Identification Of Regulatory Genes Research Articles

The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice.

Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.

Expression Quantitative Trait Locus of Wood Formation-Related Genes in Salix suchowensis.

Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis.

The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes.

Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These datasets add valuable transcriptomic resources for further study of developmental gene expression, transcriptional regulations and functional gene activities involved in the development of M. plana. Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an RNAi-mediated pest control management by targeting certain pathways, and functional studies of the genes in M. plana.

Identification of Regulatory Genes and Metabolic Processes Important for Alginate Biosynthesis in Azotobacter vinelandii by Screening of a Transposon Insertion Mutant Library.

Azotobacter vinelandii produces the biopolymer alginate, which has a wide range of industrial and pharmaceutical applications. A random transposon insertion mutant library was constructed from A. vinelandii ATCC12518Tc in order to identify genes and pathways affecting alginate biosynthesis, and about 4,000 mutant strains were screened for altered alginate production. One mutant, containing a mucA disruption, displayed an elevated alginate production level, and several mutants with decreased or abolished alginate production were identified. The regulatory proteins AlgW and AmrZ seem to be required for alginate production in A. vinelandii, similarly to Pseudomonas aeruginosa. An algB mutation did however not affect alginate yield in A. vinelandii although its P. aeruginosa homolog is needed for full alginate production. Inactivation of the fructose phosphoenolpyruvate phosphotransferase system protein FruA resulted in a mutant that did not produce alginate when cultivated in media containing various carbon sources, indicating that this system could have a role in regulation of alginate biosynthesis. Furthermore, impaired or abolished alginate production was observed for strains with disruptions of genes involved in peptidoglycan biosynthesis/recycling and biosynthesis of purines, isoprenoids, TCA cycle intermediates, and various vitamins, suggesting that sufficient access to some of these compounds is important for alginate production. This hypothesis was verified by showing that addition of thiamine, succinate or a mixture of lysine, methionine and diaminopimelate increases alginate yield in the non-mutagenized strain. These results might be used in development of optimized alginate production media or in genetic engineering of A. vinelandii strains for alginate bioproduction.

Repair, regenerate and reconstruct: meeting the state-of-the-art.

The seventh EMBO meeting on the Molecular and Cellular Basis of Regeneration and Tissue Repair took place in Valletta, Malta, in September 2018. Researchers from all over the world gathered together with the aim of sharing the latest advances in wound healing, repair and regeneration. The meeting covered a wide range of regeneration models and tissues, identification of regulatory genes and signals, and striking advances toward regenerative therapies. Here, we report some of the exciting topics discussed during this conference, highlighting important discoveries in regeneration and the perspectives for regenerative medicine.

P3029 Identification of regulatory genes involved in longissimus dorsi transcriptomic differences between pig genotypes

P3029 Identification of regulatory genes involved in longissimus dorsi transcriptomic differences between pig genotypes

Identification of regulatory genes to reduce N2O production

Siciliano, S. D. 2014. Identification of regulatory genes to reduce N2O production. Can. J. Plant Sci. 94: 1033-1036. The production of nitrous oxide occurs predominantly by microbial activity. This microbial activity can be broadly sub-divided into denitrification, the sequential reduction of nitrate to nitrous oxide or dinitrogen gas, or into nitrification, the sequential oxidation of ammonia to nitrite. The consumption of nitrous oxide occurs by microbial activity as well, but only by a single pathway, i.e., the activity of nitrous oxide reductase (nos). The purpose of this investigation was to determine the dominant producer of nitrous oxide in our agricultural ecosystems, and then explore how these producers interacted with other biological and edaphic factors to regulate overall nitrous oxide production. Finally, we also investigated what controlled nitrous oxide consumption in these agricultural ecosystems. Much to our surprise, the dominant production of nitrous oxide in these upland agricultural ...

Identification of regulatory genes to reduce N2O production

Siciliano, S. D. 2014. Identification of regulatory genes to reduce N2O production. Can. J. Plant Sci. 94: 1033–1036. The production of nitrous oxide occurs predominantly by microbial activity. This microbial activity can be broadly sub-divided into denitrification, the sequential reduction of nitrate to nitrous oxide or dinitrogen gas, or into nitrification, the sequential oxidation of ammonia to nitrite. The consumption of nitrous oxide occurs by microbial activity as well, but only by a single pathway, i.e., the activity of nitrous oxide reductase (nos). The purpose of this investigation was to determine the dominant producer of nitrous oxide in our agricultural ecosystems, and then explore how these producers interacted with other biological and edaphic factors to regulate overall nitrous oxide production. Finally, we also investigated what controlled nitrous oxide consumption in these agricultural ecosystems. Much to our surprise, the dominant production of nitrous oxide in these upland agricultural soils occurred by nitrification, likely the nitrification-denitrification pathway. In addition, a root exudate, formate, was a large driver of nitrous oxide release via its interaction with the fungal biomass under micro-aerophilic conditions. Despite these unusual sources of production, what became apparent was that the net flux of nitrous oxide in an agricultural soil was linked to denitrifier consumption of nitrous oxide. In conclusion, this project found that there was a wide variety of non-bacterial denitrifier producers of nitrous oxide in an agricultural soil and that they interact not only between themselves but with the plant community. However, the net production of nitrous oxide in agricultural fields was still tightly linked to bacterial denitrification, but through the consumption of nitrous oxide by bacterial denitrifiers.

Identification of regulatory genes to improve nitrogen use efficiency

Guevara, D. R., Bi, Y.-M. and Rothstein, S. J. 2014. Identification of regulatory genes to improve nitrogen use efficiency. Can. J. Plant Sci. 94: 1009–1012. Crop production on soils containing sub-optimal levels of nitrogen (N) severely compromises yield potential. The development of crop varieties displaying high N use efficiency (NUE) is necessary in order to optimize N fertilizer use, and reduce the environmental damage caused by the current excessive application of N in agricultural areas. Genome-wide microarray analysis of rice plants grown under N-limiting environments was performed to identify NUE candidate genes. An early nodulin gene, OsENOD93-1, was strongly up-regulated during plant growth under low N. A constitutive Ubiquitin promoter was used to drive the expression of the OsENOD93-1 gene in transgenic plants to determine the importance of OsENOD93-1 for rice NUE. Transgenic rice plants over-expressing the OsENOD93-1 gene achieved ∼23% and 16% more yield and biomass, respectively, compared with wild-type plants when grown under N-limitation conditions. OsENOD93-1-OX transgenic plants accumulated a higher amount of total amino acids in the roots and xylem sap under N stress, suggesting that OsENOD93-1 plays a role in the transportation of amino acids. Taken together, we demonstrate that an effective way to identify NUE gene candidates involves both transcriptional profiling coupled with a transgenic validation approach to improve complex traits such as NUE in important crops.

Identification of regulatory genes to improve nitrogen use efficiency

Guevara, D. R., Bi, Y.-M. and Rothstein, S. J. 2014. Identification of regulatory genes to improve nitrogen use efficiency. Can. J. Plant Sci. 94: 1009-1012. Crop production on soils containing sub-optimal levels of nitrogen (N) severely compromises yield potential. The development of crop varieties displaying high N use efficiency (NUE) is necessary in order to optimize N fertilizer use, and reduce the environmental damage caused by the current excessive application of N in agricultural areas. Genome-wide microarray analysis of rice plants grown under N-limiting environments was performed to identify NUE candidate genes. An early nodulin gene, OsENOD93-1, was strongly up-regulated during plant growth under low N. A constitutive Ubiquitin promoter was used to drive the expression of the OsENOD93-1 gene in transgenic plants to determine the importance of OsENOD93-1 for rice NUE. Transgenic rice plants over-expressing the OsENOD93-1 gene achieved ~23% and 16% more yield and biomass, respectively, compared w...

Application of polymerase chain reaction with disposable amplicon detection device for identification of regulatory gene introduced into genetically modified maize

A novel genetically modified organism (GMO) detection method was developed using a simple and rapid procedure to identify a regulatory gene introduced into genetically modified (GM) maize. After DNA extraction from GM maize flours, fragments of the conserved sequence of the cauliflower masaic virus (CaMV) 35S promoter gene along with a competitive internal control gene were amplified using duplex polymerase chain reaction (PCR). Amplification products were then detected using a disposable detection device. The quantitative detection limit for GM maize 59122 was found to be 1.0% (w/w). Because the combination-method involving PCR technology coupled with a disposable detection device does not require expensive instrumentation or expertise, it will serve as a valuable alternative to immunoassays and traditional PCR-based tests in the detection of GMOs.

Plant–Pathogen Interactions: What Microarray Tells About It?

Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

Advances in plant disease and pest management

SUMMARYPests and diseases impact on crop yield and quality, and also reduce resource-use efficiency. Improved crop protection strategies to prevent such damage and loss can increase production and make a substantial contribution to food security. DNA-based technologies are likely to greatly increase the speed, sensitivity and accuracy of pest and pathogen detection and diagnosis. Rapid sequencing of nucleic acids from infected plants will aid identification of novel disease agents. Biomarkers of disease or crop damage such as volatile chemicals or blends may also be used to detect pest outbreaks. Biosensors coupled to information networks will provide real-time monitoring and surveillance of crops or stored produce and hence early warning of emerging problems and new invasive species. Challenges remain in the dissemination of new technologies and information to resource poor farmers in developing countries, although the rapid extension of the internet, mobile phones and other communication networks will provide new opportunities. Defining the genetic and molecular basis of innate plant immunity has been a major advance in plant biology with the potential to identify new targets for intervention via novel chemistry or genetic modification (GM). Identification of regulatory genes, signal molecules, pathways and networks controlling induced plant defence should lead to the development of a new generation of defence modulators, delivered either as crop protection products, or via biological agents on seeds or in the root zone. There should also be opportunities to select more responsive crop genotypes, or to develop transgenic crops tailored to respond to specific chemical cues or molecular patterns diagnostic for particular biotic threats. Sequencing of the genomes of the major crop species and their wild relatives will expand enormously the known gene pool and diversity of genetic resources available for plant breeders to access. It should be possible to identify genomic regions and genes conferring more durable, quantitative resistance to pathogens. The breeding cycle will be accelerated by high-throughput phenotyping and more efficient selection of resistance traits using within-gene markers. GM approaches will facilitate pyramiding (combining) resistance genes with different specificities and modes of action, thereby reducing the risk of directional selection for virulence. Analysis of the genomes of plant pathogens and invertebrate pests is already providing new information on genes, gene families and processes involved in host colonization and pathogenicity. Comparative genomics of species with diverse host ranges, contrasting feeding habits and different pathogenic lifestyles will identify new targets for inhibiting pest attack and aid the development of novel antimicrobial drugs and pesticides. Understanding the natural ecology of pests and pathogens, such as the factors determining host location, resource exploitation and interactions with other organisms, will improve our ability to manipulate behaviour, or exploit natural enemies or other antagonists of pest species. Volatile signals, either from natural plant sources, or engineered in transgenic crops, will be more widely used to modify pest behaviour. It may also be possible to manipulate microbial communities regulating pathogen populations and activity, and thereby recruit and retain more effective biocontrol agents. Insights into the natural diversity and activity of soil and microbial populations in the zones surrounding roots and seeds will provide new information on mechanisms of suppression regulating pest species. Fully effective interventions are unlikely, due to the complexity and diversity of the soil system, but there should be progress towards integrated control regimes combining more resistant crop genotypes (either selected or GM) with targeted management of natural suppressive processes. Harnessing new technologies and knowledge to create more durable resistant crops and sustainable disease and pest management systems will require improved understanding of the factors driving pest and pathogen adaptation and evolution. There must also be an increased emphasis on translational research and delivery, and developing strategies appropriate for lower-input production systems, if the second ‘green revolution’ is to become a reality.

Creating new knowledge for ruminant reproduction from rapidly expanding and evolving scientific databases

Declining fertility is a major problem for the dairy industry. Recent developments of Omics-technologies facilitate a comprehensive analysis of molecular patters in gametes, embryos and tissues of the reproductive tract which may help to identify the reasons for impaired fertility. Large Omics-datasets require appropriate bioinformatics analysis in the context of rapidly expanding and evolving scientific databases. This overview summarizes the current status of ruminant genome projects, describes currently existing resources for ruminant genomics, transcriptomics and proteomics as well as databases and tools for the interpretation and exploitation of transcriptomics and proteomics datasets. Gene set enrichment analysis (GSEA) and transcription factor binding site (TFBS) analyses are strategies for the identification of regulatory genes. In general, the comprehensive analysis of molecular traits by Omics-technologies can enhance the interpretation of genome-wide association studies, providing insights into the biological pathways linking genotype and phenotype, and their modulation by endogenous and environmental factors.

The secondary growth in plant and its molecular regulation

The secondary growth is a significant biological activity for plant development, and the secondary xylem (i.e. wood) plays an important role for human life. The secondary growth includes several consecutive processes such as vascular tissue differentiation, secondary cell wall deposition, lignification, PCD and heart wood formation. Considerable evidence indicated that auxin is the major signal involved in several aspects of the ontogeny of the vascular system. At the same time, a suite of putative transcription factors such as MYB, NAC, AP2/EREBP, homeobox and MADS have been implicated in the regulation of the secondary growth. The candidate genes in the signaling and transcriptional regulation which have been identified will assist future investigations to unravel the molecular mechanisms of secondary growth. The important aspect in secondary growth and the identification of regulatory genes were reviewed here.

Genetic Mechanisms of Cell Transdifferentiation

Studies have been considered, which concern identification of regulatory genes in adult newts and their expression during retinal and lens regeneration. B.L. Astaurov repeatedly urged to join efforts of geneticists and embryologists in studies of the mechanisms underlying biological phenomena. This was also true for studies of regeneration. Such studies became possible only after introduction of molecular biology methods. Studies of the mechanisms underlying regeneration have been recently carried out jointly by geneticists and developmental biologists. This review presented at the conference dedicated to the 100th anniversary of B.L. Astaurov deals with these aspects in studies of regeneration.

Identification and characterization of two novel zinc finger genes, ZNF359 and ZFP28, in human development

Transcription factors play an essential role in controlling gene expression during cardiac and vascular pathogeneses. Identification of regulatory genes in the cardiovascular system is a necessary step toward an understanding of the pathogenesis of congenital heart disease and acquired cardiovascular diseases. The Cys2/His2 type zinc finger genes are the single largest class of transcription factors in the human genome and many numbers of these kr ü pple-like zinc finger genes have been found to be involved in cardiac development or cardiovascular diseases. In this study, we have identified two novel human kr ü pple-like zinc finger genes named ZNF359 and ZFP28 from the human heart cDNA library. The complete human ZNF359 cDNA sequence is 3270 bp and contains a 1932-bp open reading frame (ORF) that encodes a 643 amino acid protein with an N-terminal KRAB domain and 16 C-terminus zinc finger C 2H 2 motifs. The ZFP28 cDNA sequence is 4104 bp and contains a 2076-bp ORF that encodes an 868 amino acid protein with an N-terminal signal peptide, two KRAB domains, and 14 C-terminal C 2H 2 zinc finger motifs. Northern blot analyses showed a strong expression of ZNF359 and ZFP28 in various tissues of adult human. A further analysis using human embryonic tissues (18–23 weeks) showed a development-specific expression pattern in heart, skeletal muscle, liver, lung, kidney, and brain, suggesting a role for these genes in embryonic development.

LIM-domain protein cysteine- and glycine-rich protein 2 (CRP2) is a novel marker of hepatic stellate cells and binding partner of the protein inhibitor of activated STAT1.

Activation of hepatic stellate cells is considered to be the main step in the development of liver fibrosis, which is characterized by the transition of quiescent vitamin-A-rich cells to proliferative, fibrogenic and contractile myofibroblasts. The identification of regulatory genes during early cell activation and transdifferentiation is essential to extend our knowledge of hepatic fibrogenesis. In liver, the gene CSRP2 is exclusively expressed by stellate cells, whereas no transcripts are detectable in hepatocytes, sinusoidal endothelial cells or Kupffer cells. The early activation of stellate cells induced by platelet-derived growth factor is accompanied by an enhanced expression of CSRP2. During later stages of transdifferentiation, the expression of CSRP2 in these cells is suppressed in vitro and in vivo. The CSRP2-encoded cysteine- and glycine-rich double-LIM-domain protein (CRP)2 is proposed to function as a molecular adapter, arranging two or more as yet unidentified protein constituents into a macromolecular complex. To identify these proteins and assign a cellular function to CRP2, a human cDNA library was screened with full-length CRP2 as bait in a yeast two-hybrid screen. The protein inhibitor of activated STAT1 ('PIAS1') was shown to associate selectively with the C-terminal LIM domain of CRP2. Physical interaction of both proteins in the cellular environment was confirmed by co-localization experiments with confocal laser scanning microscopy and co-immunoprecipitation analysis. These results establish CRP2 as a potential new factor in the JAK/STAT-signalling pathway and suggest that the suppression of CSRP2 might be a prerequisite for the myofibroblastic transition of hepatic stellate cells.

LIM-domain protein cysteine- and glycine-rich protein 2 (CRP2) is a novel marker of hepatic stellate cells and binding partner of the protein inhibitor of activated STAT1

Activation of hepatic stellate cells is considered to be the main step in the development of liver fibrosis, which is characterized by the transition of quiescent vitamin-A-rich cells to proliferative, fibrogenic and contractile myofibroblasts. The identification of regulatory genes during early cell activation and transdifferentiation is essential to extend our knowledge of hepatic fibrogenesis. In liver, the gene CSRP2 is exclusively expressed by stellate cells, whereas no transcripts are detectable in hepatocytes, sinusoidal endothelial cells or Kupffer cells. The early activation of stellate cells induced by platelet-derived growth factor is accompanied by an enhanced expression of CSRP2. During later stages of transdifferentiation, the expression of CSRP2 in these cells is suppressed in vitro and in vivo. The CSRP2-encoded cysteine- and glycine-rich double-LIM-domain protein (CRP)2 is proposed to function as a molecular adapter, arranging two or more as yet unidentified protein constituents into a macromolecular complex. To identify these proteins and assign a cellular function to CRP2, a human cDNA library was screened with full-length CRP2 as bait in a yeast two-hybrid screen. The protein inhibitor of activated STAT1 (‘PIAS1’) was shown to associate selectively with the C-terminal LIM domain of CRP2. Physical interaction of both proteins in the cellular environment was confirmed by co-localization experiments with confocal laser scanning microscopy and co-immunoprecipitation analysis. These results establish CRP2 as a potential new factor in the JAK/STAT-signalling pathway and suggest that the suppression of CSRP2 might be a prerequisite for the myofibroblastic transition of hepatic stellate cells.