The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

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The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

10.1101/2020.09.15.298612 ◽

2020 ◽

Author(s):

Alexandre Hild Aono ◽

Ricardo José Gonzaga Pimenta ◽

Ana Letycia Basso Garcia ◽

Fernando Henrique Correr ◽

Guilherme Kenichi Hosaka ◽

...

Keyword(s):

Sorghum Bicolor ◽

Expression Profiles ◽

Expression Patterns ◽

Saccharum Spontaneum ◽

Rna Seq ◽

Kinase Gene ◽

Molecular Features ◽

History Of ◽

Allele Specificity ◽

Coexpression Networks

AbstractThe protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs.HighlightThis study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor, providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.

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Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.2929 ◽

2019 ◽

Vol 286 (1897) ◽

pp. 20182929 ◽

Cited By ~ 2

Author(s):

Elena A. Ritschard ◽

Robert R. Fitak ◽

Oleg Simakov ◽

Sönke Johnsen

Keyword(s):

Signal Transduction ◽

Positive Selection ◽

G Protein ◽

Evolutionary History ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Genomic Signatures ◽

History Of ◽

G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

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Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

10.1101/2021.01.15.426908 ◽

2021 ◽

Author(s):

Jakub Jankowski ◽

Hye Kyung Lee ◽

Julia Wilflingseder ◽

Lothar Hennighausen

Keyword(s):

Gene Expression ◽

Proximal Tubule ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Regulatory Elements ◽

Rna Seq ◽

Angiotensin Converting Enzyme 2 ◽

Genome Wide ◽

Cytokine Stimulation

SummaryRecently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFNα and IFNβ, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.

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Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis

Frontiers in Genetics ◽

10.3389/fgene.2021.802953 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yani Dong ◽

Likang Lyu ◽

Haishen Wen ◽

Bao Shi

Keyword(s):

Molecular Mechanisms ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Interaction ◽

Cynoglossus Semilaevis ◽

Rna Seq ◽

Tongue Sole ◽

Gene Interaction Networks ◽

Half Smooth Tongue Sole ◽

The Brain

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.

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Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

Frontiers in Genetics ◽

10.3389/fgene.2021.769690 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pengpeng Zhang ◽

Mingxuan Sheng ◽

Chunyu Du ◽

Zhe Chao ◽

Haixia Xu ◽

...

Keyword(s):

Binding Sites ◽

Expression Profiles ◽

Expression Patterns ◽

Potential Functions ◽

Rna Seq ◽

Specific Expression ◽

Protein Coding ◽

Multiple Binding Sites ◽

Brown Adipose ◽

Brown Adipogenesis

Brown adipose tissue (BAT) is specialized for energy expenditure, thus a better understanding of the regulators influencing BAT development could provide novel strategies to defense obesity. Many protein-coding genes, miRNAs, and lncRNAs have been investigated in BAT development, however, the expression patterns and functions of circRNA in brown adipogenesis have not been reported yet. This study determined the circRNA expression profiles across brown adipogenesis (proliferation, early differentiated, and fully differentiated stages) by RNA-seq. We identified 3,869 circRNAs and 36.9% of them were novel. We found the biogenesis of circRNA was significantly related to linear mRNA transcription, meanwhile, almost 70% of circRNAs were generated by alternative back-splicing. Next, we examined the cell-specific and differentiation stage-specific expression of circRNAs. Compared to white adipocytes, nearly 30% of them were specifically expressed in brown adipocytes. Further, time-series expression analysis showed circRNAs were dynamically expressed, and 117 differential expression circRNAs (DECs) in brown adipogenesis were identified, with 77 upregulated and 40 downregulated. Experimental validation showed the identified circRNAs could be successfully amplified and the expression levels detected by RNA-seq were reliable. For the potential functions of the circRNAs, GO analysis suggested that the decreased circRNAs were enriched in cell proliferation terms, while the increased circRNAs were enriched in development and thermogenic terms. Bioinformatics predictions showed that DECs contained numerous binding sites of functional miRNAs. More interestingly, most of the circRNAs contained multiple binding sites for the same miRNA, indicating that they may facilitate functions by acting as microRNA sponges. Collectively, we characterized the circRNA expression profiles during brown adipogenesis and provide numerous novel circRNAs candidates for future brown adipogenesis regulating studies.

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Involvement of the p38 Mitogen-activated Protein Kinase α, β, and γ Isoforms in Myogenic Differentiation

Molecular Biology of the Cell ◽

10.1091/mbc.e07-08-0817 ◽

2008 ◽

Vol 19 (4) ◽

pp. 1519-1528 ◽

Cited By ~ 35

Author(s):

Haixia Wang ◽

Qing Xu ◽

Fang Xiao ◽

Yong Jiang ◽

Zhenguo Wu

Keyword(s):

Protein Kinase ◽

Target Genes ◽

Myogenic Differentiation ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

C2c12 Cells ◽

Mitogen Activated Protein Kinase ◽

Cyclin D3 ◽

Mitogen Activated Protein

We and others previously showed that p38 mitogen-activated protein kinase is indispensable for myogenic differentiation. However, it is less clear which of the four p38 isoforms in the mouse genome participates in this process. Using C2C12 myogenic cells as a model, we showed here that p38α, β, and γ are expressed with distinct expression patterns during differentiation. Knockdown of any of them by small interfering RNA inhibits myogenic differentiation, which suggests that the functions of the three p38 isoforms are not completely redundant. To further elucidate the unique role of each p38 isoform in myogenic differentiation, we individually knocked down one p38 isoform at a time in C2C12 cells, and we compared the whole-genome gene expression profiles by microarrays. We found that some genes are coregulated by all three p38 isoforms, whereas others are uniquely regulated by one particular p38 isoform. Furthermore, several novel p38 target genes (i.e., E2F2, cyclin D3, and WISP1) are found to be required for myogenin expression, which provides a molecular basis to explain why different p38 isoforms are required for myogenic differentiation.

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Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi

PeerJ ◽

10.7717/peerj.8768 ◽

2020 ◽

Vol 8 ◽

pp. e8768 ◽

Cited By ~ 1

Author(s):

Kunyuan Guo ◽

Yiwei Yao ◽

Meng Yang ◽

Yanni Li ◽

Bin Wu ◽

...

Keyword(s):

Expression Profiles ◽

Pearson Correlation ◽

Expression Patterns ◽

Phosphate Transporter ◽

Molecular Response ◽

Pueraria Lobata ◽

Rna Seq ◽

Structural Genes ◽

Ros Scavenging ◽

Isoflavone Biosynthesis

Pueraria lobata (willd.) Ohwi is a consumable selenium-enriched plant used for medicinal purposes. The molecular response to selenium (Se) stimuli in P. lobata is currently unknown. We used RNA-Seq to identify potential genes involved in selenite metabolism and analyzed their expression profiles. We obtained a total of 150,567 unigenes, of which 90,961 were annotated, including 16 structural genes, 14 sulfate transporters, and 13 phosphate transporters that may be involved in Se metabolism, and 33 candidate structural genes involved in isoflavone biosynthesis. The genes with a —foldchange— >2 and q value <0.05 after sodium selenite treatment were identified as differentially expressed genes (DEGs). We obtained a total of 4,246 DEGs, which were enriched in GO terms that included “response to stimulus”, “response to stress”, “signal transduction”, “response to abiotic stimulus”, and “response to chemical”. Of the 4,246 DEGs, one sulfate transporter and five phosphate transporter genes involved Se metabolism, and nine structural genes involved in isoflavone biosynthesis were up-regulated. The expression patterns of 10 DEGs were selected randomly and validated using qRT-PCR. The Pearson Correlation Coefficient (r) was 0.86, indicating the reliability of RNA-Seq results. 22 Reactive Oxygen Species (ROS) scavenging DEGs were found, 11 of which were up-regulated. 436, 624 transcription factors (TFs) correlated with structural genes were identified that may be involved in Se and isoflavone biosynthesis, respectively, using r (r > 0.7 or r < − 0.7). 556 TFs were related to at least one sulfate and phosphate transporter. Our results provided a comprehensive description of gene expression and regulation in response to Se stimuli in P. lobata.

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HMGR overexpression and interference affects the expression of steroidogenic genes and cholesterol content in bovine intramuscular adipocytes

10.21203/rs.2.10141/v1 ◽

2019 ◽

Author(s):

Xiaomu Liu ◽

Wei You ◽

Xianglun Zhang ◽

Qing Jin ◽

Xiuwen Tan ◽

...

Keyword(s):

Energy Metabolism ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Mevalonic Acid ◽

Cholesterol Content ◽

Rna Seq ◽

Theoretical Understanding ◽

Bovine Adipocytes ◽

Steroidogenic Genes

Abstract Background:Previously, we found that mevalonic acid stimulates HMGR expression in bovine intramuscular adipocytes, and influences adipocyte differentiation. However, it remains unclear whether there is any direct link between HMGR, steroidogenic genes, and cholesterol content. RNA-Seq was conducted to determine the differences between the gene expression profiles of bovine adipocytes containing different HMGR expression constructs. Results:In total, 10 234 differentially expressed genes (DEGs) were found. Of these, 35 and 6 DEGs between the control and the overexpression groups were functionally related to lipid and energy metabolisms, respectively. Additionally, 43 and 8 DEGs between the control and the HMGR inhibition groups were related to lipid and energy metabolism. Additionally, several DEGs related to lipid and energy metabolism were identified between the HMGR overexpression group and the HMGR interference group. Several DEGs correlated positively or negatively with overexpression or inhibition of HMGR. We also found that, following activation or inhibition of the HMGR gene, AMPK and SIRT1 had opposite expression patterns in bovine intramuscular adipocytes. Interestingly, the HMGR gene was downregulated when HMGR was overexpressed, and upregulated when HMGR was inhibited. Conclusion:Our findings establish a theoretical understanding of signaling pathways involved in cholesterol synthesis by elucidating the relationships between key genes.

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Identification of Isoflavonoid Biosynthesis-Related R2R3-MYB Transcription Factors in Callerya speciosa (Champ. ex Benth.) Schot Using Transcriptome-Based Gene Coexpression Analysis

International Journal of Genomics ◽

10.1155/2021/9939403 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Linchan Yu ◽

Ding Huang ◽

Jinyuan Gu ◽

Dongjin Pan ◽

Yong Tan ◽

...

Keyword(s):

Genetic Manipulation ◽

Sequence Similarity ◽

Expression Profiles ◽

Expression Patterns ◽

Structural Genes ◽

Chinese Medicinal Herb ◽

Tuberous Roots ◽

Repeat Domain ◽

R2r3 Myb ◽

Coexpression Networks

The R2R3-MYB family is one of the largest plant transcription factor (TF) families playing vital roles in defense, plant growth, and secondary metabolism biosynthesis. Although this gene family has been studied in many species, isoflavonoid biosynthesis-related R2R3-MYB TFs in Callerya speciosa (Champ. ex Benth.) Schot, a traditional Chinese medicinal herb, are poorly understood. Here, a total of 101 R2R3-MYB TFs were identified from C. speciosa transcriptome dataset. 25 clades divided into five functional groups were clustered based on the sequence similarity and phylogenetic tree. Conserved motifs and domain distribution, expression patterns, and coexpression networks were also employed to identify the potential R2R3-MYB TFs in the regulation of isoflavonoid biosynthesis. In silico evaluation showed that the deduced R2R3-CsMYB proteins contain highly conserved R2R3 repeat domain at the N-terminal region, that is the signature motif of R2R3-type MYB TFs. Eight potential TFs (CsMYB17, CsMYB36, CsMYB41, CsMYB44, CsMYB45, CsMYB46, CsMYB72, and CsMYB81) had high degrees of coexpression with four key isoflavonoid biosynthetic genes (CsIFS, CsCHS7, CsHID-1, and CsCHI3), in which CsMYB36 as a potential regulator possessed the highest degree. HPLC analysis showed that formononetin and maackiain contents were significantly increased during the development of tuberous roots, which might be controlled by both related R2R3-CsMYBs and structural genes involved in the isoflavonoid biosynthesis pathway. The transcriptome data were further validated by reverse transcription real-time PCR (RT-qPCR) analysis, and similar expression profiles between TFs and key structural genes were identified. This study was the first step toward the understanding of the R2R3-MYB TFs regulating isoflavonoid biosynthesis in C. speciosa. The results will provide information for further functional analysis and quality improvement through genetic manipulation of these potential R2R3-CsMYB genes in C. speciosa.

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Genome-wide sequence and expression analysis of the NAC transcription factor family in polyploid wheat

10.1101/141747 ◽

2017 ◽

Author(s):

Philippa Borrill ◽

Sophie A. Harrington ◽

Cristobal Uauy

Keyword(s):

Transcription Factors ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Phylogenetic Groups ◽

Future Studies ◽

Nac Transcription Factors ◽

Wide Range ◽

Nac Family

ARTICLE SUMMARYTranscription factors are vital in plants to regulate gene expression in response to environmental stimuli and to control developmental processes. In this study, we annotated and classified transcription factors in polyploid bread wheat into gene families and explored the NAC family in detail. We combined phylogenetic analysis and transcriptome analysis, using publicly available RNA-seq data, to characterize the NAC gene family and provide hypotheses for putative functions of many NAC transcription factors. This study lays the groundwork for future studies on transcription factors in wheat which may be of great agronomic relevance.ABSTRACTMany important genes in agriculture correspond to transcription factors which regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5,776 transcription factors in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain conservation and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). C-terminal domain motifs were frequently conserved between wheat, rice and barley within phylogenetic groups, however this conservation was not maintained across phylogenetic groups. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a co-expression analysis on all wheat genes and identified 37 modules of co-expressed genes of which 23 contained NACs. Using GO term enrichment we obtained putative functions for NACs within co-expressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC transcription factors in wheat.

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