Carlos Hotta

Carlos Hotta
University of São Paulo | USP · Department of Biochemistry (IQ)

About

78
Publications
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1,675
Citations
Additional affiliations
October 2007 - present
Universidade de São Paulo
Position
  • Circadian rhythms in plants
September 2003 - September 2007
University of Cambridge
Position
  • Circadian rhythms of intracellular calcium in Arabidopsis
January 1998 - December 2002
University of São Paulo
Position
  • Melatonin as a signalling molecule in Plasmodium
Education
September 2003 - September 2007
University of Cambridge
Field of study
  • Plant Sciences

Publications

Publications (78)
Article
Full-text available
The l-DOPA dioxygenase of Amanita muscaria (AmDODA) participates in the biosynthesis of betalain- and hygroaurin-type natural pigments. AmDODA is encoded by the dodA gene, whose DNA sequence was inferred from cDNA and gDNA libraries almost 30 years ago. However, reports on its heterologous expression rely on either the original 5'-truncated cDNA pl...
Article
Full-text available
Starch is a polysaccharide that is stored to be used in different timescales. Transitory starch is used during nighttime when photosynthesis is unavailable. Long-term starch is stored to support vegetative or reproductive growth, reproduction, or stress responses. Starch is not just a reserve of energy for most plants but also has many other roles,...
Article
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...
Article
Most research in plant chronobiology has been done in laboratory conditions. However, they usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High‐density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments with specific light and temperature due to mutual shadi...
Article
Full-text available
Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SnRK1, a key mediator of responses to low energy. ● We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growt...
Preprint
Full-text available
Most research in plant chronobiology was done in laboratory conditions. However, they usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane ( Saccharum hybrid), generate field microenvironments with specific light and temperature due to mutual shading....
Preprint
L-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 descri...
Article
Full-text available
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 trans...
Article
Full-text available
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 gene...
Article
Full-text available
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 ri...
Preprint
Full-text available
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 ri...
Preprint
Full-text available
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 le...
Article
Full-text available
Growth rate is an informative measurement for the culture of any organism, as it provides cues about fitness and allows selection of strains. For seaweeds, the gain of mass has been the most used methodology at the laboratory, but it can be laborious and increase the contamination. In this work, we present an easy, accessible, and sensitive method...
Article
Full-text available
Author summary Circadian oscillators are internal timing devices that produce rhythms with a period of about 24 hours to regulate a wide range of biological processes for nearly all organisms. Circadian oscillators adjust phase and period in response to external cues such as light and temperatures and internal cues such as metabolites to maintain s...
Data
Networks inferred by DyDE in both untreated and NAM-treated plants, with the regulation loss networks. (A) Network inferred in absence of NAM. (B) Network inferred in presence of NAM. (C) Regulation loss network. (D) Common regulation network. On these graphs, genes are organized by their peaking time during diel cycles. Genes that are represented...
Data
Phytochrome and cryptochrome modulate [Ca2+]cyt under monochromatic light. 35S:AEQ luminescence measured over 96 hours in constant 65 umol m-2 s-1 monochromatic red or blue light in light signaling mutants. Bars on the X axis indicate red and blue mixed light (white), dark (black), monochromatic red (red), or monochromatic blue (blue). Darker boxes...
Data
Details of the dynamical interactions inferred by DyDE between the genes of the Arabidopsis thaliana circadian oscillator. The tables describe the connections modelled for the circadian oscillator in the untreated plants, NAM treated, regulation loss and common networks. Network connections are described gene by gene and a comparison with the known...
Data
Circadian rhythms of CCA1:LUC, LHY:LUC, PRR7:LUC, PRR9:LUC, TOC1:LUC and GI:LUC activity in constant red and blue mixed light, constant red or constant blue light (70 umol m-2 s-1). Grey indicates the presence and white indicates the absence of 20 mM NAM. Light conditions indicated by the colored boxes on the X axes. White is red/blue mix, monochro...
Data
Blue light-sensitive circadian [Ca2+]cyt oscillations are inhibited by nicotinamide. 35S:AEQ luminescence measured over 96 hours in constant 65 umol m-2 s-1 monochromatic red or blue light in light signaling mutants in the presence (grey circles) and absence (open circles) of 20 mM NAM. Bars on the X axis indicate light treatment of red and blue mi...
Data
Circadian transcriptomes of untreated and nicotinamide-treated plants. Circadian time-series for the transcripts on the ATH1 microarray for the untreated and nicotinamide-treated (NAM) datasets are presented on three separate sheets. Gene lists are provided describing the genes that were identified by PEAL to be circadian-regulated, along with the...
Data
GO enrichment terms of transcripts rhythmic. The tables list the most enriched terms in the rhythmic transcripts, split in to the three ontologies: Biological process, Molecular function, and Cellular component. The analysis is split in eight categories, each corresponding to a column in the table: GO term (unique identifier in the GO database), GO...
Data
Assessment of circadian regulated transcripts from both the learning methodology and standard tools. (A) Results correspond to untreated plants. The trained algorithm, COSOPT [33] and JTK [32] respectively identified 3859, 1856 and 3698 circadian regulated transcripts. JTK and the trained algorithm identified most of the genes labelled as periodic...
Data
Coverage and false positive curves of the known regulatory links involved in the circadian oscillator of Arabidopsis Thaliana, as inferred by DyDE. In DyDE, linear Ordinary Differential equations (ODEs) of order one are computed between each pair of genes to describe the dynamics of the whole system. To be further considered as a good approximation...
Data
Circadian rhythms of leaf movement are insensitive to nicotinamide in prr7-11. Rhythms of leaf movement were measured in constant white light for 120 h in the presence (yellow) or absence (white) of 20 mM NAM. n = 22 Col-0, and n = 30 prr7-11. (EPS)
Data
Detrended time-series of circadian transcript in both untreated and NAM condition. Data were gathered for 44 hours every 4 hours, 2 replicates, starting from 49 hours after the switch to constant light (i.e., third day of constant light). Data showed are detrended, so that the rhythmic pattern is clear. LUX does not appear on this list, as the prob...
Data
The effect of nicotinamide on circadian rhythms in circadian, light and ABA signaling mutants. Rhythms of luciferase activity were measured in the presence (grey) or absence (white) of 20 mM NAM. Col-0 CCA1:LUC, Col-0 TOC1:LUC, WS CAB:LUC+ and C24 CAB:LUC backgrounds are shown with respective mutants. Traces represent mean values of n > 16 biologic...
Data
Comparative analysis of the network reconstruction accuracy of our algorithm with state-of-the-art network inference methodologies. The Area Under the ROC Curve and the Precision-Recall Curve are shown for each algorithm and simulation run. For this comparison, only 10 stochastic simulations were carried to limit the overall computation time of met...
Article
Full-text available
The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or profes...
Article
Full-text available
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 Ca2+ ([Ca2+]cyt), though their purpose has not been fully c...
Article
Full-text available
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 re...
Article
Full-text available
Ethylene is a phytohormone involved in the regulation of several aspects of plant development as well as in responses to biotic and abiotic stress. The effects of exogenous application of ethylene to sugarcane plants are well characterized: growth inhibition of immature internodes and stimulation of sucrose accumulation. However, the molecular netw...
Article
Full-text available
Gracilaria tenuistipitata is a red macroalga often found in intertidal environments, where it is frequently under drought stress due to tidal water scarcity. In order to be able to study the molecular mechanisms involved in G. tenuistipitata resistance to dehydration, we have done a dehydration assay, tested different RNA extraction protocols, and...
Article
Full-text available
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 expr...
Article
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 c...
Article
Full-text available
Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-...
Article
Full-text available
Commercial sugarcane (Saccharum hybrid) is a highly polyploid and aneuploid grass that stores large amounts of sucrose in its stem. We have measured circadian rhythms of sense and antisense transcription in a commercial cultivar (RB855453) using a custom oligoarray with 14,521 probes that hybridize to sense transcripts (SS) and 7,380 probes that hy...
Data
Identification of rhythmic probes in other datasets. (A) A maize dataset [18], (B) a rice dataset [17]and (C–D) two Arabidopsis circadian datasets [20], [39] were reanalysed using our analysis pipeline. Venn diagrams showing the number of transcripts in each dataset that were considered rhythmic by three algorithms: JTK_CYCLE, COSOPT and Fisher's G...
Data
Rhythmic probes associated with several pathways. Z-score normalized time courses of rhythmic probes for transcripts associated with the photosynthetic pathway were separated into (A–B) amino acid metabolism; (C–D) lipid metabolism; (E) nitrogen metabolism; and (F) flowering regulation. Lines in different colours indicate transcripts with contrasti...
Data
More than one sugarcane assembled sequences (SAS) may align to a same gene model. The SbTOC1 CDS (1,732 bp) was blasted against the Sugarcane EST database and two different SAS were selected: SCEPLB1042B08.g (381 bp) and SCCCSB1002H04.g (1,256 bp). (TIF)
Data
Real-time PCR validation of array time courses. Z-score normalized expression levels from the arrays (darker colour) and from real-time PCR (lighter colour) for (A) ScCCA1 (SCCCLR1048E10.g), (B) ScTOC1 (SCCCSB1002H04.g and SCEPLB1042B08.g), (C) ScGI (SCJFAD1014B07.b), (D) ScPRR3 (SCACLR1057G02.g), (E) ScPRR59 (SCCCLR1077F09.g), (F) ScPRR7 (SCACLR10...
Data
Rhythmic probes associated with several hormone signalling pathways. Z-score normalized time courses of rhythmic probes for transcripts associated with the photosynthetic pathway were separated into (A) brassinosteroids signalling (green) and (B) ethylene signalling (red). Lines in different colours indicate transcripts with contrasting phases. Whi...
Data
Levels of photosynthetic pigments remained constant in constant light. Leaf pigments were extracted using chilled 80% acetone and measured using a spectrophotometer. Briefly, 100 mg of frozen ground leaf tissue was homogenized in 10 ml 80% acetone for 72 h, protected from light at 4°C. Samples were measured in sealed 96-well plates, to avoid aceton...
Data
Ortholog clusters validation using enzymes involved in sucrose synthesis and degradation. The ortholog clusters generated using InParanoid and MultiParanoid were compared with genes annotated manually. The number of false positives is the number of sequences that were present in an ortholog cluster but did not match the other genes. The number of f...
Data
Term enrichment of rhythmic probes in the sense direction. (DOCX)
Data
Term enrichment of rhythmic probes in the antisense direction. (DOCX)
Article
Full-text available
The understanding of the regulatory networks that drive sugarcane physiology and agronomic traits becomes increasingly necessary for the improvement of sugarcane. We are interested in understanding the regulation of carbon partitioning, sugar content, fibre yield and drought tolerance. Different field and greenhouse experiments have been done to ob...
Article
Full-text available
Modern sugarcane cultivars are complex hybrids resulting from crosses among several Saccharum species. Traditional breeding methods have been employed extensively in different countries over the past decades to develop varieties with increased sucrose yield and resistance to pests and diseases. Conventional variety improvement, however, may be limi...
Article
In recent years, efforts to improve sugarcane have focused on the development of biotechnology for this crop. It has become clear that sugarcane lacks tools for the biotechnological route of improvement and that the initial efforts in sequencing ESTs had limited impact for breeding. Until recently, the models used by breeders in statistical genetic...
Article
Full-text available
Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in t...
Article
Full-text available
Due to the strategic importance of sugarcane to Brazil, FAPESP, the main São Paulo state research funding agency, launched in 2008 the FAPESP Bioenergy Research Program (BIOEN, http://bioenfapesp.org). BIOEN aims to generate new knowledge and human resources for the improvement of the sugarcane and ethanol industry. As part of the BIOEN program, a...
Article
Full-text available
Xu et al. were unable to measure circadian oscillations of cyclic adenosine diphosphate ribose (cADPR). Their experiments showing very low concentrations of cADPR lack appropriate controls, which suggests that technical limitations might explain their negative result. Xu et al. also report that chemically induced ADP ribosyl cyclase did not alter c...
Article
Full-text available
We have previously shown that in vivo and in vitro the hormone melatonin is responsible for the synchronous development of Plasmodia. Melatonin can also mobilize calcium from internal stores in these parasites and this response is abolished by luzindole, a melatonin antagonist. We here demonstrate that in vivo alteration of parasite synchronous de-...
Article
Full-text available
We have reported that Arabidopsis might have genetically distinct circadian oscillators in multiple cell-types.1 Rhythms of CHLOROPHYLL A/B BINDING PROTEIN2 (CAB2) promoter activity are 2.5 h longer in phytochromeB mutants in constant red light and in cryptocrome1 cry2 double mutant (hy4-1 fha-1) in constant blue light than the wild-type.2 However,...
Article
Transcriptional feedback loops are a feature of circadian clocks in both animals and plants. We show that the plant circadian clock also incorporates the cytosolic signaling molecule cyclic adenosine diphosphate ribose (cADPR). cADPR modulates the circadian oscillator's transcriptional feedback loops and drives circadian oscillations of Ca2+ releas...
Article
Full-text available
Plants have circadian oscillations in the concentration of cytosolic free calcium ([Ca(2+)](cyt)). To dissect the circadian Ca(2+)-signaling network, we monitored circadian [Ca(2+)](cyt) oscillations under various light/dark conditions (including different spectra) in Arabidopsis thaliana wild type and photoreceptor and circadian clock mutants. Bot...