scholarly journals Transcriptome Profiling of Cu Stressed Petunia Petals Reveals Candidate Genes Involved in Fe and Cu Crosstalk

2021 ◽  
Vol 22 (21) ◽  
pp. 11604
Author(s):  
Jinglei Wu ◽  
Kai Li ◽  
Jian Li ◽  
Henk Schat ◽  
Yanbang Li

Copper (Cu) is an essential element for most living plants, but it is toxic for plants when present in excess. To better understand the response mechanism under excess Cu in plants, especially in flowers, transcriptome sequencing on petunia buds and opened flowers under excess Cu was performed. Interestingly, the transcript level of FIT-independent Fe deficiency response genes was significantly affected in Cu stressed petals, probably regulated by basic-helix-loop-helix 121 (bHLH121), while no difference was found in Fe content. Notably, the expression level of bHLH121 was significantly down-regulated in petals under excess Cu. In addition, the expression level of genes related to photosystem II (PSII), photosystem I (PSI), cytochrome b6/f complex, the light-harvesting chlorophyll II complex and electron carriers showed disordered expression profiles in petals under excess Cu, thus photosynthesis parameters, including the maximum PSII efficiency (FV/FM), nonphotochemical quenching (NPQ), quantum yield of the PSII (ΦPS(II)) and photochemical quenching coefficient (qP), were reduced in Cu stressed petals. Moreover, the chlorophyll a content was significantly reduced, while the chlorophyll b content was not affected, probably caused by the increased expression of chlorophyllide a oxygenase (CAO). Together, we provide new insight into excess Cu response and the Cu–Fe crosstalk in flowers.

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Victoria Yu Shtratnikova ◽  
Mikhail I. Sсhelkunov ◽  
Victoria V. Fokina ◽  
Eugeny Y. Bragin ◽  
Andrey A. Shutov ◽  
...  

Abstract Background Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. Results Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. Conclusion The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.


2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Melika Ameli-Mojarad ◽  
Mandana Ameli-Mojarad ◽  
Mitra Nourbakhsh ◽  
Ehsan Nazemalhosseini-Mojarad

Breast cancer (BC) is one of the most common lethal diseases in women worldwide. Recent evidence has shown that covalently closed Circular RNA (circRNA) deregulation is observed in different human malignancies and cancers. Lately, circRNAs are being considered as a new diagnostic biomarker; however, the mechanism and the correlation of action between circRNAs and BC are still unclear. In the present study, we try to investigate the expression level of hsa_circ_0005046 and hsa_circ_0001791 in BC. By using quantitative real-time polymerase chain reaction (qRT-PCR), expression profiles of candidate circRNAs were detected in 60 BC tissue and paired adjacent normal tissues. Furthermore, the clinicopathological relation and diagnostic value were estimated. Our results showed the higher expression levels of hsa_circ_0005046 and hsa_circ_0001791 in BC tissues compared to paired adjacent normal tissues with P value ( P < 0.0001 ) for both circRNAs, and the area under the receiver operating characteristic (ROC) curve was 0.857 and 1.0, respectively; in addition, a total 10 miRNAs that can be targeted by each candidate circRNAs was predicted base on bioinformatics databases. Taken together, for the first time, the results of our study presented high expression levels of hsa_circ_0005046 and hsa_circ_00017916 in BC; although there was no direct correlation between the high expression level of both circRNAs with clinic pathological factors, except hsa_circ_0001791 association with estrogen receptors (ER), high ROC curve in expressed samples indicated that both circRNAs could be used as a new diagnostic biomarker for BC. Moreover, miRNAs selection tools predicted that miR-215 and mir-383-5p which have a tumor suppressor role in BC can be targeted by our candidate circRNAs to affect the PI3K/AKT pathway; in conclusion, further studies are required to validate the oncogene role of our candidate circRNAs through the PI3k pathway.


2020 ◽  
Author(s):  
Mizuki Honda ◽  
Shinya Oki ◽  
Akihito Harada ◽  
Kazumitsu Maehara ◽  
Kaori Tanaka ◽  
...  

ABSTRACTIn multicellular organisms, individual cells are characterized by their gene expression profiles and the spatial interactions among cells enable the elaboration of complex functions. Expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of whole tissues. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. After photo-irradiation of limited areas, gene expression was detected from at least 10 cells in the tissue sections. PIC transcriptome analysis detected genes specifically expressed in small distinct areas of the mouse embryo. Thus, PIC enables transcriptome profiles to be determined from limited regions at a spatial resolution up to the diffraction limit.


Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 2081 ◽  
Author(s):  
Xiaohui Li ◽  
Xuexia Xing ◽  
Pei Tian ◽  
Mingzhen Zhang ◽  
Zhaoguang Huo ◽  
...  

Root-knot nematodes Meloidogyne incognita are one of the most destructive pathogens, causing severe losses to tobacco productivity and quality. However, the underlying resistance mechanism of tobacco to M. incognita is not clear. In this study, two tobacco genotypes, K326 and Changbohuang, which are resistant and susceptible to M. incognita, respectively, were used for RNA-sequencing analysis. An average of 35 million clean reads were obtained. Compared with their expression levels in non-infected plants of the same genotype, 4354 and 545 differentially expressed genes (DEGs) were detected in the resistant and susceptible genotype, respectively, after M. incognita invasion. Overall, 291 DEGs, involved in diverse biological processes, were common between the two genotypes. Genes encoding toxic compound synthesis, cell wall modification, reactive oxygen species and the oxidative burst, salicylic acid signal transduction, and production of some other metabolites were putatively associated with tobacco resistance to M. incognita. In particular, the complex resistance response needed to overcome M. incognita invasion may be regulated by several transcription factors, such as the ethylene response factor, MYB, basic helix–loop–helix transcription factor, and indole acetic acid–leucine-resistant transcription factor. These results may aid in the identification of potential genes of resistance to M. incognita for tobacco cultivar improvement.


Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 914
Author(s):  
Shan ◽  
Zhang ◽  
Yu ◽  
Wang ◽  
Li ◽  
...  

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.


PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8465 ◽  
Author(s):  
Yongguo Zhao ◽  
Hua Kong ◽  
Yunling Guo ◽  
Zhi Zou

The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.


2020 ◽  
Vol 64 (3) ◽  
Author(s):  
Aubrie O’Rourke ◽  
Sinem Beyhan ◽  
Yongwook Choi ◽  
Pavel Morales ◽  
Agnes P. Chan ◽  
...  

ABSTRACT Antimicrobial resistance (AMR) is an ever-growing public health problem worldwide. The low rate of antibiotic discovery coupled with the rapid spread of drug-resistant bacterial pathogens is causing a global health crisis. To facilitate the drug discovery processes, we present a large-scale study of reference antibiotic challenge bacterial transcriptome profiles, which included 37 antibiotics across 6 mechanisms of actions (MOAs) and provide an economical approach to aid in antimicrobial dereplication in the discovery process. We demonstrate that classical MOAs can be sorted based upon the magnitude of gene expression profiles despite some overlap in the secondary effects of antibiotic exposures across MOAs. Additionally, using gene subsets, we were able to subdivide broad MOA classes into subMOAs. Furthermore, we provide a biomarker gene set that can be used to classify most antimicrobial challenges according to their canonical MOA. We also demonstrate the ability of this rapid MOA diagnostic tool to predict and classify the expression profiles of pure compounds and crude extracts to their expression profile-associated MOA class.


2020 ◽  
Vol 21 (5) ◽  
pp. 1815
Author(s):  
Katarzyna Marciniak ◽  
Krzysztof Przedniczek

Precise control of generative organ development is of great importance for the productivity of crop plants, including legumes. Gibberellins (GAs) play a key role in the regulation of flowering, and fruit setting and development. The major repressors of GA signaling are DELLA proteins. In this paper, the full-length cDNA of LlDELLA1 gene in yellow lupine (Lupinus luteus L.) was identified. Nuclear-located LlDELLA1 was clustered in a second phylogenetic group. Further analyses revealed the presence of all conserved motifs and domains required for the GA-dependent interaction with Gibberellin Insensitive Dwarf1 (GID1) receptor, and involved in the repression function of LlDELLA1. Studies on expression profiles have shown that fluctuating LlDELLA1 transcript level favors proper flower and pod development. Accumulation of LlDELLA1 mRNA slightly decreases from the flower bud stage to anther opening (dehiscence), while there is rapid increase during pollination, fertilization, as well as pod setting and early development. LlDELLA1 expression is downregulated during late pod development. The linkage of LlDELLA1 activity with cellular and tissue localization of gibberellic acid (GA3) offers a broader insight into the functioning of the GA pathway, dependent on the organ and developmental stage. Our analyses provide information that may be valuable in improving the agronomic properties of yellow lupine.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2552-2552
Author(s):  
Sylvie Nadvornikova ◽  
Marketa Zackova ◽  
Tereza Lopotova ◽  
Hana Klamova ◽  
Jana Moravcova

Abstract Abstract 2552 The Musashi (MSI) gene family members, MSI1 and MSI2, represent an evolutionarily conserved family of RNA-binding proteins that regulate mRNA translation through binding in their N-termini. High levels of MSI2 protein are associated with increased cell proliferation, decreased cell maturation, more aggressive hematologic malignancy diseases and worse clinical prognosis. Recently obtained data pointed to MSI2 playing an important role in acute myeloid leukemia (AML) and in deadly blast crisis of chronic myeloid leukemia (CML) (Ito et al. 2010 Nature 5; 466). In this study we screened the level of MSI2 mRNA in 49 patients in different phases of CML and with different response to therapy – 18 patients at diagnosis (DG), 5 in major molecular response (MMR), 4 in complete molecular response (CMR), 2 after bone marrow transplantation (BMT), 10 in hematology relaps (HR), 6 in accelerrated phase (AP), and 4 in blast crisis (BC), and in 6 healthy donors. The level of MSI2 mRNA was quantified by real-time reverse-transcriptase-polymerase chain reaction using in-house designed specific primers and TaqMan probe and normalized to B2M endogenous control. Expression ratios were calculated by ΔΔCt method, and the differences between groups were statistically evaluated using Mann Whitney test. We detected MSI2 expression in all samples. The median expression of mRNA MSI2 in patients at DG was 1,43 (0,33–3,28), in MMR 0,52 (0,20–0,62), in CMR 0,37 (0,30–0,63), after BMT 1,28 (1,02–1,54), in HR 0,41 (0,16–0,58), in AP 3,78 (1,94–13,69), in BC 15,17 (2,61–28,15). MSI2 expression was statistically up-regulated in patients in advanced phases of CML (AP, BC) when compared with patients in CP (P<0.0001). The difference between patients in DG and remaining patients in CP was also statistically significant (P= 0,0006). No correlation of MSI2 expression level in DG patients with their responsiveness to treatment, BCR-ABL transcript level or survival was found. No significant differences were observed among groups of patients in MMR, CMR, HR, and after BMT. In addition, in order to check whether MSI2 expression level can serve as a marker of CML progression we also retrospectively screened kinetics of MSI2 transcript in 5 CML patients monitored on average 27 months (18–48). During this period, 3 patients developed HR, 1 patient AP and 1 BC. In BC patient the MSI2 transcript level increased with progression of CML in accordance with the increase of leucocytes and BCR-ABL transcript level. In 1 patient with a rising AP BCR-ABL levels remained constant compared to sevenfold increase of the MSI2 transcript level. On the other hand in HR patients we detected a constant or even decreasing level of MSI2 transcript regardless of the increase of leucocytes and BCR-ABL. In summary, our results confirm the association of high MSI2 mRNA level with advanced phases of CML and indicate that increase of MSI2 mRNA level may serve as a valuable marker of advanced phases of CML. In particular for CML patients with constantly high level of BCR-ABL mRNA the monitoring of MSI2 level can be important tool for early recognition of CML progression. Potential contributions of MSI2 to leukemic pathogenesis and its regulation in CML progression remain unknown. Grant support: NT/12392-4 IGA MZ-CR. Disclosures: No relevant conflicts of interest to declare.


2015 ◽  
Vol 18 (4) ◽  
pp. 677-682 ◽  
Author(s):  
P. Rzymski ◽  
P. Niedzielski ◽  
P. Dąbrowski

AbstractIron (Fe) represents a highly essential element for various biological processes. In spite of this very little is known as regards its status in mammalian reproductive tissues and factors that may potentially influence it. At the same time, there is an ongoing debate as to whether analyses of the Fe content in hair can provide reliable information on its tissue burden. Therefore, the aim of the present study was to investigate the content of Fe in the testicular and uterine tissues, and hair of the domestic cat (Felis catus) and how this content relates to an animal’s age, weight, physical activity, inhabited environment and diet. The median Fe content in the feline reproductive tissues amounted to 50.8 ppm and in hair to 180.2 ppm. As found, free-ranging cats were characterized by a significantly higher Fe content in reproductive tissues, particularly in the uterus. Age, weight and physical activity had no effect on determined Fe levels. The type of commercial diet (wet, dry or combined) given to household cats also had no influence upon Fe status in hair and tissue although males fed exclusively on dry food had a lower Fetestis:Fehairratio. Hair Fe level was positively correlated with that found in the reproductive tissues (Rs=0.30). This study extends the body of information on Fe distribution in felines, demonstrates the difference between free-ranging and household cats and provides evidence that Fe hair status may, at least partially, reflect the status of this element in the feline reproductive system.


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