Knowledge about environmental and biological rhythms can lead to more sustainable agriculture in ... more Knowledge about environmental and biological rhythms can lead to more sustainable agriculture in a climate crisis and resource scarcity scenario. When rhythms are considered, more efficient and cost-effective management practices can be designed for food production. The circadian clock is used to anticipate daily and seasonal changes, organise the metabolism during the day, integrate internal and external signals, and optimise interaction with other organisms. Plants with a circadian clock in synchrony with the environment are more productive and use fewer resources. In medicine, chronotherapy is used to increase drug efficacy, reduce toxicity, and understand the health effects of circadian clock disruption. Here, I show evidence of why circadian biology can be helpful in agriculture. However, as evidence is scattered among many areas, they frequently lack field testing, integrate poorly with other rhythms, or suffer inconsistent results. These problems can be mitigated if researche...
Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circad... more Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs — the networks that generate circadian rhythms — had similar dynamics, albeit with different amplitudes. The differences in rhythmi...
ABSTRACTl-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurin... more ABSTRACTl-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurins pigments. The sequence of the DODAs found in Caryophyllales and Basidiomycetes are not conserved, although betalains are produced both by plants and fungi. Here we revise the coding region of the dodA gene of fly agaric [Amanita muscaria (L.) Lam.] and describe an alternative start codon downstream that enables the heterologous expression of AmDODA, a promiscuous l-DOPA dioxygenase. AmDODA is 43-amino acid residues shorter than the recombinant DODA previously reported but catalyzes the formation of two isomeric seco-DOPAs that are the biosynthetic precursors of betalains and hygroaurins. The putative active site of AmDODA contains two distinct His-His-Glu motifs that can explain the dual cleavage of l-DOPA according to the mechanism proposed for non-heme iron-dependent dioxygenases. Upon addition of excess l-DOPA, both the betaxanthin and hygroaurin adducts of l-DOPA are produced. The ...
Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically wi... more Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose...
Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precurs... more Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to identify AS events in core circadian clock genes and the dynamic adjustment of the events as a response to temperature changes in field-grown sugarcane. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95 and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and org...
We investigated whether different specialized organs in field-grown sugarcane follow the same tem... more We investigated whether different specialized organs in field-grown sugarcane follow the same temporal rhythms in transcription. We assayed the transcriptomes of three organs during the day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the two types of internodes were more similar to each other than to those of the leaves. More transcripts were rhythmic under field conditions than under circadian conditions and most of their peaks were during the day. Among the transcripts that were considered expressed in all three organs, only 7.4% showed the same rhythmic time course pattern. The central oscillators of these three organs - the networks that generate circadian rhythms - had similar dynamics with different amplitudes. The differences between the rhythmic transcriptomes ...
In the last decade, the view of circadian oscillators has expanded from transcriptional feedback ... more In the last decade, the view of circadian oscillators has expanded from transcriptional feedback to incorporate post-transcriptional, post-translational, metabolic processes and ionic signalling. In plants and animals, there are circadian oscillations in the concentration of cytosolic free Ca ([Ca]), though their purpose has not been fully characterized. We investigated whether circadian oscillations of [Ca] regulate the circadian oscillator of Arabidopsis thaliana. We report that in Arabidopsis, [Ca] circadian oscillations can regulate circadian clock function through the Ca-dependent action of CALMODULIN-LIKE24 (CML24). Genetic analyses demonstrate a linkage between CML24 and the circadian oscillator, through pathways involving the circadian oscillator gene TIMING OF CAB2 EXPRESSION1 (TOC1).
Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biologic... more Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment [1], to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4-6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis [5]. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7-9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian o...
cyclic ADP-ribose (cADPR) is a Ca2+-mobilising intracellular second messenger synthesised from ni... more cyclic ADP-ribose (cADPR) is a Ca2+-mobilising intracellular second messenger synthesised from nicotinamide adenine dinucleotide (NAD) by ADP-ribosyl cyclases (ADPR cyclases). In animals, cADPR targets the ryanodine receptor (RyR) present in the sarco/endoplasmic reticulum (SR/ER) to promote Ca2+ release from intracellular stores to increases the concentration of cytosolic free Ca2+ ([Ca2+]cyt) in Arabidopsis cADPR has been proposed to play a central role in signal transduction pathways evoked by the drought and stress hormone, abscisic acid (ABA) and the circadian clock. Despite evidence for the action of cADPR in Arabidopsis, no predicted proteins with significant similarity to the known ADPR cyclases have been reported in any plant genome database, suggesting either that there is a unique route for cADPR synthesis or a that homolog of ADPR cyclase with low similarity might exist in plants. We sought to determine whether the low-levels of ADPR cyclase activity reported in Arabidop...
Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions... more Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. ...
We are interested in understanding the complexity of the sugarcane genome, the contribution of di... more We are interested in understanding the complexity of the sugarcane genome, the contribution of different alleles to traits of interest and the definition of gene networks. We are sequencing the sugarcane genome using several plataforms. In this work we will describe data for 109 Bacterial Artificial Chromosomes (BACs) from the library of sugarcane hybrid R570. On these BACs we predicted genes and performed an initial categorization of the corresponding proteins. We have also used a whole genome shotgun approach to sequence the commercial variety SP80-3280. The BACs were assembled using PHRAP and manual curation. An initial assembly of the WGS data using Newbler produced 1.1 million contigs (totaling 830Mpb assembled). We are using sorghum genes as an initial quality indicator of the assemblies. In parallel we are also developing an experimental pipeline to automatically obtain high quality assemblies of the promoter regions. For gene prediction we are using Augustus, a widely used g...
Knowledge about environmental and biological rhythms can lead to more sustainable agriculture in ... more Knowledge about environmental and biological rhythms can lead to more sustainable agriculture in a climate crisis and resource scarcity scenario. When rhythms are considered, more efficient and cost-effective management practices can be designed for food production. The circadian clock is used to anticipate daily and seasonal changes, organise the metabolism during the day, integrate internal and external signals, and optimise interaction with other organisms. Plants with a circadian clock in synchrony with the environment are more productive and use fewer resources. In medicine, chronotherapy is used to increase drug efficacy, reduce toxicity, and understand the health effects of circadian clock disruption. Here, I show evidence of why circadian biology can be helpful in agriculture. However, as evidence is scattered among many areas, they frequently lack field testing, integrate poorly with other rhythms, or suffer inconsistent results. These problems can be mitigated if researche...
Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circad... more Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs — the networks that generate circadian rhythms — had similar dynamics, albeit with different amplitudes. The differences in rhythmi...
ABSTRACTl-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurin... more ABSTRACTl-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurins pigments. The sequence of the DODAs found in Caryophyllales and Basidiomycetes are not conserved, although betalains are produced both by plants and fungi. Here we revise the coding region of the dodA gene of fly agaric [Amanita muscaria (L.) Lam.] and describe an alternative start codon downstream that enables the heterologous expression of AmDODA, a promiscuous l-DOPA dioxygenase. AmDODA is 43-amino acid residues shorter than the recombinant DODA previously reported but catalyzes the formation of two isomeric seco-DOPAs that are the biosynthetic precursors of betalains and hygroaurins. The putative active site of AmDODA contains two distinct His-His-Glu motifs that can explain the dual cleavage of l-DOPA according to the mechanism proposed for non-heme iron-dependent dioxygenases. Upon addition of excess l-DOPA, both the betaxanthin and hygroaurin adducts of l-DOPA are produced. The ...
Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically wi... more Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2–6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose...
Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precurs... more Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, a wide range of physiological and metabolic events are related to AS, as well as fast responses to changes in temperature. AS is present in around 60% of intron-containing genes in Arabidopsis, 46% in rice and 38% in maize and it is widespread among the circadian clock genes. Little is known about how AS influences the circadian clock of C4 plants, like commercial sugarcane, a C4 crop with a complex hybrid genome. This work aims to identify AS events in core circadian clock genes and the dynamic adjustment of the events as a response to temperature changes in field-grown sugarcane. A systematic search for AS in five sugarcane clock genes, ScLHY, ScPRR37, ScPRR73, ScPRR95 and ScTOC1 using different organs of sugarcane sampled during winter, with 4 months old plants, and during summer, with 9 months old plants, revealed temperature- and org...
We investigated whether different specialized organs in field-grown sugarcane follow the same tem... more We investigated whether different specialized organs in field-grown sugarcane follow the same temporal rhythms in transcription. We assayed the transcriptomes of three organs during the day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the two types of internodes were more similar to each other than to those of the leaves. More transcripts were rhythmic under field conditions than under circadian conditions and most of their peaks were during the day. Among the transcripts that were considered expressed in all three organs, only 7.4% showed the same rhythmic time course pattern. The central oscillators of these three organs - the networks that generate circadian rhythms - had similar dynamics with different amplitudes. The differences between the rhythmic transcriptomes ...
In the last decade, the view of circadian oscillators has expanded from transcriptional feedback ... more In the last decade, the view of circadian oscillators has expanded from transcriptional feedback to incorporate post-transcriptional, post-translational, metabolic processes and ionic signalling. In plants and animals, there are circadian oscillations in the concentration of cytosolic free Ca ([Ca]), though their purpose has not been fully characterized. We investigated whether circadian oscillations of [Ca] regulate the circadian oscillator of Arabidopsis thaliana. We report that in Arabidopsis, [Ca] circadian oscillations can regulate circadian clock function through the Ca-dependent action of CALMODULIN-LIKE24 (CML24). Genetic analyses demonstrate a linkage between CML24 and the circadian oscillator, through pathways involving the circadian oscillator gene TIMING OF CAB2 EXPRESSION1 (TOC1).
Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biologic... more Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment [1], to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4-6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis [5]. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7-9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian o...
cyclic ADP-ribose (cADPR) is a Ca2+-mobilising intracellular second messenger synthesised from ni... more cyclic ADP-ribose (cADPR) is a Ca2+-mobilising intracellular second messenger synthesised from nicotinamide adenine dinucleotide (NAD) by ADP-ribosyl cyclases (ADPR cyclases). In animals, cADPR targets the ryanodine receptor (RyR) present in the sarco/endoplasmic reticulum (SR/ER) to promote Ca2+ release from intracellular stores to increases the concentration of cytosolic free Ca2+ ([Ca2+]cyt) in Arabidopsis cADPR has been proposed to play a central role in signal transduction pathways evoked by the drought and stress hormone, abscisic acid (ABA) and the circadian clock. Despite evidence for the action of cADPR in Arabidopsis, no predicted proteins with significant similarity to the known ADPR cyclases have been reported in any plant genome database, suggesting either that there is a unique route for cADPR synthesis or a that homolog of ADPR cyclase with low similarity might exist in plants. We sought to determine whether the low-levels of ADPR cyclase activity reported in Arabidop...
Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions... more Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. ...
We are interested in understanding the complexity of the sugarcane genome, the contribution of di... more We are interested in understanding the complexity of the sugarcane genome, the contribution of different alleles to traits of interest and the definition of gene networks. We are sequencing the sugarcane genome using several plataforms. In this work we will describe data for 109 Bacterial Artificial Chromosomes (BACs) from the library of sugarcane hybrid R570. On these BACs we predicted genes and performed an initial categorization of the corresponding proteins. We have also used a whole genome shotgun approach to sequence the commercial variety SP80-3280. The BACs were assembled using PHRAP and manual curation. An initial assembly of the WGS data using Newbler produced 1.1 million contigs (totaling 830Mpb assembled). We are using sorghum genes as an initial quality indicator of the assemblies. In parallel we are also developing an experimental pipeline to automatically obtain high quality assemblies of the promoter regions. For gene prediction we are using Augustus, a widely used g...
Uploads
Papers by Carlos Hotta