Correlating the structure and activity of Y. pestis Ail in a bacterial cell envelope

ABSTRACTUnderstanding microbe-host interactions at the molecular level is a major goal of fundamental biology and therapeutic drug development. Structural biology strives to capture biomolecular structures in action, but the samples are often highly simplified versions of the complex native environment. Here we present an E. coli model system that allows us to probe the structure and function of Ail, the major surface protein of the deadly pathogen Yersinia pestis. We show that cell surface expression of Ail produces Y. pestis virulence phenotypes in E. coli, including resistance to human serum, co-sedimentation of human vitronectin and pellicle formation. Moreover, isolated bacterial cell envelopes, encompassing inner and outer membranes, yield high-resolution solid-state nuclear magnetic resonance (NMR) spectra that reflect the structure of Ail and reveal Ail sites that are sensitive to the bacterial membrane environment and involved in the interactions with human serum components. The data capture the structure and function of Ail in a bacterial outer membrane and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum.SIGNIFICANCEAil is a critical virulence factor of Y. pestis, and its interactions with human serum are central for promoting the immune resistance of bacteria to the human host defenses. Here we capture the action of Ail in a functional bacterial environment and set the stage for probing its interactions with the complex milieu of immune response proteins present in human serum. The development of an E. coli model system of Y. pestis for biophysical studies is new and biologically important. Finally, the work extends the range in-situ NMR spectroscopy to include models of microbial infection.

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Depletion and Reconstitution of Active E. Coli Ribosomes

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100116826 ◽

1975 ◽

Vol 33 ◽

pp. 640-641

Author(s):

M. Boublik ◽

W. Hellmann ◽

F. Jenkins

Keyword(s):

Protein Biosynthesis ◽

Large Subunit ◽

High Resolution Electron Microscopy ◽

Small Subunit ◽

Structure And Function ◽

Biologically Active ◽

Biological Macromolecules ◽

E Coli ◽

Resolution Electron ◽

And Function

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

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Glycation of Human Serum Albumin in Diabetes: Impacts on the Structure and Function

Current Medicinal Chemistry ◽

10.2174/0929867321666140912155738 ◽

2014 ◽

Vol 22 (1) ◽

pp. 4-13 ◽

Cited By ~ 18

Author(s):

Hui Cao ◽

Tingting Chen ◽

Yujun Shi

Keyword(s):

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Structure And Function ◽

And Function

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Impact of DNA methylation on 3D genome structure

Nature Communications ◽

10.1038/s41467-021-23142-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Diana Buitrago ◽

Mireia Labrador ◽

Juan Pablo Arcon ◽

Rafael Lema ◽

Oscar Flores ◽

...

Keyword(s):

Dna Methylation ◽

Chromatin Structure ◽

Chromatin Condensation ◽

Genome Structure ◽

Dna Methyltransferases ◽

Model System ◽

Structure And Function ◽

3D Genome ◽

Cellular Machinery ◽

And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

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Conserved Structure and Function in the Granulysin and NK-Lysin Peptide Family

Infection and Immunity ◽

10.1128/iai.73.10.6332-6339.2005 ◽

2005 ◽

Vol 73 (10) ◽

pp. 6332-6339 ◽

Cited By ~ 33

Author(s):

Charlotte M. A. Linde ◽

Susanna Grundström ◽

Erik Nordling ◽

Essam Refai ◽

Patrick J. Brennan ◽

...

Keyword(s):

Mycobacterium Smegmatis ◽

Three Dimensional ◽

Antimycobacterial Activity ◽

Structure And Function ◽

Loop Structure ◽

E Coli ◽

Short Loop ◽

Peptide Family ◽

And Function ◽

Related Proteins

ABSTRACT Granulysin and NK-lysin are homologous bactericidal proteins with a moderate residue identity (35%), both of which have antimycobacterial activity. Short loop peptides derived from the antimycobacterial domains of granulysin, NK-lysin, and a putative chicken NK-lysin were examined and shown to have comparable antimycobacterial but variable Escherichia coli activities. The known structure of the NK-lysin loop peptide was used to predict the structure of the equivalent peptides of granulysin and chicken NK-lysin by homology modeling. The last two adopted a secondary structure almost identical to that of NK-lysin. All three peptides form very similar three-dimensional (3-D) architectures in which the important basic residues assume the same positions in space. The basic residues in granulysin are arginine, while those in NK-lysin and chicken NK-lysin are a mixture of arginine and lysine. We altered the ratio of arginine to lysine in the granulysin fragment to examine the importance of basic residues for antimycobacterial activity. The alteration of the amino acids reduced the activity against E. coli to a larger extent than that against Mycobacterium smegmatis. In granulysin, the arginines in the loop structure are not crucial for antimycobacterial activity but are important for cytotoxicity. We suggest that the antibacterial domains of the related proteins granulysin, NK-lysin, and chicken NK-lysin have conserved their 3-D structure and their function against mycobacteria.

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Influence of aqueous extracts of urban airborne particulate matter on the structure and function of human serum albumin

Environmental Pollution ◽

10.1016/j.envpol.2020.114667 ◽

2020 ◽

Vol 263 ◽

pp. 114667 ◽

Cited By ~ 2

Author(s):

Olga Mazuryk ◽

Przemysław Gajda-Morszewski ◽

Monika Flejszar ◽

Przemysław Łabuz ◽

Rudi van Eldik ◽

...

Keyword(s):

Particulate Matter ◽

Human Serum Albumin ◽

Serum Albumin ◽

Human Serum ◽

Airborne Particulate Matter ◽

Structure And Function ◽

Aqueous Extracts ◽

Airborne Particulate ◽

And Function

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High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x20001132 ◽

2020 ◽

Vol 76 (2) ◽

pp. 94-102 ◽

Cited By ~ 2

Author(s):

Maria A. Schumacher ◽

Tomoo Ohashi ◽

Lauren Corbin ◽

Harold P. Erickson

Keyword(s):

Escherichia Coli ◽

Staphylococcus Aureus ◽

Cell Division ◽

High Resolution ◽

Crystal Structures ◽

Bacterial Cell ◽

Model System ◽

E Coli ◽

Z Ring ◽

Main Model

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

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Changes in the trace element concentrations of developing chick embryo brain tissue

Proceedings of the British Society of Animal Production (1972) ◽

10.1017/s0308229600024867 ◽

1993 ◽

Vol 1993 ◽

pp. 163-163

Author(s):

A. MacPherson ◽

J. Dixon ◽

R.C. Noble ◽

B. Speake ◽

M. Cocchi

Keyword(s):

Model System ◽

Structure And Function ◽

Superoxide Dismutases ◽

Avian Embryo ◽

Membrane Structure And Function ◽

Free Radical Attack ◽

And Function ◽

Radical Attack ◽

Embryo Brain ◽

Pufa Metabolism

Polyunsaturated fatty acids(PUFA) are vitally important for normal neonatal development. As well as providing a source of energy they are intrinsically involved in the establishment and maintenance of cell membrane structure and function. High PUFA levels, however, are subject to peroxidation and consequently require to be protected against free radical attack via an adequate antioxidant supply. The avian embryo was used as a model system as it is particularly dependent on PUFA and poor hatchability has recently been linked to inadequate PUFA metabolism. The micronutrient elements Se, Cu, Zn, Fe and Mn are involved in the antioxidant complex through their presence in the enzymes glutathione peroxidase (GSH-PX), superoxide dismutases (SOD) and catalase. The concentrations of these elements were measured in eggs and in chick embryonic and post hatch brains at different stages of development in order to elucidate their roles in the maintenance of PUFA metabolism.

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Bacterial ß-Barrel Outer Membrane Proteins

Handbook of Research on Systems Biology Applications in Medicine ◽

10.4018/978-1-60566-076-9.ch010 ◽

2009 ◽

pp. 182-207

Author(s):

Pantelis G. Bagos ◽

Stavros J. Hamodrakas

Keyword(s):

Membrane Proteins ◽

Outer Membrane ◽

Bacterial Cell ◽

Outer Membrane Proteins ◽

Structural Features ◽

Structure And Function ◽

Structural Motif ◽

Functional Roles ◽

Bacterial Outer Membrane ◽

And Function

ß-barrel outer membrane proteins constitute the second and less well-studied class of transmembrane proteins. They are present exclusively in the outer membrane of Gram-negative bacteria and presumably in the outer membrane of mitochondria and chloroplasts. During the last few years, remarkable advances have been made towards an understanding of their functional and structural features. It is now wellknown that ß-barrels are performing a large variety of biologically important functions for the bacterial cell. Such functions include acting as specific or non-specific channels, receptors for various compounds, enzymes, translocation channels, structural proteins, and adhesion proteins. All these functional roles are of great importance for the survival of the bacterial cell under various environmental conditions or for the pathogenic properties expressed by these organisms. This chapter reviews the currently available literature regarding the structure and function of bacterial outer membrane proteins. We emphasize the functional diversity expressed by a common structural motif such as the ß-barrel, and we provide evidence from the current literature for dozens of newly discovered families of transmembrane ß-barrels.

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