RETRACTED: Role of the Sigma Factor in Transcription Initiation in the Absence of Core RNA Polymerase

Hsu, Hsin-Hsien; Chung, Kuei‐Min; Chen, Tsung-Ching; Chang, Ban‐Yang

doi:10.1016/j.cell.2006.08.042

Cited by 4 publications

(2 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The C2H2-type zinc finger proteins belong to the largest family of regulatory transcription factors, playing important roles in growth and development in animals and also in plant systems (Hsu et al 2006). Similarly, the HLH and homeobox families are widespread in the biosphere.…”

Section: Introductionmentioning

confidence: 99%

Bombyx moriTranscription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

Huang

Cheng

et al. 2012

Journal of Insect Science

View full text Add to dashboard Cite

Transcription factors are present in all living organisms, and play vital roles in a wide range of biological processes. Studies of transcription factors will help reveal the complex regulation mechanism of organisms. So far, hundreds of domains have been identified that show transcription factor activity. Here, 281 reported transcription factor domains were used as seeds to search the transcription factors in genomes of Bombyx mori L. (Lepidoptera: Bombycidae) and four other model insects. Overall, 666 transcription factors including 36 basal factors and 630 other factors were identified in B. mori genome, which accounted for 4.56% of its genome. The silkworm transcription factors' expression profiles were investigated in relation to multiple tissues, developmental stages, sexual dimorphism, and responses to oral infection by pathogens and direct bacterial injection. These all provided rich clues for revealing the transcriptional regulation mechanism of silkworm organ differentiation, growth and development, sexual dimorphism, and response to pathogen infection.

show abstract

Section: Introductionmentioning

confidence: 99%

Bombyx moriTranscription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

Huang

Cheng

et al. 2012

Journal of Insect Science

View full text Add to dashboard Cite

show abstract

“…Sigma factors are bacterial transcription factors that bind core RNAP and direct transcription initiation at a specific promoter site. 3 – 5 Recognition of a promoter sequence is directed by the σ-subunit of the RNAP holoenzyme. 6 …”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche

Nazir

Ibrahim

Zaman

et al. 2018

Evol Bioinform Online

View full text Add to dashboard Cite

Sigma factors are bacterial transcription factors that bind the core RNA polymerase and direct transcription initiation at a specific promoter site. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions and selectively increase the transcription of those genes. Here, we attempt to identify sigma factors in 5 genomes belonging to the Enterobacter cloacae complex (Ecc), a group of gram-negative bacteria that are important nosocomial pathogens. This process includes the identification of orthologous sequences, conserved motifs, domains, families, phylogenetic profiles, and protein-protein associations of these components. Based on the reference genome, genome-wide comparison revealed that the genomes of Enterobacter asburiae JCM6051, Enterobacter nimipressuralis CIP 104980, Enterobacter hormaechei ATCC49162, Enterobacter kobei JCM 8580, and Enterobacter ludwigii EN-119 encode 10 sigma factors that exist in the reference strain Enterobacter cloacae subsp cloacae ATCC13047. Moreover, the sequence similarity, protein domains and families of the sigma factors, protein-protein association, and phylogenetic profile indicate that the sigma factor proteins of these 5 strains may have evolutionary relatedness and functional characteristics important to their various environmental niches. Interestingly, the absence of RpoS in E kobei, which contributes to bacterial survival under environmental stress conditions, indicates that RpoS might have been independently acquired and may play different roles relating to pathogenicity, host range determination, and/or niche adaptation. Future work such as RNA sequencing will be directed towards investigating the roles that these sigma factors play in the biology of the Ecc.

show abstract

Genome-wide investigation of transcription factors provides insights into transcriptional regulation in Plutella xylostella

Zhao

Huang

et al. 2017

Mol Genet Genomics

View full text Add to dashboard Cite

Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P. xylostella or Lepidoptera. RNA-seq analysis showed that some of the TF families, such as zinc fingers, homeobox, bZIP, bHLH, and MADF_DNA_bdg genes, were highly expressed in certain tissues including midgut, salivary glands, fat body, and hemocytes, with an obvious sex-biased expression pattern. In addition, a number of TFs showed significant differences in expression between insecticide susceptible and resistant strains, suggesting that these TFs play a role in regulating genes related to insecticide resistance. Finally, we identified an expansion of the HOX cluster in Lepidoptera, which might be related to Lepidoptera-specific evolution. Knockout of this cluster using CRISPR/Cas9 showed that the egg cannot hatch, indicating that this cluster may be related to egg development and maturation. This is the first comprehensive study on identifying and characterizing TFs in P. xylostella. Our results suggest that some TF families are expanded in the P. xylostella genome, and these TFs may have important biological roles in growth, development, sexual dimorphism, and resistance to insecticides. The present work provides a solid foundation for understanding regulation via TFs in P. xylostella and insights into the evolution of the P. xylostella genome.

show abstract

RETRACTED: Role of the Sigma Factor in Transcription Initiation in the Absence of Core RNA Polymerase

Cited by 4 publications

References 41 publications

Bombyx moriTranscription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

Bombyx moriTranscription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche

Genome-wide investigation of transcription factors provides insights into transcriptional regulation in Plutella xylostella

Contact Info

Product

Resources

About