Role of multiprotein bridging factor 1 in archaea: bridging the domains?

2009 ◽  
Vol 37 (1) ◽  
pp. 52-57 ◽  
Author(s):  
Bart de Koning ◽  
Fabian Blombach ◽  
Hao Wu ◽  
Stan J.J. Brouns ◽  
John van der Oost
Keyword(s):  
Yeast Genome ◽  
Terminal Part ◽  
Context Analysis ◽  
Eukaryotic Transcription ◽  
Translation Fidelity ◽  
Genome Context Analysis ◽  
Tata Box Binding Protein ◽  
Genome Context ◽  
Regulatory Dna

MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge between distinct regulatory DNA-binding proteins and the TATA-box-binding protein. MBF1 consists of two parts: a C-terminal part that contains a highly conserved helix–turn–helix, and an N-terminal part that shows a clear divergence: in eukaryotes, it is a weakly conserved flexible domain, whereas, in archaea, it is a conserved zinc-ribbon domain. Although its function in archaea remains elusive, its function as a transcriptional co-activator has been deduced from thorough studies of several eukaryotic proteins, often indicating a role in stress response. In addition, MBF1 was found to influence translation fidelity in yeast. Genome context analysis of mbf1 in archaea revealed conserved clustering in the crenarchaeal branch together with genes generally involved in gene expression. It points to a role of MBF1 in transcription and/or translation. Experimental data are required to allow comparison of the archaeal MBF1 with its eukaryotic counterpart.

Genome-wide Analysis of the Distribution of Riboswitches and Function Analyses of the Corresponding Downstream Genes in Prokaryotes

2018 ◽  
Vol 14 (1) ◽  
pp. 53-61
Author(s):  
Xinfeng Li ◽  
Fang Chen ◽  
Jinfeng Xiao ◽  
Shan-Ho Chou ◽  
Xuming Li ◽  
...  
Keyword(s):  
Functional Categories ◽  
Gene Expressions ◽  
Context Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Genome Context Analysis ◽  
Genome Context ◽  
And Function

Background: Riboswitches are structured elements that usually reside in the noncoding regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene expressions. To date, more than twenty different classes of riboswitches have been characterized to sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal ions, etc. </P><P> Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and function analyses of the corresponding downstream genes in prokaryotes. Results: In this study, we have completed a genome context analysis of 27 riboswitches to elucidate their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079 prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was applied to predict and classify the possible functions of corresponding downstream genes of these riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG functional categories, in which the two main clusters &quot;coenzyme metabolism [H]&quot; and &quot;amino acid transport and metabolism [E]&quot; were the most significantly enriched. Conclusion: Riboswitches are found to be widespread in bacteria, among which three main classes of TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of functions were associated with the corresponding downstream genes, suggesting that a wide extend of regulatory roles were mediated by these riboswitches in prokaryotes.

scholarly journals Transcription Factor E Is a Part of Transcription Elongation Complexes

2007 ◽  
Vol 282 (49) ◽  
pp. 35482-35490 ◽  
Author(s):  
Sebastian Grünberg ◽  
Michael S. Bartlett ◽  
Souad Naji ◽  
Michael Thomm
Keyword(s):  
Transcription Factor ◽  
Terminal Part ◽  
Eukaryotic Transcription ◽  
Α Subunit ◽  
Winged Helix ◽  
Transcription Bubble ◽  
Template Strand ◽  
Transcription Complexes ◽  
Dna Strand

A homologue of the N-terminal domain of the α subunit of the general eukaryotic transcription factor TFE is encoded in the genomes of all sequenced archaea, but the position of archaeal TFE in transcription complexes has not yet been defined. We show here that TFE binds nonspecifically to single-stranded DNA, and photochemical cross-linking revealed TFE binding to a preformed open transcription bubble. In preinitiation complexes, the N-terminal part of TFE containing a winged helix-turn-helix motif is cross-linked specifically to DNA of the nontemplate DNA strand at positions –9 and –11. In complexes stalled at +20, TFE cross-linked specifically to positions +9, +11, and +16 of the non-template strand. Analyses of transcription complexes stalled at position +20 revealed a TFE-dependent increase of the resumption efficiency of stalled RNA polymerase and a TFE-induced enhanced permanganate sensitivity of thymine residues in the transcription bubble. These results demonstrate the presence of TFE in early elongation complexes and suggest a role of TFE in stabilization of the transcription bubble during elongation.

scholarly journals The Salmonella enterica serovar Typhimurium virulence factor STM3169 is a hexuronic acid binding protein component of a TRAP transporter

Microbiology ◽  
2020 ◽  
Vol 166 (10) ◽  
pp. 981-987 ◽  
Author(s):  
Reyme Herman ◽  
Cavan Bennett-Ness ◽  
Abbas Maqbool ◽  
Amna Afzal ◽  
Andrew Leech ◽  
...  
Keyword(s):  
Carbon Source ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Binding Protein ◽  
Context Analysis ◽  
Gene Coding ◽  
Serovar Typhimurium ◽  
Genes Encoding ◽  
Genome Context Analysis ◽  
Genome Context ◽  
Substrate Binding Protein

The intracellular pathogen S. Typhimurium is a leading cause of foodborne illness across the world and is known to rely on a range of virulence factors to colonize the human host and cause disease. The gene coding for one such factor, stm3169, was determined to be upregulated upon macrophage entry and its disruption reduces survival in the macrophage. In this study we characterize the STM3169 protein, which forms the substrate binding protein (SBP) of an uncharacterized tripartite ATP-independent periplasmic (TRAP) transporter. Genome context analysis of the genes encoding this system in related bacteria suggests a function in sugar acid transport. We demonstrate that purified STM3169 binds d-glucuronic acid with high affinity and specificity. S. Typhimurium LT2 can use this sugar acid as a sole carbon source and the genes for a probable catabolic pathway are present in the genome. As this gene was previously implicated in macrophage survival, it suggests a role for d-glucuronate as an important carbon source for S. Typhimurium in this environment.

scholarly journals Comprehensive analysis of protein acetyltransferases of human pathogen Mycobacterium tuberculosis

2019 ◽  
Vol 39 (12) ◽  
Author(s):  
Longxiang Xie ◽  
Wenmin Yang ◽  
Xiangyu Fan ◽  
Jianping Xie
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Comprehensive Analysis ◽  
Therapeutic Interventions ◽  
Lysine Acetylation ◽  
Human Pathogen ◽  
Tuberculosis Control ◽  
Context Analysis ◽  
H37rv Strain ◽  
Genome Context Analysis ◽  
Genome Context

Abstract Tuberculosis (TB), a leading infectious disease caused by Mycobacterium tuberculosis strain, takes four human lives every minute globally. Paucity of knowledge on M. tuberculosis virulence and antibiotic resistance is the major challenge for tuberculosis control. We have identified 47 acetyltransferases in the M. tuberculosis, which use diverse substrates including antibiotic, amino acids, and other chemical molecules. Through comparative analysis of the protein file of the virulent M. tuberculosis H37Rv strain and the avirulent M. tuberculosis H37Ra strain, we identified one acetyltransferase that shows significant variations with N-terminal deletion, possibly influencing its physicochemical properties. We also found that one acetyltransferase has three types of post-translation modifications (lysine acetylation, succinylation, and glutarylation). The genome context analysis showed that many acetyltransferases with their neighboring genes belong to one operon. By data mining from published transcriptional profiles of M. tuberculosis exposed to diverse treatments, we revealed that several acetyltransferases may be functional during M. tuberculosis infection. Insights obtained from the present study can potentially provide clues for developing novel TB therapeutic interventions.

scholarly journals Investigating the role of noncoding regulatory DNA in plasmid development for Yarrowia lipolytica

2020 ◽  
Author(s):  
Carmen Lopez ◽  
Mingfeng Cao ◽  
Zhanyi Yao ◽  
Zengyi Shao
Keyword(s):  
Yarrowia Lipolytica ◽  
Plasmid Stability ◽  
Critical Role ◽  
Fold Increase ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Expression Platform ◽  
Regulatory Dna ◽  
Selection Of

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 4.5-fold increase in gene expression and higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

scholarly journals Identification of C-terminal motifs responsible for transmission of inhibition by ATP of mammalian phosphofructokinase, and their contribution to other allosteric effects

2004 ◽  
Vol 377 (1) ◽  
pp. 77-84 ◽  
Author(s):  
Oscar H. MARTÍNEZ-COSTA ◽  
Carmen HERMIDA ◽  
Cristina SÁNCHEZ-MARTÍNEZ ◽  
Belén SANTAMARÍA ◽  
Juan J. ARAGÓN
Keyword(s):  
Point Mutations ◽  
Terminal Part ◽  
Protein Fluorescence ◽  
Binding Studies ◽  
C Terminus ◽  
Allosteric Effectors ◽  
Inhibitory Site ◽  
Intrinsic Protein Fluorescence ◽  
Strong Activator

Systematic deletions and point mutations in the C-terminal extension of mammalian PFK (phosphofructokinase) led us to identify Leu-767 and Glu-768 of the M-type isoform (PFK-M) as the motifs responsible for the role of this region in inhibition by MgATP. These amino acids are the only residues of the C-terminus that are conserved in all mammalian isoforms, and were found to have a similar function in the C-type isoenzyme. Both residues in PFK-C and Leu-767 in PFK-M were also observed to be critical for inhibition by citrate, which is synergistic with that by MgATP. Binding studies utilizing titration of intrinsic protein fluorescence indicated that the C-terminal part of the enzyme participates in the signal transduction route from the MgATP inhibitory site to the catalytic site, but does not contribute to the binding of this inhibitor, whereas it is essential for the binding of citrate. Mutations of the identified structural motifs did not alter either the action of other allosteric effectors that also interact with MgATP, such as the inhibitor phosphoenolpyruvate and the strong activator fructose 2,6-bisphosphate, or the co-operative effect of fructose 6-phosphate. The latter data provide evidence that activation by fructose 2,6-bisphosphate and fructose 6-phosphate co-operativity are not linked to the same allosteric transition as that mediating inhibition by MgATP.

scholarly journals Overexpression of peroxisomal testis-specific 1 protein induces germ cell apoptosis and leads to infertility in male mice

2011 ◽  
Vol 22 (10) ◽  
pp. 1766-1779 ◽  
Author(s):  
Karina Kaczmarek ◽  
Maja Studencka ◽  
Andreas Meinhardt ◽  
Krzysztof Wieczerzak ◽  
Sven Thoms ◽  
...  
Keyword(s):  
Cell Death ◽  
Germ Cell ◽  
Germ Cells ◽  
Specific Gene ◽  
Male Mice ◽  
Terminal Part ◽  
Male Germ Cells ◽  
Germ Cell Apoptosis ◽  
Induced Apoptosis

 Peroxisomal testis-specific 1 gene (Pxt1) is the only male germ cell–specific gene that encodes a peroxisomal protein known to date. To elucidate the role of Pxt1 in spermatogenesis, we generated transgenic mice expressing a c-MYC-PXT1 fusion protein under the control of the PGK2 promoter. Overexpression of Pxt1 resulted in induction of male germ cells’ apoptosis mainly in primary spermatocytes, finally leading to male infertility. This prompted us to analyze the proapoptotic character of mouse PXT1, which harbors a BH3-like domain in the N-terminal part. In different cell lines, the overexpression of PXT1 also resulted in a dramatic increase of apoptosis, whereas the deletion of the BH3-like domain significantly reduced cell death events, thereby confirming that the domain is functional and essential for the proapoptotic activity of PXT1. Moreover, we demonstrated that PXT1 interacts with apoptosis regulator BAT3, which, if overexpressed, can protect cells from the PXT1-induced apoptosis. The PXT1-BAT3 association leads to PXT1 relocation from the cytoplasm to the nucleus. In summary, we demonstrated that PXT1 induces apoptosis via the BH3-like domain and that this process is inhibited by BAT3.

scholarly journals Leading role of TBP in the Establishment of Complexity in Eukaryotic Transcription Initiation Systems

Cell Reports ◽  
2017 ◽  
Vol 21 (13) ◽  
pp. 3941-3956 ◽  
Author(s):  
Eiryo Kawakami ◽  
Naruhiko Adachi ◽  
Toshiya Senda ◽  
Masami Horikoshi
Keyword(s):  
Transcription Initiation ◽  
Eukaryotic Transcription ◽  
Leading Role

scholarly journals Expression and nuclear localization of the TATA-box-binding protein during baculovirus infection

2014 ◽  
Vol 95 (6) ◽  
pp. 1396-1407 ◽  
Author(s):  
Daniela Mainz ◽  
Ilja Quadt ◽  
Andrea K. Stranzenbach ◽  
Daniel Voss ◽  
Linda A. Guarino ◽  
...  
Keyword(s):  
Binding Protein ◽  
Degradation Pathway ◽  
Tata Box ◽  
Viral Dna ◽  
Eukaryotic Transcription ◽  
Protein Levels ◽  
Baculovirus Infection ◽  
Rnap Ii ◽  
Tata Box Binding Protein ◽  
Nuclear Domains

The TATA-box-binding protein (TBP) plays a key role in initiating eukaryotic transcription and is used by many viruses for viral transcription. We previously reported increased TBP levels during infection with the baculovirus Autographa californica multicapsid nuclear polyhedrovirus (AcMNPV). The TBP antiserum used in that study, however, cross-reacted with a baculoviral protein. Here, we reported that increased amounts of nuclear TBP were detected upon infection of Spodoptera frugiperda and TN-368 cells with a TBP-specific antiserum. TBP levels increased until 72 h post-infection (p.i.), whilst tbp transcripts decreased by 16 h p.i., which suggested a virus-induced influence on the TBP protein levels. To address a potential modification of the TBP degradation pathway during infection, we investigated the possible role of viral ubiquitin. Infection studies with AcMNPV recombinants carrying a mutated viral ubiquitin gene revealed that the TBP increase during infection was not altered. In addition, pulse–chase experiments indicated a high TBP half-life of ~60 h in uninfected cells, suggesting that a virus-induced increase of TBP stability was unlikely. This increase in TBP correlated with a redistribution to nuclear domains resembling sites of viral DNA synthesis. Furthermore, we observed colocalization of TBP with host RNA polymerase (RNAP) II, but only until 8 h p.i., whilst TBP, but not RNAPII, was present in the enlarged replication domains late during infection. Thus, we suggested that AcMNPV adapted a mechanism to accumulate the highly stable cellular TBP at sites of viral DNA replication and transcription.

Sign in / Sign up

Export Citation Format

Share Document