scholarly journals Dynamic landscape of protein occupancy across the Escherichia coli chromosome

PLoS Biology ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. e3001306
Author(s):  
Peter L. Freddolino ◽  
Haley M. Amemiya ◽  
Thomas J. Goss ◽  
Saeed Tavazoie
Keyword(s):  
Escherichia Coli ◽  
Genetic Manipulation ◽  
Dynamic Condition ◽  
Bacterial Genome ◽  
Structural Features ◽  
Sequence Specificity ◽  
Bacterial Physiology ◽  
Transcriptional Regulatory ◽  
Protein Occupancy

Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein–DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (in vivo protein occupancy display—high resolution, IPOD-HR) and present a pilot application to Escherichia coli. We observe that the E. coli protein–DNA interactome organizes into 2 distinct prototypic features: (1) highly dynamic condition-dependent transcription factor (TF) occupancy; and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence specificity models for the majority of active TFs. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria that are not amenable to routine genetic manipulation.

scholarly journals Dynamic landscape of protein occupancy across the Escherichia coli chromosome

2020 ◽  
Author(s):  
Peter L. Freddolino ◽  
Thomas J. Goss ◽  
Haley M. Amemiya ◽  
Saeed Tavazoie
Keyword(s):  
Genetic Manipulation ◽  
Dynamic Condition ◽  
Bacterial Genome ◽  
Structural Features ◽  
Sequence Specificity ◽  
Bacterial Physiology ◽  
E Coli ◽  
Transcriptional Regulatory ◽  
Protein Occupancy

AbstractFree living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using a modification of in vivo protein occupancy display technology (IPOD-HR) applied to E. coli. We observe that the E. coli protein-DNA interactome organizes into two distinct prototypic features: (1) highly dynamic condition-dependent transcription factor occupancy by dedicated transcriptional regulators, and (2) condition-invariant kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence-specificity models for the majority of active transcription factors. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria which are not amenable to routine genetic manipulation.

scholarly journals Targeted Transposition by the V(D)J Recombinase

2002 ◽  
Vol 22 (7) ◽  
pp. 2068-2077 ◽  
Author(s):  
Gregory S. Lee ◽  
Matthew B. Neiditch ◽  
Richard R. Sinden ◽  
David B. Roth
Keyword(s):  
Signal Sequence ◽  
Target Selection ◽  
Structural Features ◽  
Sequence Specificity ◽  
Recombination Signal ◽  
Chromosome Translocations ◽  
Hybrid Joints ◽  
Sequence Elements ◽  
Rag Proteins

ABSTRACT Cleavage by the V(D)J recombinase at a pair of recombination signal sequences creates two coding ends and two signal ends. The RAG proteins can integrate these signal ends, without sequence specificity, into an unrelated target DNA molecule. Here we demonstrate that such transposition events are greatly stimulated by—and specifically targeted to—hairpins and other distorted DNA structures. The mechanism of target selection by the RAG proteins thus appears to involve recognition of distorted DNA. These data also suggest a novel mechanism for the formation of alternative recombination products termed hybrid joints, in which a signal end is joined to a hairpin coding end. We suggest that hybrid joints may arise by transposition in vivo and propose a new model to account for some recurrent chromosome translocations found in human lymphomas. According to this model, transposition can join antigen receptor loci to partner sites that lack recombination signal sequence elements but bear particular structural features. The RAG proteins are capable of mediating all necessary breakage and joining events on both partner chromosomes; thus, the V(D)J recombinase may be far more culpable for oncogenic translocations than has been suspected.

scholarly journals Separate physiological roles of specific and non-specific DNA binding of HU protein in Escherichia coli

2021 ◽  
Author(s):  
Sankar Adhya ◽  
Subhash Verma
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Protein Interactions ◽  
Specific Binding ◽  
Bacterial Genome ◽  
Dna Structure ◽  
Binding Modes ◽  
Chromosomal Dna

Conserved in bacteria, the histone-like protein HU is crucial for genome organization and expression of many genes. It binds DNA regardless of the sequence and exhibits two binding affinities in vitro, low-affinity to any B-DNA (non-specific) and high-affinity to DNA with distortions like kinks and cruciforms (structure-specific), but the physiological relevance of the two binding modes needed further investigation. We validated and defined the three conserved lysine residues, K3, K18, and K83, in Escherichia coli HU as critical amino acid residues for both non-specific and structure-specific binding and the conserved proline residue P63 additionally for only the structure-specific binding. By mutating these residues in vivo, we showed that two DNA binding modes of HU play separate physiological roles. The DNA structure-specific binding, occurring at specific sites in the E. coli genome, promotes higher-order DNA structure formation, regulating the expression of many genes, including those involved in chromosome maintenance and segregation. The non-specific binding participates in numerous associations of HU with the chromosomal DNA, dictating chromosome structure and organization. Our findings underscore the importance of DNA structure in transcription regulation and promiscuous DNA-protein interactions in a dynamic organization of a bacterial genome.

scholarly journals Comparison of Escherichia coli surface attachment methods for single-cell microscopy

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yao-Kuan Wang ◽  
Ekaterina Krasnopeeva ◽  
Ssu-Yuan Lin ◽  
Fan Bai ◽  
Teuta Pilizota ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Cell ◽  
Super Resolution ◽  
Bacterial Cells ◽  
Surface Attachment ◽  
Bacterial Physiology ◽  
E Coli ◽  
Single Cell Imaging ◽  
Atomic Force

AbstractFor in vivo, single-cell imaging bacterial cells are commonly immobilised via physical confinement or surface attachment. Different surface attachment methods have been used both for atomic force and optical microscopy (including super resolution), and some have been reported to affect bacterial physiology. However, a systematic comparison of the effects these attachment methods have on the bacterial physiology is lacking. Here we present such a comparison for bacterium Escherichia coli, and assess the growth rate, size and intracellular pH of cells growing attached to different, commonly used, surfaces. We demonstrate that E. coli grow at the same rate, length and internal pH on all the tested surfaces when in the same growth medium. The result suggests that tested attachment methods can be used interchangeably when studying E. coli physiology.

scholarly journals BldD-based bimolecular fluorescence complementation for in vivo detection of the second messenger cyclic di-GMP

2021 ◽  
Author(s):  
Manuel Halte ◽  
Mirka E. Wörmann ◽  
Maxim Bogisch ◽  
Marc Erhardt ◽  
Natalia Tschowri
Keyword(s):  
Escherichia Coli ◽  
Single Cell ◽  
Salmonella Enterica ◽  
Second Messenger ◽  
Bimolecular Fluorescence Complementation ◽  
Bacterial Physiology ◽  
Serovar Typhimurium ◽  
Fluorescence Complementation ◽  
Bimolecular Fluorescence

AbstractThe widespread bacterial second messenger bis-(3’-5’)-cyclic diguanosine monophosphate (c-di-GMP) is an important regulator of biofilm formation, virulence and cell differentiation. C-di-GMP-specific biosensors that allow detection and visualization of c-di-GMP levels in living cells are key to our understanding of how c-di-GMP fluctuations drive cellular responses. Here, we describe a novel c-di-GMP biosensor, CensYBL, that is based on c-di-GMP-induced dimerization of the effector protein BldD from Streptomyces resulting in bimolecular fluorescence complementation of split-YPet fusion proteins. As a proof-of-principle, we demonstrate that CensYBL is functional in detecting fluctuations in intracellular c-di-GMP levels in the Gram-negative model bacteria Escherichia coli and Salmonella enterica serovar Typhimurium. Using deletion mutants of c-di-GMP diguanylate cyclases and phosphodiesterases, we show that c-di-GMP dependent dimerization of CBldD-YPet results in fluorescence complementation reflecting intracellular c-di-GMP levels. Overall, we demonstrate that the CensYBL biosensor is a user-friendly and versatile tool that allows to investigate c-di-GMP variations using single-cell and population-wide experimental set-ups.ImportanceThe second messenger c-di-GMP controls various bacterial functions including development of resistant biofilm communities and transition into dormant spores. In vivo detection of c-di-GMP levels is therefore crucial for a better understanding of how intracellular c-di-GMP levels induce changes of bacterial physiology. Here, we describe the design of a novel c-di-GMP biosensor and demonstrate its effective application in investigating fluctuations in intracellular c-di-GMP levels in Escherichia coli and Salmonella enterica serovar Typhimurium on a population-based and single-cell level.

scholarly journals The yefM-yoeB Toxin-Antitoxin Systems of Escherichia coli and Streptococcus pneumoniae: Functional and Structural Correlation

2006 ◽  
Vol 189 (4) ◽  
pp. 1266-1278 ◽  
Author(s):  
Concha Nieto ◽  
Izhack Cherny ◽  
Seok Kooi Khoo ◽  
Mario García de Lacoba ◽  
Wai Ting Chan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Streptococcus Pneumoniae ◽  
Structural Features ◽  
E Coli ◽  
Modeled Structure ◽  
The Family ◽  
Bona Fide ◽  
K 12

ABSTRACT Toxin-antitoxin loci belonging to the yefM-yoeB family are located in the chromosome or in some plasmids of several bacteria. We cloned the yefM-yoeB locus of Streptococcus pneumoniae, and these genes encode bona fide antitoxin (YefM Spn ) and toxin (YoeB Spn ) products. We showed that overproduction of YoeB Spn is toxic to Escherichia coli cells, leading to severe inhibition of cell growth and to a reduction in cell viability; this toxicity was more pronounced in an E. coli B strain than in two E. coli K-12 strains. The YoeB Spn -mediated toxicity could be reversed by the cognate antitoxin, YefM Spn , but not by overproduction of the E. coli YefM antitoxin. The pneumococcal proteins were purified and were shown to interact with each other both in vitro and in vivo. Far-UV circular dichroism analyses indicated that the pneumococcal antitoxin was partially, but not totally, unfolded and was different than its E. coli counterpart. Molecular modeling showed that the toxins belonging to the family were homologous, whereas the antitoxins appeared to be specifically designed for each bacterial locus; thus, the toxin-antitoxin interactions were adapted to the different bacterial environmental conditions. Both structural features, folding and the molecular modeled structure, could explain the lack of cross-complementation between the pneumococcal and E. coli antitoxins.

Streptonigrin toxicity in Escherichia coli: oxygen dependence and the role of the intracellular oxidation–reduction state

1982 ◽  
Vol 28 (5) ◽  
pp. 545-552 ◽  
Author(s):  
John B. Harley ◽  
Caroline J. Fetterolf ◽  
Cesar A. Bello ◽  
Joel G. Flaks
Keyword(s):  
Escherichia Coli ◽  
Superoxide Dismutase ◽  
Superoxide Dismutase Activity ◽  
Lethal Concentration ◽  
Bacterial Physiology ◽  
E Coli ◽  
Escherichia Coli K12 ◽  
Oxidation Reduction

The bacterial physiology of streptonigrin toxicity was further investigated. An optimal oxygen concentration for toxicity was inferred from data showing that steptonigrin at 5 µg/mL was rapidly lethal to aerobic cultures of Escherichia coli K12 JF361, but was without effect on anaerobic cultures and was bacteriostatic to cultures incubated in 5 atm of oxygen plus 1 atm of air (5 atm O2 plus air) (1 atm = 101.325 kPa). Escherichia coli were protected from a potentially lethal concentration of streptonigrin during anaerobic incubation, whether previously grown anaerobically, aerobically, or in 5 atm O2 plus air. Superoxide dismutase activity increased with increasing oxygen tension in the medium, but was not significantly changed by a lethal concentration of streptonigrin. Although the superoxide dismutase activity was four times greater in E. coli grown in 5 atm O2 plus air than those grown in air alone, the aerobic survival in 5 µg/mL streptonigrin was identical, which suggested that superoxide dismutase was not rate limiting for toxicity. Escherichia coli K12 strains deficient in glutathione (KMBL54-129, AB1157-821, and AB1157-830) were protected from streptonigrin poisoning. Dithiothreotol (5.0 mM), diamide (1 mM), methyl viologen (1 mM), and cyanide (10 mM) protected aerobic E. coli from 5 µg/mL streptonigrin.These data are also consistent with a model of in vivo streptonigrin toxicity that requires a favorable intracellular oxidation–reduction state and an optimal concentration of molecular oxygen.

scholarly journals The yeast alpha2 and Mcm1 proteins interact through a region similar to a motif found in homeodomain proteins of higher eukaryotes.

1996 ◽  
Vol 16 (5) ◽  
pp. 2135-2143 ◽  
Author(s):  
J Mead ◽  
H Zhong ◽  
T B Acton ◽  
A K Vershon
Keyword(s):  
Dna Binding ◽  
Transcriptional Repression ◽  
Direct Interaction ◽  
Homeodomain Protein ◽  
Sequence Specificity ◽  
Homeodomain Proteins ◽  
Yeast Saccharomyces Cerevisiae ◽  
Transcriptional Regulatory

Homeodomain proteins are transcriptional regulatory factors that, in general, bind DNA with relatively low sequence specificity and affinity. One mechanism homeodomain proteins use to increase their biological specificity is through interactions with other DNA-binding proteins. We have examined how the yeast (Saccharomyces cerevisiae) homeodomain protein alpha2 specifically interacts with Mcm1, a MADS box protein, to bind DNA specifically and repress transcription. A patch of predominantly hydrophobic residues within a region preceding the homeodomain of alpha2 has been identified that specifies direct interaction with Mcm1 in the absence of DNA. This hydrophobic patch is required for cooperative DNA binding with Mcm1 in vitro and for transcriptional repression in vivo. We have also found that a conserved motif, termed YPWM, frequently found in homeodomain proteins of insects and mammals, partially functions in place of the patch in alpha2 to interact with Mcm1. These findings suggest that homeodomain proteins from diverse organisms may use analogous interaction motifs to associate with other proteins to achieve high levels of DNA binding affinity and specificity.

scholarly journals Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

2019 ◽  
Author(s):  
Matthew L. Jenior ◽  
Thomas J. Moutinho ◽  
Bonnie V. Dougherty ◽  
Jason A. Papin
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Network Models ◽  
Growth Conditions ◽  
Flux Analysis ◽  
Bacterial Physiology ◽  
Context Specific ◽  
K 12 ◽  
Genome Scale

AbstractThe metabolic responses of bacteria to dynamic extracellular conditions drives not only the behavior of single species, but also entire communities of microbes. Over the last decade, genome-scale metabolic network reconstructions have assisted in our appreciation of important metabolic determinants of bacterial physiology. These network models have been a powerful force in understanding the metabolic capacity that species may utilize in order to succeed in an environment. Increasingly, an understanding of context-specific metabolism is critical for elucidating metabolic drivers of larger phenotypes and disease. However, previous approaches to use network models in concert with omics data to better characterize experimental systems have met challenges due to assumptions necessary by the various integration platforms or due to large input data requirements. With these challenges in mind, we developed RIPTiDe (Reaction Inclusion by Parsimony and Transcript Distribution) which uses both transcriptomic abundances and parsimony of overall flux to identify the most cost-effective usage of metabolism that also best reflects the cell’s investments into transcription. Additionally, in biological samples where it is difficult to quantify specific growth conditions, it becomes critical to develop methods that require lower amounts of user intervention in order to generate accurate metabolic predictions. Utilizing a metabolic network reconstruction for the model organism Escherichia coli str. K-12 substr. MG1655 (iJO1366), we found that RIPTiDe correctly identifies context-specific metabolic pathway activity without supervision or knowledge of specific media conditions. We also assessed the application of RIPTiDe to in vivo metatranscriptomic data where E. coli was present at high abundances, and found that our approach also effectively predicts metabolic behaviors of host-associated bacteria. In the setting of human health, understanding metabolic changes within bacteria in environments where growth substrate availability is difficult to quantify can have large downstream impacts on our ability to elucidate molecular drivers of disease-associated dysbiosis across the microbiota. Our results indicate that RIPTiDe may have potential to provide understanding of context-specific metabolism of bacteria within complex communities.Author SummaryTranscriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment. While traditional analyses have been informative, leveraging these datasets within genome-scale metabolic network reconstructions (GENREs) can provide greatly improved context for shifts in pathway utilization and downstream/upstream ramifications for changes in metabolic regulation. Many previous techniques for GENRE transcript integration have focused on creating maximum consensus with input datasets, but these approaches were recently shown to generate less accurate metabolic predictions than a transcript-agnostic method of flux minimization (pFBA), which identifies the most efficient/economic patterns of metabolism given certain growth constraints. Despite this success, growth conditions are not always easily quantifiable and highlights the need for novel platforms that build from these findings. Our new method, RIPTiDe, combines these concepts and utilizes overall minimization of flux weighted by transcriptomic analysis to identify the most energy efficient pathways to achieve growth that include more highly transcribed enzymes, without previous insight into extracellular conditions. Utilizing a well-studied GENRE from Escherichia coli, we demonstrate that this new approach correctly predicts patterns of metabolism utilizing a variety of both in vitro and in vivo transcriptomes. This platform could be important for revealing context-specific bacterial phenotypes in line with governing principles of adaptive evolution, that drive disease manifestation or interactions between microbes.

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