Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors

We built a complete and non-redundant database of bZIP transcriptional regulatory factors from the Arabidopsis reference genome. These Arabidopsis bZIP factors were ordered into thirteen families of evolutionary related proteins and this classification was used to identify and organize sugarcane cDNAs encoding bZIP proteins. We also show how this classification should help in defining putative clusters of orthologous groups of higher plant bZIP regulators and briefly discuss the expected benefits of this procedure to efficiently characterize sugarcane bZIP transcriptional regulators.

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Selective DNA bending by a variety of bZIP proteins.

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5479 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5479-5489 ◽

Cited By ~ 95

Author(s):

T K Kerppola ◽

T Curran

Keyword(s):

Dna Bending ◽

Major Groove ◽

Bent Dna ◽

Dna Structures ◽

Protein Dimers ◽

Bzip Proteins ◽

Related Proteins ◽

Combinatorial Interactions ◽

Bend Angles ◽

Bzip Family

We have investigated DNA bending by bZIP family proteins that can bind to the AP-1 site. DNA bending is widespread, although not universal, among members of this family. Different bZIP protein dimers induced distinct DNA bends. The DNA bend angles ranged from virtually 0 to greater than 40 degrees as measured by phasing analysis and were oriented toward both the major and the minor grooves at the center of the AP-1 site. The DNA bends induced by the various heterodimeric complexes suggested that each component of the complex induced an independent DNA bend as previously shown for Fos and Jun. The Fos-related proteins Fra1 and Fra2 bent DNA in the same orientation as Fos but induced smaller DNA bend angles. ATF2 also bent DNA toward the minor groove in heterodimers formed with Fos, Fra2, and Jun. CREB and ATF1, which favor binding to the CRE site, did not induce significant DNA bending. Zta, which is a divergent member of the bZIP family, bent DNA toward the major groove. A variety of DNA structures can therefore be induced at the AP-1 site through combinatorial interactions between different bZIP family proteins. This diversity of DNA structures may contribute to regulatory specificity among the plethora of proteins that can bind to the AP-1 site.

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The Escherichia coli transcriptome mostly consists of independently regulated modules

Nature Communications ◽

10.1038/s41467-019-13483-w ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 29

Author(s):

Anand V. Sastry ◽

Ye Gao ◽

Richard Szubin ◽

Ying Hefner ◽

Sibei Xu ◽

...

Keyword(s):

Escherichia Coli ◽

Transcriptional Regulatory Network ◽

Transcriptional Regulators ◽

Specific Gene ◽

E Coli ◽

Gene Sets ◽

Transcriptional Regulatory ◽

Genetic Perturbations ◽

Function Discovery ◽

Multiple Strains

AbstractUnderlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome.

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Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators

Physiological Genomics ◽

10.1152/physiolgenomics.00055.2006 ◽

2006 ◽

Vol 28 (1) ◽

pp. 114-128 ◽

Cited By ~ 37

Author(s):

M. A. Keller ◽

S. Addya ◽

R. Vadigepalli ◽

B. Banini ◽

K. Delgrosso ◽

...

Keyword(s):

Network Analysis ◽

Blood Cell ◽

Regulatory Network ◽

Target Genes ◽

Transcriptional Regulatory Network ◽

Expression Patterns ◽

Transcriptional Regulators ◽

Erythroid Progenitors ◽

Hematopoietic Stem ◽

Transcriptional Regulatory

Deciphering the molecular basis for human erythropoiesis should yield information benefiting studies of the hemoglobinopathies and other erythroid disorders. We used an in vitro erythroid differentiation system to study the developing red blood cell transcriptome derived from adult CD34+ hematopoietic progenitor cells. mRNA expression profiling was used to characterize developing erythroid cells at six time points during differentiation ( days 1, 3, 5, 7, 9, and 11). Eleven thousand seven hundred sixty-three genes (20,963 Affymetrix probe sets) were expressed on day 1, and 1,504 genes, represented by 1,953 probe sets, were differentially expressed (DE) with 537 upregulated and 969 downregulated. A subset of the DE genes was validated using real-time RT-PCR. The DE probe sets were subjected to a cluster metric and could be divided into two, three, four, five, or six clusters of genes with different expression patterns in each cluster. Genes in these clusters were examined for shared transcription factor binding sites (TFBS) in their promoters by comparing enrichment of each TFBS relative to a reference set using transcriptional regulatory network analysis. The sets of TFBS enriched in genes up- and downregulated during erythropoiesis were distinct. This analysis identified transcriptional regulators critical to erythroid development, factors recently found to play a role, as well as a new list of potential candidates, including Evi-1, a potential silencer of genes upregulated during erythropoiesis. Thus this transcriptional regulatory network analysis has yielded a focused set of factors and their target genes whose role in differentiation of the hematopoietic stem cell into distinct blood cell lineages can be elucidated.

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Screening of Virulence-Related Transcriptional Regulators in Streptococcus suis

Genes ◽

10.3390/genes11090972 ◽

2020 ◽

Vol 11 (9) ◽

pp. 972

Author(s):

Liang Liu ◽

Qiang Zhang ◽

Zhongmin Xu ◽

Bo Chen ◽

Anding Zhang ◽

...

Keyword(s):

Virulence Factors ◽

Streptococcus Suis ◽

Transcriptional Regulators ◽

Rna Seq ◽

Related Factors ◽

Transcriptional Regulatory ◽

Mutant Strains ◽

Whole Transcriptome

Streptococcus suis (S.suis) is an important zoonotic pathogen that causes many severe diseases in pigs and humans. Virulence-related transcriptional regulators have been widely reported in pathogenic microorganisms, but only a few have been identified in S.suis. Our aim was to screen virulence-related transcriptional regulators in S.suis. A total of 89 such genes were predicted in the S.suis genome, of which 22 were up-regulated and 18 were down-regulated during S.suis infection in mice. To evaluate the roles of these differentially expressed factors in S.suis virulence, deletion mutants were constructed, and 10 mutants were successfully obtained. Among these genes, the deletion of comR, sitR, or sxvR caused significantly decreased virulence in mice, compared to that with the wild-type strain. Moreover, the survival of ΔcomR, ΔsitR, and ΔsxvR mutant strains in blood was significantly reduced both in vitro and in vivo. Furthermore, their pro-inflammatory abilities were also obviously decreased in vivo. The regulatory mechanisms of comR, sitR, and sxvR were then analyzed by whole transcriptome RNA sequencing (RNA-Seq). Results indicated that the absence of comR induced the down-regulation of 17 virulence factors or virulence-related factors, including genes involved in the synthesis of capsules, oxidative stress tolerance, immune evasion, and cell division. Furthermore, three and two virulence factors or virulence-related factors were down-regulated upon deletion of sitR and sxvR, respectively. Thus, this study reports the discovery of three virulence-associated transcriptional regulatory factors in S.suis. These factors could ultimately be targeted to control infection caused by these bacteria.

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The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Animals ◽

10.3390/ani10010034 ◽

2019 ◽

Vol 10 (1) ◽

pp. 34

Author(s):

Hu Chen ◽

Siqi Huang ◽

Ye Jiang ◽

Fuyao Han ◽

Qingyong Ni ◽

...

Keyword(s):

Gene Duplication ◽

Positive Selection ◽

Phylogenetic Relationships ◽

Molecular Mechanisms ◽

Coding Region ◽

Evolutionary Mechanisms ◽

Evolutionary Patterns ◽

Mhc Genes ◽

Mhc Class Ia ◽

Related Proteins

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

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Identification of an IRF10 gene in common carp (Cyprinus carpio L.) and analysis of its function in the antiviral and antibacterial immune response

BMC Veterinary Research ◽

10.1186/s12917-020-02674-z ◽

2020 ◽

Vol 16 (1) ◽

Author(s):

Yaoyao Zhu ◽

Shijuan Shan ◽

Huaping Zhao ◽

Rongrong Liu ◽

Hui Wang ◽

...

Keyword(s):

Common Carp ◽

Cyprinus Carpio ◽

Head Kidney ◽

Ctenopharyngodon Idella ◽

Poly I:C ◽

Type I ◽

Regulatory Factors ◽

Polyinosinic:Polycytidylic Acid ◽

Transcriptional Regulatory ◽

Localization Signal

Abstract Background Interferon (IFN) regulatory factors (IRFs), as transcriptional regulatory factors, play important roles in regulating the expression of type I IFN and IFN- stimulated genes (ISGs) in innate immune responses. In addition, they participate in cell growth and development and regulate oncogenesis. Results In the present study, the cDNA sequence of IRF10 in common carp (Cyprinus carpio L.) was characterized (abbreviation, CcIRF10). The predicted protein sequence of CcIRF10 shared 52.7–89.2% identity with other teleost IRF10s and contained a DNA-binding domain (DBD), a nuclear localization signal (NLS) and an IRF-associated domain (IAD). Phylogenetic analysis showed that CcIRF10 had the closest relationship with IRF10 of Ctenopharyngodon idella. CcIRF10 transcripts were detectable in all examined tissues, with the highest expression in the gonad and the lowest expression in the head kidney. CcIRF10 expression was upregulated in the spleen, head kidney, foregut and hindgut upon polyinosinic:polycytidylic acid (poly I:C) and Aeromonas hydrophila stimulation and induced by poly I:C, lipopolysaccharide (LPS) and peptidoglycan (PGN) in peripheral blood leucocytes (PBLs) and head kidney leukocytes (HKLs) of C. carpio. In addition, overexpression of CcIRF10 was able to decrease the expression of the IFN and IFN-stimulated genes PKR and ISG15. Conclusions These results indicate that CcIRF10 participates in antiviral and antibacterial immunity and negatively regulates the IFN response, which provides new insights into the IFN system of C. carpio.

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Altered gene expression of transcriptional regulatory factors in tumor marker-positive cells during chemically induced hepatocarcinogenesis

Toxicology Letters ◽

10.1016/j.toxlet.2006.08.014 ◽

2006 ◽

Vol 167 (2) ◽

pp. 106-113 ◽

Cited By ~ 13

Author(s):

Shigehiro Osada ◽

Ayako Naganawa ◽

Masashi Misonou ◽

Soken Tsuchiya ◽

Shigero Tamba ◽

...

Keyword(s):

Gene Expression ◽

Tumor Marker ◽

Regulatory Factors ◽

Altered Gene Expression ◽

Chemically Induced ◽

Transcriptional Regulatory ◽

Altered Gene

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Identification of an IRF10 gene in common carp (Cyprinus carpio L.) and analysis of its function in the antiviral and antibacterial immune response

10.21203/rs.3.rs-63536/v2 ◽

2020 ◽

Author(s):

Yaoyao Zhu ◽

Shijuan Shan ◽

Huaping Zhao ◽

Rongrong Liu ◽

Hui Wang ◽

...

Keyword(s):

Common Carp ◽

Cyprinus Carpio ◽

Head Kidney ◽

Ctenopharyngodon Idella ◽

Poly I:C ◽

Type I ◽

Regulatory Factors ◽

Common Carp Cyprinus Carpio ◽

Transcriptional Regulatory ◽

Carp Cyprinus Carpio

Abstract Background: Interferon (IFN) regulatory factors (IRFs), as transcriptional regulatory factors, play important roles in regulating the expression of type I IFN and IFN stimulated genes (ISGs) in innate immune responses. In addition, they participate in cell growth and development and regulate oncogenesis. Results: In the present study, the cDNA sequence of IRF10 in common carp (Cyprinus carpio L.) was characterized (abbreviation, CcIRF10). The predicted protein sequence of CcIRF10 shared 52.7-89.2% identity with other teleost IRF10s and contained a DNA-binding domain (DBD), a nuclear localization signal (NLS) and an IRF-associated domain (IAD). Phylogenetic analysis showed that CcIRF10 had the closest relationship with IRF10 of Ctenopharyngodon idella. CcIRF10 transcripts were detectable in all examined tissues, with the highest expression in the gonad and the lowest expression in the head kidney. CcIRF10 expression was upregulated in the spleen, head kidney, foregut and hindgut upon polyinosinic:polycytidylic acid (poly I:C) and Aeromonas hydrophila stimulation and induced by poly I:C, lipopolysaccharide (LPS) and peptidoglycan (PGN) in peripheral blood leucocytes (PBLs) and head kidney leukocytes (HKLs) of C. carpio. In addition, overexpression of CcIRF10 was able to decrease the expression of the IFN and IFN stimulated genes PKR and ISG15. Conclusions: These results indicate that CcIRF10 participates in antiviral and antibacterial immunity and negatively regulates the IFN response, which provides new insights into the IFN system of C. carpio.

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Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

10.1101/2021.07.28.454220 ◽

2021 ◽

Author(s):

Akanksha Rajput ◽

Hannah Tsunemoto ◽

Anand V Sastry ◽

Richard Szubin ◽

Kevin Rychel ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Transcriptional Regulatory Network ◽

Critical Role ◽

Gene Clusters ◽

Transcriptional Regulators ◽

Critical Conditions ◽

Future Research ◽

Secretion Systems ◽

Metabolism Regulation ◽

Transcriptional Regulatory

The transcriptional regulatory network (TRN) of Pseudomonas aeruginosa plays a critical role in coordinating numerous cellular processes. We extracted and quality controlled all publicly available RNA-sequencing datasets for P. aeruginosa to find 281 high-quality transcriptomes. We produced 83 new RNAseq data sets under critical conditions to generate a comprehensive compendium of 364 transcriptomes. We used this compendium to reconstruct the TRN of P. aeruginosa using independent component analysis (ICA). We identified 104 independently modulated sets of genes (called iModulons), among which 81 (78%) reflect the effects of known transcriptional regulators. We show that iModulons: 1) play an important role in defining the genomic boundaries of biosynthetic gene clusters (BGCs); 2) show increased expression of the BGCs and associated secretion systems in conditions that emulate cystic fibrosis (CF); 3) show the presence of a novel BGC named RiPP (bacteriocin producer) which might have a role in worsening CF outcomes; 4) exhibit the interplay of amino acid metabolism regulation and central metabolism across carbon sources, and 5) clustered according to their activity changes to define iron and sulfur stimulons. Finally, we compare the iModulons of P. aeruginosa with those of E. coli to observe conserved regulons across two gram negative species. This comprehensive TRN framework covers almost every aspect of the transcriptional regulatory machinery in P. aeruginosa, and thus could prove foundational for future research of its physiological functions.

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