Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations

Carvalho, Maria Helena Cruz de; Sun, Hai‐Xi; Bowler, Chris; Chua, Nam‐Hai

doi:10.1111/nph.13787

Cited by 98 publications

(198 citation statements)

References 74 publications

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“…Also, C. reinhardtii exhibited 14 putative P i transporters, indicating either gene loss in Nannochloropsis spp. or gene expansion in the other studied algae (Grossman and Aksoy, 2015;Cruz de Carvalho et al, 2016). The high-affinity P transporters encoded by No_1557/1558 show closer relation to Pho4-type P transporters in green algae, plants, and mosses, while five Na+/P i cotransporters of P. tricornutum share sequence homology to mammalian renal transporters (Supplemental Fig.…”

Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 94%

“…The amount of responsive P transporter to low P i concentration varies significantly between algae species. While P. tricornutum cells up-regulated 12 of 24 putative P transporters, N. oceanica exhibited four of six identified P transporters up-regulated under low P i concentration (Cruz de Carvalho et al, 2016). Also, C. reinhardtii exhibited 14 putative P i transporters, indicating either gene loss in Nannochloropsis spp.…”

Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 98%

“…The specific P stress response genes were shown to differ notably from other stramenopile P acquisition genes, as Nannochloropsis spp. lack APs and P acquisition genes have bacterial or green algal origins (Cruz de Carvalho et al, 2016;Lin et al, 2016).…”

Section: P Acquisitionmentioning

confidence: 99%

“…The high-affinity P transporters encoded by No_1557/1558 show closer relation to Pho4-type P transporters in green algae, plants, and mosses, while five Na+/P i cotransporters of P. tricornutum share sequence homology to mammalian renal transporters (Supplemental Fig. S6; Cruz de Carvalho et al, 2016). Closer relation to green algae, plants, and mosses also holds true for the phylogenetic affiliation of the VTC1-type protein (No_7919), which likely is involved in trafficking P to a potential polyP compartment (Aksoy et al, 2014).…”

Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 99%

“…These studies showed a taxonomically diverse lipid response under P stress with unresolved questions related to the diversified mechanism behind the lipid responses. So far, only cursory insights into the lipidremodeling process have been provided by either transcriptomic or lipidomic studies on P limitation (Riekhof et al, 2005;Cruz de Carvalho et al, 2016;Shemi et al, 2016;Cañavate et al, 2017b). To capture the taxonomically diverse response and niche partitioning, studies include ecological successful algae, such as Emiliania huxleyi and Thalassiosira pseudonana (Lessard et al, 2005;Van Mooy et al, 2009), and algae featuring high resilience and lipid content during low P, like Phaeodactylum tricornutum and Nannochloropsis spp.…”

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confidence: 99%

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Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga

et al. 2017

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. Previous studies point to P limitation-induced changes in lipid composition. As, in microalgae, the molecular mechanisms of this specific P stress adaptation remain unresolved, we reveal a detailed phospholipid-recycling scheme in Nannochloropsis oceanica and describe important P acquisition genes based on highly corresponding transcriptome and lipidome data. Initial responses to P limitation showed increased expression of genes involved in P uptake and an expansion of the P substrate spectrum based on purple acid phosphatases. Increase in P trafficking displayed a rearrangement between compartments by supplying P to the chloroplast and carbon to the cytosol for lipid synthesis. We propose a novel phospholipid-recycling scheme for algae that leads to the rapid reduction of phospholipids and synthesis of the P-free lipid classes. P mobilization through membrane lipid degradation is mediated mainly by two glycerophosphoryldiester phosphodiesterases and three patatin-like phospholipases A on the transcriptome level. To compensate for low phospholipids in exponential growth, N. oceanica synthesized sulfoquinovosyldiacylglycerol and diacylglyceroltrimethylhomoserine. In this study, it was shown that an N. oceanica strain has a unique repertoire of genes that facilitate P acquisition and the degradation of phospholipids compared with other stramenopiles. The novel phospholipid-recycling scheme opens new avenues for metabolic engineering of lipid composition in algae.Phosphorus (P) availability is often a limiting factor in aquatic ecosystems (Van Mooy et al., 2009). In some microalgae, nutrient starvation limits cell division and leads to the accumulation of organic carbon (e.g. in the form of triacylglycerols [TAGs]). To cope with P limitation, the interplay of P recycling and changes in lipid classes is observed in the open sea and in culture studies of several stramenopiles and green algae (Van Mooy et al., 2009;Martin et al., 2011;Cañavate et al., 2017b). These studies showed a taxonomically diverse lipid response under P stress with unresolved questions related to the diversified mechanism behind the lipid responses. So far, only cursory insights into the lipidremodeling process have been provided by either transcriptomic or lipidomic studies on P limitation (Riekhof et al., 2005;Cruz de Carvalho et al., 2016;Shemi et al., 2016;Cañavate et al., 2017b). To capture the taxonomically diverse response and niche partitioning, studies include ecological successful algae, such as Emiliania huxleyi and Thalassiosira pseudonana (Lessard et al., 2005;Van Mooy et al., 2009), and algae featuring high resilience and lipid content during low P, like Phaeodactylum tricornutum and Nannochloropsis spp. (Rodolfi et al., 2009;Yang et al., 2013;Mayers et al., 2014;Abida et al., 2015). During these studies, focus is often on changes of long-chain fatty acids (FAs) and their contribution to lipid classes in specific pathways [OPEN] Articles can be viewed without a subscription. www.plantphysiol.org/cgi

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Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 94%

Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 98%

Section: P Acquisitionmentioning

confidence: 99%

Section: Novel Assigned P Transporter and Vtcsmentioning

confidence: 99%

mentioning

confidence: 99%

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Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga

et al. 2017

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Particulate polyphosphate and alkaline phosphatase activity across a latitudinal transect in the tropical Indian Ocean

Martin

Lauro

Sarkar

et al. 2018

Limnology & Oceanography

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Polyphosphate (polyP) is an essential chemical constituent of microbial cells, and is hypothesized to play important roles in the marine biogeochemistry of phosphorus. However, polyP has only rarely been measured in the oceans. Here, we present data on the distribution of polyP across a latitudinal transect in the tropical Indian Ocean. PolyP concentrations (quantified as molar equivalents of a synthetic polyP standard) and ratios of polyP to total particulate phosphorus (TPP) along the transect ranged between 3-7 nmol eq. L 21 (polyP concentration) and 0.2-0.4 nmol eq. nmol 21 (polyP : TPP ratio), which is very similar to values reported from the North Pacific Subtropical Gyre. Yet unlike in the North Pacific, soluble reactive phosphorus was depleted to low concentrations ( 0.03 lmol L 21 ), and alkaline phosphatase activity was relatively high (1-4 nmol P L 21 h 21 ) along our cruise track. We attribute these results to the unique seasonal changes in iron and macronutrient supply in the Indian Ocean, which are caused by the monsoonal reversal in ocean currents. PolyP concentrations and polyP : TPP ratios decreased sharply with depth down to 150 m, suggesting that polyP was preferentially recycled relative to TPP, unlike in the North Pacific Subtropical Gyre. We hypothesize that alkaline phosphatase exerts a significant control over marine polyP biogeochemistry.

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The Role of Long Noncoding RNAs in Plant Stress Tolerance

Song

Zhang

2017

Methods in Molecular Biology

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Plants must adapt to multiple biotic and abiotic stresses ; thus, sensing and responding to environmental signals is imperative for their survival. Moreover, understanding these responses is imperative for efforts to improve plant yield and consistency. Regulation of transcript levels is a key aspect of the plant response to environmental signals. Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years with the advance of high-throughput sequencing technologies. As important biological regulators, lncRNAs have been implicated in a wide range of developmental processes and diseases in animals. However, knowledge of the role that lncRNAs play in plant stress tolerance remains limited. Here, we review recent studies on the identification, characteristics, classification, and biological functions of lncRNAs in response to various stresses, including bacterial pathogens, excess light, drought, salinity, hypoxia, extreme temperatures, and nitrogen/phosphate deficiency. We also discuss possible directions for future research.

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Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations

Cited by 98 publications

References 74 publications

Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga

Mechanisms of Phosphorus Acquisition and Lipid Class Remodeling under P Limitation in a Marine Microalga

Particulate polyphosphate and alkaline phosphatase activity across a latitudinal transect in the tropical Indian Ocean

The Role of Long Noncoding RNAs in Plant Stress Tolerance

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