Expression of Genes Associated with Nickel Resistance in White Spruce (&amp;lt;i&amp;gt;Picea glauca&amp;lt;/i&amp;gt;) under Nickel Stress: Analysis of AT2G16800 and &amp;lt;i&amp;gt;NRAMP&amp;lt;/i&amp;gt; Genes

Boyd, Meagan; Nkongolo, K. K.

doi:10.4236/ajps.2020.118082

Cited by 6 publications

(2 citation statements)

References 21 publications

(27 reference statements)

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“…Effects of nickel ions on gene expression in conifer species has been recently studied. Boyd and Nkongolo [ 56 ] reported a significant increase of AT2G16800 , and NRAMP expression in Picea glauca root samples treated with different concentrations of Ni compared to water. They also revealed that Ni induces an upregulation of ACCD at low and high doses tested in roots.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Czajka

Nkongolo²

2022

PLoS ONE

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Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Czajka

Nkongolo²

2022

PLoS ONE

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“…In Pinus banksiana and Pinus strobus, excess nickel prompted downregulation of the gene encoding the natural resistance-associated macrophage protein (NRAMP3) [22]. In contrast, this gene was upregulated in Picea glauca under conditions of excess nickel [23]. In some species, NRAMP3 is localized to the vacuole membrane, implying a possible role in nickel sequestration into the vacuole [24,25].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana)

Moy

Czajka

Paul

et al. 2023

Plants

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Understanding the genetic response of plants to nickel stress is a necessary step to improving the utility of plants in environmental remediation and restoration. The main objective of this study was to generate whole genome expression profiles of P. banksiana exposed to nickel ion toxicity compared to reference genotypes. Pinus banksiana seedlings were screened in a growth chamber setting using a high concentration of 1600 mg of nickel per 1 kg of soil. RNA was extracted and sequenced using the Illumina platform, followed by de novo transcriptome assembly. Overall, 25,552 transcripts were assigned gene ontology. The biological processes in water-treated samples were analyzed, and 55% of transcripts were distributed among five categories: DNA metabolic process (19.3%), response to stress (13.3%), response to chemical stimuli (8.7%), signal transduction (7.7%) and response to biotic stimulus (6.0%). For molecular function, the highest percentages of genes were involved in nucleotide binding (27.6%), nuclease activity (27.3%) and kinase activity (10.3%). Sixty-two percent of genes were associated with cellular compartments. Of these genes, 21.7% were found in the plasma membrane, 16.1% in the cytosol, 12.4% with the chloroplast and 11.9% in the extracellular region. Nickel ions induced changes in gene expression, resulting in the emergence of differentially regulated categories. Overall, there were significant changes in gene expression with a total 4128 genes upregulated and 3754 downregulated genes detected in nickel-treated genotypes compared to water-treated control plants. For biological processes, the highest percentage of upregulated genes in plants exposed to nickel were associated with the response to stress (15%), the response to chemicals (11,1%), carbohydrate metabolic processes (7.4%) and catabolic processes (7.4%). The largest proportions of downregulated genes were associated with the biosynthetic process (21%), carbohydrate metabolic process (14.3%), response to biotic stimulus (10.7%) and response to stress (10.7%). For molecular function, genes encoding for enzyme regulatory and hydrolase activities represented the highest proportion (61%) of upregulated gene. The majority of downregulated genes were involved in the biosynthetic processes. Overall, 58% of upregulated genes were located in the extracellular region and the nucleus, while 42% of downregulated genes were localized to the plasma membrane and 33% to the extracellular region. This study represents the first report of a transcriptome from a conifer species treated with nickel.

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Gene Regulation and Global DNA Methylation Changes in White Spruce (Picea glauca) in Response to Copper Contaminations

McKergow

Nkongolo

2023

Water Air Soil Pollut

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Expression of Genes Associated with Nickel Resistance in White Spruce (<i>Picea glauca</i>) under Nickel Stress: Analysis of AT2G16800 and <i>NRAMP</i> Genes

Cited by 6 publications

References 21 publications

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana)

Gene Regulation and Global DNA Methylation Changes in White Spruce (Picea glauca) in Response to Copper Contaminations

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