scholarly journals New insights into the evolution of glutamine synthetase isoenzymes in plants

2021 ◽  
Author(s):  
José Miguel Valderrama-Martín ◽  
Francisco Ortigosa ◽  
Concepción Ávila ◽  
Francisco M. Cánovas ◽  
Bertrand Hirel ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Expression Profiles ◽  
Inorganic Nitrogen ◽  
Phylogenetic Analyses ◽  
Gene Expression Profiles ◽  
Phylogenetic Study ◽  
Genes Encoding ◽  
Terrestrial Life ◽  
Key Enzyme ◽  
Living Organisms

Glutamine synthetase (GS) is a key enzyme responsible for the incorporation of inorganic nitrogen in the form of ammonium into the amino acid glutamine. The genes encoding GS are among the oldest existing genes in living organisms. In plants, two groups of functional GS enzymes are found: eubacterial GSIIb (GLN2) and eukaryotic GSIIe (GLN1/GS). Phylogenetic analyses have shown that the GLN2 group originated from bacteria following horizontal gene transfer. Only GLN1/GS genes are found in vascular plants, which suggests that they are involved in the final adaptation of plants to terrestrial life. The present phylogenetic study reclassifies the different GS of seed plants into three clusters: GS1a, GS1b and GS2. The presence of genes encoding GS2 has been expanded to Cycadopsida gymnosperms, which suggests the origin of this gene in a common ancestor of Cycadopsida, Ginkgoopsida and angiosperms. GS1a genes have been identified in all gymnosperms, basal angiosperms and some Magnoliidae species. Previous studies in conifers and the gene expression profiles obtained in ginkgo and magnolia in the present work could explain the absence of GS1a in more recent angiosperm species (e.g., monocots and eudicots) due to the redundant roles of GS1a and GS2 in photosynthetic cells. Altogether, the results provide a better understanding of the evolution of plant GS isoenzymes and their physiological roles, which is valuable for improving crop nitrogen use efficiency and productivity.

scholarly journals Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 500
Author(s):  
Jeeyong Lee ◽  
Junhye Kwon ◽  
DaYeon Kim ◽  
Misun Park ◽  
KwangSeok Kim ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Expression Profiles ◽  
Cell Cycle Control ◽  
Methylation Status ◽  
Locally Advanced ◽  
Gene Expression Profiles ◽  
Advanced Rectal Cancer ◽  
Bioinformatic Analysis ◽  
Locally Advanced Rectal Cancer ◽  
Genes Encoding

LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.

scholarly journals Expression of sugarcane genes induced by inoculation with Gluconacetobacter diazotrophicus and Herbaspirillum rubrisubalbicans

2001 ◽  
Vol 24 (1-4) ◽  
pp. 199-206 ◽  
Author(s):  
Eduardo de Matos Nogueira ◽  
Fabiano Vinagre ◽  
Hana Paula Masuda ◽  
Claudia Vargas ◽  
Vânia Lúcia Muniz de Pádua ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
Expression Profiles ◽  
Inorganic Nitrogen ◽  
Gene Expression Profiles ◽  
Nitrogen Fertilizers ◽  
Gluconacetobacter Diazotrophicus ◽  
Nitrogen Fixing ◽  
Preferential Expression ◽  
Sugarcane Varieties ◽  
Exclusive Or

Several Brazilian sugarcane varieties have the ability to grow with little addition of inorganic nitrogen fertilizers, showing high contributions of Biological Nitrogen Fixation (BNF). A particular type of nitrogen-fixing association has been described in this crop, where endophytic diazotrophs such as Gluconacetobacter diazotrophicus and Herbaspirillum spp. colonize plant tissues without causing disease symptoms. In order to gain insight into the role played by the sugarcane in the interaction between this plant and endophytic diazotrophs, we investigated gene expression profiles of sugarcane plants colonized by G. diazotrophicus and H. rubrisubalbicans by searching the sugarcane expressed sequence tag SUCEST Database (<A HREF="http://sucest.lad.ic.unicamp.br/en/">http://sucest.lad.ic.unicamp.br/en/</A>). We produced an inventory of sugarcane genes, candidates for exclusive or preferential expression during the nitrogen-fixing association. This data suggests that the host plant might be actively involved in the establishment of the interaction with G. diazotrophicus and H. rubrisubalbicans.

scholarly journals Major Latex Protein MdMLP423 Negatively Regulates Defense against Fungal Infections in Apple

2020 ◽  
Vol 21 (5) ◽  
pp. 1879 ◽  
Author(s):  
Shanshan He ◽  
Gaopeng Yuan ◽  
Shuxun Bian ◽  
Xiaolei Han ◽  
Kai Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Zinc Finger Protein ◽  
Fungal Infections ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genes Encoding ◽  
Pathogenesis Related Gene ◽  
Stress Related Genes ◽  
Related Proteins

Major latex proteins (MLPs) play critical roles in plants defense and stress responses. However, the roles of MLPs from apple (Malus × domestica) have not been clearly identified. In this study, we focused on the biological role of MdMLP423, which had been previously characterized as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis indicated that MdMLP423 is a protein with a ‘Gly-rich loop’ (GXGGXG) domain belonging to the Bet v_1 subfamily. Gene expression profiles showed that MdMLP423 is mainly expressed in flowers. In addition, the expression of MdMLP423 was significantly inhibited by Botryosphaeria berengeriana f. sp. piricola (BB) and Alternaria alternata apple pathotype (AAAP) infections. Apple calli overexpressing MdMLP423 had lower expression of resistance-related genes, and were more sensitive to infection with BB and AAAP compared with non-transgenic calli. RNA-seq analysis of MdMLP423-overexpressing calli and non-transgenic calli indicated that MdMLP423 regulated the expression of a number of differentially expressed genes (DEGs) and transcription factors, including genes involved in phytohormone signaling pathways, cell wall reinforcement, and genes encoding the defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein, and ABI3. Taken together, our results demonstrate that MdMLP423 negatively regulates apple resistance to BB and AAAP infections by inhibiting the expression of defense- and stress-related genes and transcription factors.

scholarly journals Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10604
Author(s):  
Izabela Baryla ◽  
Elzbieta Pluciennik ◽  
Katarzyna Kośla ◽  
Marzena Wojcik ◽  
Andrzej Zieleniak ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Glucose Metabolism ◽  
Gestational Diabetes ◽  
Gestational Diabetes Mellitus ◽  
Expression Profiles ◽  
Hypoxia Inducible Factor ◽  
Gene Expression Profiles ◽  
Normal Pregnancy ◽  
Normal Tissues ◽  
Genes Encoding

Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.

scholarly journals Gene Expression Profiles for Recurrence of Lymph Node-positive Primary Breast Cancer in Women Over 40 Years of Age

2021 ◽  
Author(s):  
Sean Si Qian Ma ◽  
Luyi Ye ◽  
Fan Zhang ◽  
Tiansheng Xu ◽  
Zai-Si Ji ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Lymph Node ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Olfactory Receptors ◽  
Specific Gene ◽  
Node Metastasis ◽  
Genes Encoding ◽  
Ffpe Samples

Abstract Background: Specific gene expression profiles correlate with recurrence of breast cancer in lymph node-negative patients. In contrast, insufficient knowledge is available regarding tumor-specific gene expression in patients with lymph node metastasis before surgery. Furthermore, such patients experience cumulative incidences of relapse greater than 50%. Methods: Sections of formalin-fixed paraffin embedded (FFPE) were prepared from breast tumors of 37 patients who were followed for at least 5 years. FFPE samples of patients with recurrent ductal breast cancer (n = 25) and 12 FFPE samples of such patients without recurrence were subjected to microarray analysis to identify gene expression profiles specifically associated with positive lymph nodes confirmed during surgery that were accompanied by lymphocytic invasion. Immunohistochemistry was employed to determine the estrogen receptor (ER) status of cancer tissues. All patients were administered tamoxifen after surgery, and this treatment continued for more than 5 years, or until cancer recurred. This strategy eliminated interactions between different therapeutics as potential confounding factors that influenced patients' outcomes.Results: Sixteen genes were expressed at significantly higher levels in patients with ER-positive (+) breast cancer with recurrence compared with those without recurrence. Gene Set Enrichment Analysis of The Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 73 genes encoding olfactory receptors included in the “Olfactory transduction” pathway that were enriched in the ER+ recurrence group (FDR P < 0.05). The KEGG “Histidine metabolism” and “Retinol metabolism” pathways were enriched in patients with ER-negative (–) breast cancer with recurrence (FDR P < 0.05). Conclusions: The present study is the first, to our knowledge, to identify 16 genes encoding proteins with diverse functions as well as 73 genes encoding olfactory receptors. These genes may serve as presurgical biomarkers for the recurrence of ER+ breast cancers with lymph node metastasis before surgery. These findings identify potential therapeutic targets for preventing cancer relapse, particularly after lymph nodes metastasis.

scholarly journals Different statins produce highly divergent changes in gene expression profiles of human hepatoma cells: a pilot study.

2011 ◽  
Vol 58 (4) ◽  
Author(s):  
Agata Leszczynska ◽  
Monika Gora ◽  
Danuta Plochocka ◽  
Grazyna Hoser ◽  
Anna Szkopinska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Statin Therapy ◽  
Hepg2 Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
High Dose ◽  
Human Hepatoma ◽  
Human Hepatoma Cells ◽  
Key Enzyme ◽  
Coa Reductase

Statins are inhibitors of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the key enzyme of the sterol biosynthesis pathway. Statin therapy is commonly regarded as well tolerated. However, serious adverse effects have also been reported, especially during high-dose statin therapy. The aim of our study was to investigate the effect of statins on gene expression profiles in human hepatoma HepG2 cells using Affymetrix Human Genome U133 Plus 2.0 arrays. Expression of 102, 857 and 1091 genes was changed substantially in HepG2 cells treated with simvastatin, fluvastatin and atorvastatin, respectively. Pathway and gene ontology analysis showed that many of the genes with changed expression levels were involved in a broad range of metabolic processes. The presented data clearly indicate substantial differences between the tested statins.

scholarly journals Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam

2020 ◽  
Vol 25 (6) ◽  
pp. 1111-1116 ◽  
Author(s):  
Abigail Ramsøe ◽  
Melody S. Clark ◽  
Victoria A. Sleight
Keyword(s):  
Ribosomal Proteins ◽  
Cellular Response ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Specific Gene ◽  
Heat Stress Response ◽  
Network Analyses ◽  
Genes Encoding ◽  
Response To Stress ◽  
The Antarctic

Abstract A computationally predicted gene regulatory network (GRN), generated from mantle-specific gene expression profiles in the Antarctic clam Laternula elliptica, was interrogated to test the regulation and interaction of duplicated inducible hsp70 paralogues. hsp70A and hsp70B were identified in the GRN with each paralogue falling into unique submodules that were linked together by a single shared second neighbour. Annotations associated with the clusters in each submodule suggested that hsp70A primarily shares regulatory relationships with genes encoding ribosomal proteins, where it may have a role in protecting the ribosome under stress. hsp70B, on the other hand, interacted with a suite of genes involved in signalling pathways, including four transcription factors, cellular response to stress and the cytoskeleton. Given the contrasting submodules and associated annotations of the two hsp70 paralogues, the GRN analysis suggests that each gene is carrying out additional separate functions, as well as being involved in the traditional chaperone heat stress response, and therefore supports the hypothesis that subfunctionalization has occurred after gene duplication. The GRN was specifically produced from experiments investigating biomineralization; however, this study shows the utility of such data for investigating multiple questions concerning gene duplications, interactions and putative functions in a non-model species.

scholarly journals Testosterone-induced permanent changes of hepatic gene expression in female mice sustained during Plasmodium chabaudi malaria infection

2010 ◽  
Vol 45 (6) ◽  
pp. 379-390 ◽  
Author(s):  
Denis Delić ◽  
Nicole Gailus ◽  
Hans-Werner Vohr ◽  
Mohamed Dkhil ◽  
Saleh Al-Quraishy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Malaria Infection ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Liver Metabolism ◽  
Hepatic Gene Expression ◽  
Plasmodium Chabaudi ◽  
Female Mice ◽  
Genes Encoding

Testosterone has been previously shown to induce persistent susceptibility to Plasmodium chabaudi malaria in otherwise resistant female C57BL/6 mice. Here, we investigate as to whether this conversion coincides with permanent changes of hepatic gene expression profiles. Female mice aged 10–12 weeks were treated with testosterone for 3 weeks; then, testosterone treatment was discontinued for 12 weeks before challenging with 106 P. chabaudi-infected erythrocytes. Hepatic gene expression was examined after 12 weeks of testosterone withdrawal and after subsequent infection with P. chabaudi at peak parasitemia, using Affymetrix microarrays with 22 690 probe sets representing 14 000 genes. The expression of 54 genes was found to be permanently changed by testosterone, which remained changed during malaria infection. Most genes were involved in liver metabolism: the female-prevalent genes Cyp2b9, Cyp2b13, Cyp3a41, Cyp3a44, Fmo3, Sult2a2, Sult3a1, and BC014805 were repressed, while the male-prevalent genes Cyp2d9, Cyp7b1, Cyp4a10, Ugt2b1, Ugt2b38, Hsd3b5, and Slco1a1 were upregulated. Genes encoding different nuclear receptors were not persistently changed. Moreover, testosterone induced persistent upregulation of genes involved in hepatocellular carcinoma such as Lama3 and Nox4, whereas genes involved in immune response such as Ifnγ and Igk-C were significantly decreased. Our data provide evidence that testosterone is able to induce specific and robust long-term changes of gene expression profiles in the female mouse liver. In particular, those changes, which presumably indicate masculinized liver metabolism and impaired immune response, may be critical for the testosterone-induced persistent susceptibility of mice to P. chabaudi malaria.

scholarly journals Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types

2018 ◽  
Vol 115 (45) ◽  
pp. E10672-E10681 ◽  
Author(s):  
Angela M. Magnuson ◽  
Evgeny Kiner ◽  
Ayla Ergun ◽  
Jun Seok Park ◽  
Natasha Asinovski ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Treg Cells ◽  
The Cancer Genome Atlas ◽  
Transcriptional Signature ◽  
Normal Tissues ◽  
Mouse Tumors ◽  
Tumor Stages ◽  
Genes Encoding ◽  
Tumor Types

FoxP3+T regulatory (Treg) cells are central elements of immunologic tolerance. They are abundant in many tumors, where they restrict potentially favorable antitumor responses. We used a three-pronged strategy to identify genes related to the presence and function of Tregs in the tumor microenvironment. Gene expression profiles were generated from tumor-infiltrating Tregs (TITRs) of both human and mouse tumors and were compared with those of Tregs of lymphoid organs or normal tissues from the same individuals. A computational deconvolution of whole-tumor datasets from the Cancer Genome Atlas (TCGA) was performed to identify transcripts specifically associated with Tregs across thousands of tumors from different stages and locations. We identified a set of TITR-differential transcripts with striking reproducibility between tumor types in mice, between mice and humans, and between different human patients spanning tumor stages. Many of the TITR-preferential transcripts were shared with “tissue Tregs” residing in nonlymphoid tissues, but a tumor-preferential segment could be identified. Many of these TITR signature transcripts were confirmed by mining of TCGA datasets, which also brought forth transcript modules likely representing the parenchymal attraction of, or response to, tumor Tregs. Importantly, the TITR signature included several genes encoding effective targets of tumor immunotherapy. A number of other targets were validated by CRISPR-based gene inactivation in mouse Tregs. These results confirm the validity of the signature, generating a wealth of leads for understanding the role of Tregs in tumor progression and identifying potential targets for cancer immunotherapy.

scholarly journals Global Gene Expression Responses to Cadmium Toxicity in Escherichia coli

2005 ◽  
Vol 187 (9) ◽  
pp. 3259-3266 ◽  
Author(s):  
Anyou Wang ◽  
David E. Crowley
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Cadmium Toxicity ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Temporal Gene Expression ◽  
Genes Encoding

ABSTRACT Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.

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