Biosynthetic Glycan Labeling

Glycans are ubiquitous and play important biological roles, yet chemical methods for probing their structure and function within cells remain limited. Strategies for studying other biomacromolecules, such as proteins, often exploit chemoselective reactions for covalent modification, capture, or imaging. Unlike amino acids that constitute proteins, glycan building blocks lack distinguishing reactivity because they are composed primarily of polyol isomers. Moreo-ver, encoding glycan variants through genetic manipulation is complex. Therefore, we formulated a new, generaliza-ble strategy for chemoselective glycan modification that directly takes advantage of cellular glycosyltransferases. Many of these enzymes are selective for the products they generate yet promiscuous in their donor preferences. Thus, we designed reagents with bioorthogonal handles that function as glycosyltransferase substrate surrogates. We validated the feasibility of this approach by synthesizing and testing probes of D-arabinofuranose (D-Araf), a monosaccharide found in bacteria and an essential component of the cell wall that protects mycobacteria, including Mycobacterium tuberculosis. The result is the first probe capable of selectively labeling arabinofuranose-containing glycans. Our stud-ies serve as a platform for developing new chemoselective labeling agents for other privileged monosaccharides. This probe revealed an asymmetric distribution of D-Araf residues during mycobacterial cell growth and could be used to detect mycobacteria in THP1-derived macrophages.

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Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab042 ◽

2021 ◽

Author(s):

Shen Jean Lim ◽

Brenton Davis ◽

Danielle Gill ◽

John Swetenburg ◽

Laurie C Anderson ◽

...

Keyword(s):

Amino Acids ◽

Nutrient Cycling ◽

Bacterial Communities ◽

Structure And Function ◽

Differentially Expressed ◽

Seagrass Species ◽

Bare Sand ◽

And Function

Abstract Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic, and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides, and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes, and their environment.

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Multiplatform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity

mSystems ◽

10.1128/msystems.00123-18 ◽

2018 ◽

Vol 3 (6) ◽

Cited By ~ 2

Author(s):

Jingwei Cai ◽

Robert G. Nichols ◽

Imhoi Koo ◽

Zachary A. Kalikow ◽

Limin Zhang ◽

...

Keyword(s):

Mass Spectrometry ◽

Amino Acids ◽

Flow Cytometry ◽

Free Radical ◽

Gut Microbiota ◽

Structure And Function ◽

Metabolic Phenotyping ◽

And Function

ABSTRACTThe gut microbiota is susceptible to modulation by environmental stimuli and therefore can serve as a biological sensor. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combinesin vitromicrobial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and1H nuclear magnetic resonance (NMR)-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and functionin vivo, was studied to assess its direct effect on the gut microbiota. The microbiota was isolated from mouse cecum and was exposed to tempol for 4 h under strict anaerobic conditions. The flow cytometry data suggested that short-term tempol exposure to the microbiota is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short-chain fatty acids, branched-chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating that thein vitroapproach reflectedin vivoconditions. Our results, through evaluation of microbial viability, physiology, and metabolism and a comparison ofin vitroandin vivoexposures with tempol, suggest that physiologic and metabolic phenotyping can provide unique insight into gut microbiota toxicity.IMPORTANCEThe gut microbiota is modulated physiologically, compositionally, and metabolically by xenobiotics, potentially causing metabolic consequences to the host. We recently reported that tempol, a stabilized free radical nitroxide, can exert beneficial effects on the host through modulation of the microbiome community structure and function. Here, we investigated a multiplatform phenotyping approach that combines high-throughput global metabolomics with flow cytometry to evaluate the direct effect of tempol on the microbiota. This approach may be useful in deciphering how other xenobiotics directly influence the microbiota.

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The thick waxy coat of mycobacteria, a protective layer against antibiotics and the host's immune system

Biochemical Journal ◽

10.1042/bcj20200194 ◽

2020 ◽

Vol 477 (10) ◽

pp. 1983-2006 ◽

Cited By ~ 1

Author(s):

Sarah M. Batt ◽

David E. Minnikin ◽

Gurdyal S. Besra

Keyword(s):

Infectious Disease ◽

Cell Wall ◽

Mycobacterium Tuberculosis ◽

Immune System ◽

Mortality Rate ◽

Cell Envelope ◽

Protective Layer ◽

Structure And Function ◽

Complex Lipids ◽

And Function

Tuberculosis, caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb), is the leading cause of death from an infectious disease, with a mortality rate of over a million people per year. This pathogen's remarkable resilience and infectivity is largely due to its unique waxy cell envelope, 40% of which comprises complex lipids. Therefore, an understanding of the structure and function of the cell wall lipids is of huge indirect clinical significance. This review provides a synopsis of the cell envelope and the major lipids contained within, including structure, biosynthesis and roles in pathogenesis.

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Amino acid sequence of the encephalitogenic basic protein from human myelin

Biochemical Journal ◽

10.1042/bj1230057 ◽

1971 ◽

Vol 123 (1) ◽

pp. 57-67 ◽

Cited By ~ 182

Author(s):

P. R. Carnegie

Keyword(s):

Amino Acids ◽

Central Nervous System ◽

Nervous System ◽

Amino Acid ◽

Basic Protein ◽

Structure And Function ◽

Autoimmune Encephalomyelitis ◽

The Central Nervous System ◽

And Function ◽

Experimental Autoimmune

Myelin from the central nervous system contains an unusual basic protein, which can induce experimental autoimmune encephalomyelitis. The basic protein from human brain was digested with trypsin and other enzymes and the sequence of the 170 amino acids was determined. The localization of the encephalitogenic determinants was described. Possible roles for the protein in the structure and function of myelin are discussed.

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Structure and Function Studies of GPCRs by Site-Specific Incorporation of Unnatural Amino Acids

Topics in Medicinal Chemistry - Structure and Function of GPCRs ◽

10.1007/7355_2017_20 ◽

2017 ◽

pp. 195-215

Author(s):

Meilin Tian ◽

Qian Wang ◽

Chonggang Yuan ◽

Shixin Ye

Keyword(s):

Amino Acids ◽

Unnatural Amino Acids ◽

Structure And Function ◽

Site Specific ◽

And Function

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3. Proteins

Biochemistry: A Very Short Introduction ◽

10.1093/actrade/9780198833871.003.0003 ◽

2021 ◽

pp. 34-51

Author(s):

Mark Lorch

Keyword(s):

Amino Acids ◽

Protein Folding ◽

Protein Structure ◽

Protein Structures ◽

Structure And Function ◽

Vast Array ◽

A Cell ◽

Cellular Machinery ◽

And Function ◽

The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

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Structure and Function of Multimeric G-Quadruplexes

Molecules ◽

10.3390/molecules24173074 ◽

2019 ◽

Vol 24 (17) ◽

pp. 3074 ◽

Cited By ~ 25

Author(s):

Sofia Kolesnikova ◽

Edward A. Curtis

Keyword(s):

Nucleic Acid ◽

Building Blocks ◽

Structure And Function ◽

Limited Information ◽

Functional Elements ◽

Future Studies ◽

And Function ◽

Nucleic Acid Structures ◽

Sequence Requirements ◽

Order Structures

G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.

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Frank William Ernest Gibson 1923 - 2008

Historical Records of Australian Science ◽

10.1071/hr09024 ◽

2010 ◽

Vol 21 (1) ◽

pp. 55 ◽

Cited By ~ 1

Author(s):

A. J. Pittard ◽

G. B. Cox

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Genetic Analysis ◽

Aromatic Compounds ◽

Aromatic Amino Acids ◽

Atp Synthesis ◽

Structure And Function ◽

Innovative Model ◽

Distinguished Research ◽

And Function

Frank Gibson died in Canberra on 11 July 2008. Frank was a highly distinguished research scientist who will be remembered for his pioneering studies in identifying the branch-point compound in the pathway of biosynthesis of a large number of important aromatic compounds followed by a detailed biochemical and genetic analysis of many of the pathways leading to the aromatic amino acids and the so-called aromatic vitamins. Studies on ubiquinone synthesis and function led to an examination of oxidative phosphorylation and the structure and function of the F1F0-ATPase in the bacterium Escherichia coli. This work resulted in the formulation of a highly innovative model, involving rotating subunits of the F0 segment within the membrane and offering an explanation for the mechanism linking proton flow and ATP synthesis.

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