scholarly journals Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

2020 ◽  
Vol 22 (1) ◽  
pp. 253
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Functional Groups ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Crop Improvement ◽  
Potato Virus X ◽  
Tissue Growth ◽  
Abiotic Stress Response ◽  
Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

Gene expression profiles of cardiomyocytes in rat autoimmune myocarditis by DNA microarray and increase of regenerating gene family

2008 ◽  
Vol 152 (3) ◽  
pp. 119-127 ◽  
Author(s):  
Ritsuo Watanabe ◽  
Haruo Hanawa ◽  
Tsuyoshi Yoshida ◽  
Masahiro Ito ◽  
Manabu Isoda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Dna Microarray ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Autoimmune Myocarditis

scholarly journals Distinct gene expression profiles in norepinephrine- and epinephrine-producing hereditary and sporadic pheochromocytomas: activation of hypoxia-driven angiogenic pathways in von Hippel–Lindau syndrome

2004 ◽  
Vol 11 (4) ◽  
pp. 897-911 ◽  
Author(s):  
G Eisenhofer ◽  
T-T Huynh ◽  
K Pacak ◽  
F M Brouwers ◽  
M M Walther ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Tissue Growth ◽  
Vegf Receptor ◽  
Vascular Endothelial ◽  
Biochemical Phenotype ◽  
Von Hippel Lindau ◽  
Men 2

Pheochromocytomas in von Hippel–Lindau (VHL) syndrome produce exclusively norepinephrine, whereas those in multiple endocrine neoplasia type 2 (MEN 2) produce epinephrine. This study examined the pathways activated in VHL-associated pheochromocytomas by comparing gene expression profiles in VHL and MEN 2 tumors in relationship to profiles in sporadic norepinephrine- and epinephrine-producing tumors. Larger and more distinct differences in gene expression among hereditary than sporadic tumors indicated the importance of the underlying mutation to gene expression profiles. Many of the genes over-expressed in VHL compared with MEN 2 tumors were clearly linked to the hypoxia-driven angiogenic pathways that are activated in VHL-associated tumorigenesis. Such genes included those for the glucose transporter, vascular endothelial growth factor (VEGF), placental growth factor, angiopoietin 2, tie-1, VEGF receptor 2 and its coreceptor, neuropilin-1. Other up-regulated genes, such as connective tissue growth factor, cysteine-rich 61, matrix metalloproteinase 1, vascular endothelial cadherin, tenascin C, stanniocalcin 1, and cyclooxygenases 1 and 2 are known to be involved in VEGF-regulated angiogenesis. Shared differences in expression of subsets of genes in norepinephrine- versus epinephrine-producing hereditary and sporadic pheochromocytomas indicated other differences in gene expression that may underlie the biochemical phenotype. Over-expression of the hypoxia-inducible transcription factor, HIF-2α, in norepinephrine-predominant sporadic and VHL tumors compared with epinephrine-producing tumors indicates that expression of this gene depends on the noradrenergic biochemical phenotype. The findings fit with the known expression of HIF-2α in norepinephrine-producing cells of the sympathetic nervous system and might explain both the development and noradrenergic biochemical phenotype of pheochromocytomas in VHL syndrome.

scholarly journals Dact gene expression profiles suggest a role for this gene family in integrating Wnt and TGF-β signaling pathways during chicken limb development

2013 ◽  
Vol 243 (3) ◽  
pp. 428-439 ◽  
Author(s):  
Lucimara Aparecida Sensiate ◽  
Débora R. Sobreira ◽  
Fernanda Cristina Da Veiga ◽  
Denner Jefferson Peterlini ◽  
Angelica Vasconcelos Pedrosa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Signaling Pathways ◽  
Limb Development ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1949
Author(s):  
Tian Fan ◽  
Tianxiao Lv ◽  
Chuping Xie ◽  
Yuping Zhou ◽  
Changen Tian
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress ◽  
Yeast Two Hybrid ◽  
Iq Motif ◽  
Two Hybrid

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I–III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

scholarly journals Warm seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7785 ◽  
Author(s):  
Christine Guzman ◽  
Michael Atrigenio ◽  
Chuya Shinzato ◽  
Porfirio Aliño ◽  
Cecilia Conaco
Keyword(s):  
Gene Expression ◽  
Growth Rate ◽  
Extracellular Matrix ◽  
Expression Profiles ◽  
Seawater Temperature ◽  
Scleractinian Corals ◽  
Tissue Growth ◽  
Cellular Migration ◽  
Coral Tissue ◽  
Growth Margin

Background Heliopora coerulea, the blue coral, is a reef building octocoral that is reported to have a higher optimum temperature for growth compared to most scleractinian corals. This octocoral has been observed to grow over both live and dead scleractinians and to dominate certain reefs in the Indo-Pacific region. The molecular mechanisms underlying the ability of H. coerulea to tolerate warmer seawater temperatures and to effectively compete for space on the substrate remain to be elucidated. Methods In this study, we subjected H. coerulea colonies to various temperatures for up to 3 weeks. The growth and photosynthetic efficiency rates of the coral colonies were measured. We then conducted pairwise comparisons of gene expression among the different coral tissue regions to identify genes and pathways that are expressed under different temperature conditions. Results A horizontal growth rate of 1.13 ± 0.25 mm per week was observed for corals subjected to 28 or 31 °C. This growth rate was significantly higher compared to corals exposed at 26 °C. This new growth was characterized by the extension of whitish tissue at the edges of the colony and was enriched for a matrix metallopeptidase, a calcium and integrin binding protein, and other transcripts with unknown function. Tissues at the growth margin and the adjacent calcified encrusting region were enriched for transcripts related to proline and riboflavin metabolism, nitrogen utilization, and organic cation transport. The calcified digitate regions, on the other hand, were enriched for transcripts encoding proteins involved in cell-matrix adhesion, translation, receptor-mediated endocytosis, photosynthesis, and ion transport. Functions related to lipid biosynthesis, extracellular matrix formation, cell migration, and oxidation-reduction processes were enriched at the growth margin in corals subjected for 3 weeks to 28 or 31 °C relative to corals at 26 °C. In the digitate region of the coral, transcripts encoding proteins that protect against oxidative stress, modify cell membrane composition, and mediate intercellular signaling pathways were enriched after just 24 h of exposure to 31 °C compared to corals at 28 °C. The overall downregulation of gene expression observed after 3 weeks of sustained exposure to 31 °C is likely compensated by symbiont metabolism. Discussion These findings reveal that the different regions of H. coerulea have variable gene expression profiles and responses to temperature variation. Under warmer conditions, the blue coral invests cellular resources toward extracellular matrix formation and cellular migration at the colony margins, which may promote rapid tissue growth and extension. This mechanism enables the coral to colonize adjacent reef substrates and successfully overgrow slower growing scleractinian corals that may already be more vulnerable to warming ocean waters.

scholarly journals Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Joseph M. Bliss ◽  
George A. Tollefson ◽  
Abigail Cuevas ◽  
Sarah J. Longley ◽  
Matthew N. Neale ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Candida Parapsilosis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Families ◽  
Mammalian Host ◽  
Emerging Infections ◽  
Content Type

ABSTRACT Candida parapsilosis has emerged as a frequent cause of invasive candidiasis with increasing evidence of unique biological features relative to C. albicans. As it adapts to conditions within a mammalian host, rapid changes in gene expression are necessary to facilitate colonization and persistence in this environment. Adhesion of the organism to biological surfaces is a key first step in this process and is the focus of this study. Building on previous observations showing the importance of a member of the ALS gene family in C. parapsilosis adhesion, three clinical isolates were cultured under two conditions that mimic the mammalian host and promote adhesion, incubation at 37°C in tissue culture medium 199 or in human plasma. Transcriptional profiles using RNA-seq were obtained in these adhesion-inducing conditions and compared to profiles following growth in yeast media that suppress adhesion to identify gene expression profiles associated with adhesion. Overall gene expression profiles among the three strains were similar in both adhesion-inducing conditions and distinct from adhesion-suppressing conditions. Pairwise analysis among the three growth conditions identified 133 genes that were differentially expressed at a cutoff of ±4-fold, with the most upregulated genes significantly enriched in iron acquisition and transmembrane transport, while the most downregulated genes were enriched in oxidation-reduction processes. Gene family enrichment analysis identified gene families with diverse functions that may have an important role in this important step for colonization and disease. IMPORTANCE Invasive Candida infections are frequent complications of the immunocompromised and are associated with substantive morbidity and mortality. Although C. albicans is the best-studied species, emerging infections by non-albicans Candida species have led to increased efforts to understand aspects of their pathogenesis that are unique from C. albicans. C. parapsilosis is a frequent cause of invasive infections, particularly among premature infants. Recent efforts have identified important virulence mechanisms that have features distinct from C. albicans. C. parapsilosis can exist outside a host environment and therefore requires rapid modifications when it encounters a mammalian host to prevent its clearance. An important first step in the process is adhesion to host surfaces. This work takes a global, nonbiased approach to investigate broad changes in gene expression that accompany efficient adhesion. As such, biological pathways and individual protein targets are identified that may be amenable to manipulation to reduce colonization and disease from this organism.

scholarly journals Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Triticum aestivum

2020 ◽  
Vol 71 (15) ◽  
pp. 4531-4546
Author(s):  
Huadun Wang ◽  
Yongfang Wan ◽  
Peter Buchner ◽  
Robert King ◽  
Hongxiang Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Expression Profiles ◽  
Peptide Transporter ◽  
Specific Gene ◽  
Rna Seq ◽  
Systematic Analysis ◽  
Whole Wheat ◽  
Transporter Family ◽  
Systematic Identification

Abstract NPF genes encode membrane transporters involved in the transport of a large variety of substrates including nitrate and peptides. The NPF gene family has been described for many plants, but the whole NPF gene family for wheat has not been completely identified. The release of the wheat reference genome has enabled the identification of the entire wheat NPF gene family. A systematic analysis of the whole wheat NPF gene family was performed, including responses of specific gene expression to development and nitrogen supply. A total of 331 NPF genes (113 homoeologous groups) have been identified in wheat. The chromosomal location of the NPF genes is unevenly distributed, with predominant occurrence in the long arms of the chromosomes. The phylogenetic analysis indicated that wheat NPF genes are closely clustered with Arabidopsis, Brachypodium, and rice orthologues, and subdivided into eight subfamilies. The expression profiles of wheat NPF genes were examined using RNA-seq data, and a subset of 44 NPF genes (homoeologous groups) with contrasting expression responses to nitrogen and/or development in different tissues were identified. The systematic identification of gene composition, chromosomal locations, evolutionary relationships, and expression profiles contributes to a better understanding of the roles of the wheat NPF genes and lays the foundation for further functional analysis in wheat.

scholarly journals Distribution of Kakugo Virus and Its Effects on the Gene Expression Profile in the Brain of the Worker Honeybee Apis mellifera L.

2009 ◽  
Vol 83 (22) ◽  
pp. 11560-11568 ◽  
Author(s):  
Tomoko Fujiyuki ◽  
Emiko Matsuzaka ◽  
Takayoshi Nakaoka ◽  
Hideaki Takeuchi ◽  
Akiko Wakamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Parasitic Wasp ◽  
Gene Expression Profiles ◽  
Hypothetical Protein ◽  
Brain Regions ◽  
Gene Encoding ◽  
Brain Functions ◽  
The Brain

ABSTRACT We previously identified a novel insect picorna-like virus, termed Kakugo virus (KV), obtained from the brains of aggressive honeybee worker bees that had counterattacked giant hornets. Here we examined the tissue distribution of KV and alterations of gene expression profiles in the brains of KV-infected worker bees to analyze possible effects of KV infection on honeybee neural and physiological states. By use of in situ hybridization, KV was broadly detected in the brains of the naturally KV-infected worker bees. When inoculated experimentally into bees, KV was detected in restricted parts of the brain at the early infectious stage and was later detected in various brain regions, including the mushroom bodies, optic lobes, and ocellar nerve. KV was detected not only in the brain but also in the hypopharyngeal glands and fat bodies, indicating systemic KV infection. Next, we compared the gene expression profiles in the brains of KV-inoculated and noninoculated bees. The expression of 11 genes examined was not significantly affected in KV-infected worker bees. cDNA microarray analysis, however, identified a novel gene whose expression was induced in the periphery of the brains of KV-infected bees, which was commonly observed in naturally infected and experimentally inoculated bees. The gene encoded a novel hypothetical protein with a leucine zipper motif. A gene encoding a similar protein was found in the parasitic wasp Nasonia genome but not in other insect genomes. These findings suggest that KV infection may affect brain functions and/or physiological states in honeybees.

scholarly journals Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaomin Xu ◽  
Lili Zhang ◽  
Wan Zhao ◽  
Liang Fu ◽  
Yuxuan Han ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Gene Family ◽  
Developmental Stages ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Abiotic Stress Response ◽  
Serine Carboxypeptidase ◽  
Drought And Salt Tolerance

Abstract Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat.

scholarly journals The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifang Ma ◽  
Jialu Chen ◽  
Bin Huang ◽  
Zhinuo Huang ◽  
Zhijun Zhang
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Zinc Finger Protein ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Model Organisms ◽  
Phyllostachys Edulis ◽  
Sequence Alignments ◽  
Specific Expression

Abstract Background The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown. Result In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis. Conclusions In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

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