Sylvie Garneau-Tsodikova

Bio: Sylvie Garneau-Tsodikova is an academic researcher from University of Kentucky. The author has contributed to research in topics: Aminoglycoside & Nonribosomal peptide. The author has an hindex of 39, co-authored 162 publications receiving 6190 citations. Previous affiliations of Sylvie Garneau-Tsodikova include University of California, San Diego & Life Sciences Institute.

Protein posttranslational modifications: the chemistry of proteome diversifications.

Abstract: The diversity of distinct covalent forms of proteins (the proteome) greatly exceeds the number of proteins predicted by DNA coding capacities owing to directed posttranslational modifications. Enzymes dedicated to such protein modifications include 500 human protein kinases, 150 protein phosphatases, and 500 proteases. The major types of protein covalent modifications, such as phosphorylation, acetylation, glycosylation, methylation, and ubiquitylation, can be classified according to the type of amino acid side chain modified, the category of the modifying enzyme, and the extent of reversibility. Chemical events such as protein splicing, green fluorescent protein maturation, and proteasome autoactivations also represent posttranslational modifications. An understanding of the scope and pattern of the many posttranslational modifications in eukaryotic cells provides insight into the function and dynamics of proteome compositions.

Nature's Inventory of Halogenation Catalysts: Oxidative Strategies Predominate

Abstract: Halogenated organic molecules can also arise as natural products in which the carbon -halogen bonds are generated enzymatically. To date, more than 4500 halogenated natural products have been discovered, 2 though it is likely to be a substantially incomplete inventory. Enzymatic incorporation of halogens during natural product assembly alters physical properties, including electronic and steric effects that can be consequential for determining the affinity and selectivity of interactions with biological targets. Many of the genes encoding such halogen-incorporating enzymes are embedded in specific biosynthetic gene clusters, enabling coordinate regulation to activate these secondary metabolite pathways. Biological halogenation occurs on a diverse array of organic scaffolds, from terpenes to polyketides to nonribosomal peptides. Within these scaffolds, halogen atoms are incorporated on aliphatic carbons, olefinic centers, and a wide variety of aromatic and heterocyclic rings. A recent inventory of halogen-containing natural products indicated 2300 organochlorines, 2100 organobromines, 120 organoiodines, and 30 organofluorines. 2 The larger representation of chlorinated and brominated metabolites probably reflects the abundance of chloride and bromide ions in microenvironments of terrestrial and marine producer organisms. A brief list of some chlorinated, brominated, and iodinated metabolites is noted below. Among the chlorinated natural products of therapeutic interest are vancomycin ( 1), rebeccamycin ( 2), chlortetracycline (3), and chloramphenicol ( 4; Figure 1A).3-6 The natural products1-3 carry chlorine groups on aromatic rings while chloramphenicol has a 2,2-dichloroacetyl group. As shown in Figure 1B, the cyanobacterial metabolite barbamide (5) has a trichloromethyl substituent and syringomycin E ( 6), produced by the phytotoxicPseudomonas syringae , is monochlorinated on the terminal methyl of a threonyl residue. 7,8 In the biocontrol agents pyrrolnitrin ( 7) and pyoluteorin (8; Figure 1C), also produced by Pseudomonas strains, pyrrole rings are monoand dichlorinated, respectively.9,10 Brominated metabolites are typically produced by marine microorganisms, and three such molecules are shown in Figure 2. The bromoterpene snyderol comes in three isomeric forms (9-11; R, â, and γ), reflecting three modes of quenching an intermediate carbocation. 11,12 Convolutamine A (12) has a tribromoanisole ring presumably reflecting three tandem bromination steps during maturation. 13 The terpenoid product laurallene ( 13) has two C-Br bonds, most notably the terminal bromoallene group. 14

Mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives

Abstract: Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.

Automated genome mining for natural products

Abstract: Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural product structure elucidation. Increasingly rapid and more cost-effective genome sequencing technologies coupled with advanced computational power have converged to transform this trend toward a more rational and predictive pursuit. We have developed a rapid method of scanning genome sequences for multiple polyketide, nonribosomal peptide, and mixed combination natural products with output in a text format that can be readily converted to two and three dimensional structures using conventional software. Our open-source and web-based program can assemble various small molecules composed of twenty standard amino acids and twenty two other chain-elongation intermediates used in nonribosomal peptide systems, and four acyl-CoA extender units incorporated into polyketides by reading a hidden Markov model of DNA. This process evaluates and selects the substrate specificities along the assembly line of nonribosomal synthetases and modular polyketide synthases. Using this approach we have predicted the structures of natural products from a diverse range of bacteria based on a limited number of signature sequences. In accelerating direct DNA to metabolomic analysis, this method bridges the interface between chemists and biologists and enables rapid scanning for compounds with potential therapeutic value.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Abstract: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.

Postsynthetic modification of metal–organic frameworks

Abstract: The modification of metal–organic frameworks (MOFs) in a postsynthetic scheme is discussed in this critical review. In this approach, the MOF is assembled and then modified with chemical reagents with preservation of the lattice structure. Recent findings show amide couplings, isocyanate condensations, ‘click’ chemistry, and other reactions are suitable for postsynthetic modification (PSM). In addition, a number of MOFs, from IRMOF-3 to ZIF-90, are amenable to PSM. The generality of PSM, in both scope of chemical reactions and range of suitable MOFs, clearly indicates that the approach is broadly applicable. Indeed, the rapid increase in reports on PSM demonstrates this methodology will play an increasingly important role in the development of MOFs for the foreseeable future (117 references).