scholarly journals Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation

Author(s):  
David M. Wood ◽  
Renwick C.J. Dobson ◽  
Christopher R. Horne

Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the ‘resolution revolution’ of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.

2018 ◽  
Vol 72 (1) ◽  
pp. 231-254 ◽  
Author(s):  
Chiara Rapisarda ◽  
Matteo Tassinari ◽  
Francesca Gubellini ◽  
Rémi Fronzes

Bacterial secretion systems are responsible for releasing macromolecules to the extracellular milieu or directly into other cells. These membrane complexes are associated with pathogenicity and bacterial fitness. Understanding of these large assemblies has exponentially increased in the last few years thanks to electron microscopy. In fact, a revolution in this field has led to breakthroughs in characterizing the structures of secretion systems and other macromolecular machineries so as to obtain high-resolution images of complexes that could not be crystallized. In this review, we give a brief overview of structural advancements in the understanding of secretion systems, focusing in particular on cryo–electron microscopy, whether tomography or single-particle analysis. We describe how such techniques have contributed to knowledge of the mechanism of macromolecule secretion in bacteria and the impact they will have in the future.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. SCI-30-SCI-30
Author(s):  
Jay L. Hess ◽  
Cailin Collins ◽  
Joel Bronstein ◽  
Yuqing Sun ◽  
Surya Nagaraja

Abstract Abstract SCI-30 HOXA9 plays important roles in both development and hematopoiesis and is overexpressed in more than 50 percent of acute myeloid leukemias (AML). Nearly all cases of AML with mixed lineage leukemia (MLL) translocations show increased HOXA9 expression, as well as cases with mutation of the nucleophosmin gene NPM1, overexpression of CDX2, and fusions of NUP98. In most cases, upregulation of HOXA9 is accompanied by upregulation of its homeodomain-containing cofactor MEIS1, which directly interacts with HOXA9. While HOXA9 alone is sufficient for transformation of hematopoietic stem cells in culture, the addition of MEIS1 increases the transformation efficiency and results in rapidly fatal leukemias in transplanted animals. Despite the crucial role that HOXA9 plays in development, hematopoiesis, and leukemia, its transcriptional targets and mechanisms of action are poorly understood. We have used ChIP-seq to identify Hoxa9 and Meis1 binding sites on a genome-wide level in myeloblastic cells, profiled their associated epigenetic modifications, identified the target genes regulated by HOXA9 and identified HOXA9 interacting proteins. HOXA9 and MEIS1 cobind at hundreds of promoter distal, highly evolutionarily conserved sites showing high levels of histone H3K4 monomethylation and CBP/P300 binding. These include many proleukemogenic gene loci, such as Erg, Flt3, Myb, Lmo2, and Sox4. In addition, HOXA9 binding sites overlap a subset of enhancers previously implicated in myeloid differentiation and inflammation. HOXA9 binding at enhancers stabilizes association of MEIS1 and lineage-restricted transcription factors, including C/EBPα, PU.1, and STAT5A/B thereby promoting CBP/p300 recruitment, histone acetylation, and transcriptional activation. Current efforts are focused on using both biochemical and genetic approaches to assess the role of HOXA9 “enhanceosome” components C/EBPα, PU.1, and STAT5A/B in transcriptional regulation and leukemogenesis. Studies to date suggest that C/EBPα and PU.1 binding can occur in the absence of HOXA9/MEIS1, supporting a model in which these proteins act as pioneer transcription factors for establishment of poised, but not activated, HOXA9-regulated enhancers. Work is under way to assess the impact of high-level HOXA9 and MEIS1 on enhanceosome assembly and the role of recruitment of transcriptional coactivators involved in target gene up- or downregulation, including histone acetyltransferases and chromatin remodeling complexes. Collectively, our findings suggest that HOXA9-regulated enhancers are a fundamental mechanism of HOX-mediated transcription in normal development that is deregulated in leukemia. Disclosures: No relevant conflicts of interest to declare.


Author(s):  
Ricardo D. Righetto ◽  
Leonie Anton ◽  
Ricardo Adaixo ◽  
Roman P. Jakob ◽  
Jasenko Zivanov ◽  
...  

AbstractUrease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at better than 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. Our data are of sufficient quality to support drug development efforts.


2003 ◽  
Vol 30 (9) ◽  
pp. 913 ◽  
Author(s):  
Kevin M. Davies ◽  
Kathy E. Schwinn

Plants produce secondary metabolites during development and in response to environmental stimuli such as light or pathogen attack. Transcriptional regulation provides the most important control point for the secondary metabolic pathways studied to date. In this article we review the data on the transcription factors that modulate this regulation. For the phenylpropanoid pathway, much is understood about both the specific sequences in the target genes (cis-elements) that are involved in responses to environmental and developmental stimuli, and the transcription factors involved. Most information is available for the light induction of the genes for hydroxycinnamic acid production, the production of anthocyanins in leaves and floral tissues, and the production of proanthocyanidins in seeds. Some of the functional interactions between the different types of transcription factor are now being elucidated, and upstream regulators of the genes encoding the transcription factors identified. For other secondary metabolic pathways much less is known, although good progress has been made on identifying transcription factors involved in controlling terpenoid indole alkaloid production. The identification of defined transcription factor genes provides tools for modulating both the amount and distribution of secondary metabolites in plants, and the validity of this approach has been well established by transgenic plants with modified flavonoid accumulation patterns.


2015 ◽  
Vol 112 (7) ◽  
pp. E677-E686 ◽  
Author(s):  
Rodrigo Peña-Hernández ◽  
Maud Marques ◽  
Khalid Hilmi ◽  
Teijun Zhao ◽  
Amine Saad ◽  
...  

CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ricardo D. Righetto ◽  
Leonie Anton ◽  
Ricardo Adaixo ◽  
Roman P. Jakob ◽  
Jasenko Zivanov ◽  
...  

AbstractUrease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy. Y. enterocolitica urease is a dodecameric assembly of a trimer of three protein chains, ureA, ureB and ureC. The high data quality enables detailed visualization of the urease bimetal active site and of the impact of radiation damage. The obtained structure is of sufficient quality to support drug development efforts.


Author(s):  
Jean Lepault ◽  
Hervé Delacroix ◽  
Inge Erk ◽  
Gisèle Nicolas ◽  
Jean-Luc Ranck

Cryo-electron microscopy of vitrified specimens is used to study biological objects in their native aqueous environment. Preparation artifacts are therefore minimized. In addition, due to the fast cryo-fixation associated with the vitrification process, cryo-electron microscopy may be used for dynamic structural investigations. To take full advantage of these possibilities, we are studying isolated muscular componants: actin and myosin.We observed the polymerization process of actin filaments. When the ionic strength of a globular actin suspension (G-actin-ATP) is increased, actin polymerized and filamentous actin (F-actin) is formed. During the polymerization, ATP is hydrolyzed. Three chemical forms of F-actin are then successively formed: F-actin-ATP, F-actin-ADP-Pi and F-actin-ADP. F-actin visualized in the short time of the polymerization process (F-actin-ATP; F-actin-ADP-Pi is characterized by a disordered polymer. At steady state (F-actin-ADP), F-actin appears more ordered and has its well known appearence of a helical polymer. These results show that actin has different structures which may play a role in muscular contraction.


iScience ◽  
2020 ◽  
Vol 23 (4) ◽  
pp. 101029
Author(s):  
Pablo Yubero ◽  
Juan F. Poyatos

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