolly ; Bala, Soumi ; Coe, Robert A. ; Acebron, Kelvin ; Furbank, Robert T. ; von Caemmerer, Susanne ; Quick, William Paul
    C4 photosynthesis provides an effective solution for overcoming the catalytic inefficiency of Rubisco. The pathway is characterised by a biochemical CO2 concentrating mechanism that operates across mesophyll and bundle sheath (BS) cells and relies on a gas tight BS compartment. A screen of a mutant population of Setaria viridis, an NADP-malic enzyme type C4 monocot, generated using N-nitroso-N-methylurea identified a mutant with an amino acid change in the gene coding region of the ABCG transporter, a step in the suberin synthesis pathway. Here, Nile red staining, TEM, and GC/MS confirmed the alteration in suberin deposition in the BS cell wall of the mutant. We show that this has disrupted the suberin lamellae of BS cell wall and increased BS conductance to CO2 diffusion more than two-fold in the mutant. Consequently, BS CO2 partial pressure is reduced and CO2 assimilation was impaired in the mutant. Our findings provide experimental evidence that a functional suberin lamellae is an essential anatomical feature for efficient C4 photosynthesis in NADP-ME plants like S. viridis and have implications for engineering strategies to ensure future food security.
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    Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway
    ( 2015-10-01) Rizal, Govinda ; Thakur, Vivek ; Dionora, Jacqueline ; Karki, Shanta ; Wanchana, Samart ; Acebron, Kelvin ; Larazo, Nikki ; Garcia, Richard ; Mabilangan, Abigail ; Montecillo, Florencia ; Danila, Florence ; Mogul, Reychelle ; Pablico, Paquito ; Leung, Hei ; Langdale, Jane A. ; Sheehy, John ; Kelly, Steven ; Quick, William Paul
    The specification of vascular patterning in plants has interested plant biologists for many years. In the last decade a new context has emerged for this interest. Specifically, recent proposals to engineer C4 traits into C3 plants such as rice require an understanding of how the distinctive venation pattern in the leaves of C4 plants is determined. High vein density with Kranz anatomy, whereby photosynthetic cells are arranged in encircling layers around vascular bundles, is one of the major traits that differentiate C4 species from C3 species. To identify genetic factors that specify C4 leaf anatomy, we generated ethyl methanesulfonate- and γ-ray-mutagenized populations of the C4 species sorghum (Sorghum bicolor), and screened for lines with reduced vein density. Two mutations were identified that conferred low vein density. Both mutations segregated in backcrossed F2 populations as homozygous recessive alleles. Bulk segregant analysis using next-generation sequencing revealed that, in both cases, the mutant phenotype was associated with mutations in the CYP90D2 gene, which encodes an enzyme in the brassinosteroid biosynthesis pathway. Lack of complementation in allelism tests confirmed this result. These data indicate that the brassinosteroid pathway promotes high vein density in the sorghum leaf, and suggest that differences between C4 and C3 leaf anatomy may arise in part through differential activity of this pathway in the two leaf types. Significance Statement The high vein density associated with Kranz anatomy is a defining characteristic of all plants with two-cell type C4 photosynthesis. Here we show that the brassinosteroid pathway is important for high vein density in C4 leaves.