Biology subjects

Cahill, S. M.

Publications and source records attributed to Cahill, S. M..

4 recordsLinked to original sources

bioRxiv2026

C. elegans small heat-shock protein HSP-12.6 has a highly specialized protective function towards muscle thick filaments in vivo

Small heat-shock proteins (sHSPs) are an ancient and diverse class of molecular chaperones, acting as a first line of defense against proteotoxic stresses. While the canonical sHSPs prevent uncontrollable aggregation of a broad range of non-native substrates, a subset of sHSPs do not exhibit this broad activity in vitro, and their functions in vivo are poorly understood. Interestingly, several such sHSPs are selectively expressed in muscle tissues, including by myogenic programs, indicating likely functional roles. We examined in vivo function of C. elegans HSP-12.6, which possesses no chaperone activity in vitro but regulates lifespan, and is developmentally induced in the muscles of long-lived dauer animals. We found that HSP-12.6 exhibits exceptional selectivity in protecting the muscle function against folding or assembly mutations in thick filament proteins, but not in thin filament or non-filament proteins. This reflected its exclusive chaperone-like binding to the healthy myosin-containing thick filaments, and to their aggregates. HSP-12.6 did not bind other muscle structures or aggregates, including those of thin filaments, and retained its selectivity to either healthy thick filaments or their aggregates when challenged with a toxic aggregation-prone polyQ protein. Our data establish HSP-12.6 as a highly-selective myoprotective chaperone, with client spectrum distinct from other sHSPs.

cell biology↗

bioRxiv2023

Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive

The outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread of Acinetobacter baumannii, a bacterial pathogen of global concern. In this study, we screened 12476 publicly available A. baumannii genome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17-OCL22. These were compiled with previously characterised OCL to create an updated version of the A. baumannii OCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool, Kaptive. Use of this database against the 12476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6% of sequenced genomes assigned by Kaptive with a match confidence score of Good or above. OCL1 was most common amongst isolates belonging to sequence types, ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages associated with extensive antibiotic resistance. The highest level of diversity in OCL types was found in ST2, with eight different OCL identified. The updated OCL reference database is available for download from GitHub (https://github.com/katholt/Kaptive; under version v 2.0.5), and has been integrated for use on Kaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods for A. baumannii strain identification, classification and surveillance. IMPACT STATEMENTIn the absence of effective treatment options for multi-drug resistant Acinetobacter baumannii, the highest-ranking critical priority bacterial pathogen of global concern, national and global surveillance is necessary to detect, track and subsequently curb the spread of isolates that resist current therapies. Several epidemiological markers are used to characterise A. baumannii strains by detecting genetic differences in specific regions of the genome. One of these is the chromosomal OC locus (OCL) responsible for the synthesis of the outer core (OC) component of the lipooligosaccharide (LOS). Here, we provide an update to the international A. baumannii OCL reference sequence database, extending the number of known OCL types to assist with clinical surveillance of important strains or clonal lineages. Data summaryO_LIThe updated A. baumannii OCL reference sequence database including 22 annotated OCL sequences is available for download under Kaptive v. 2.0.5 at https://github.com/katholt/Kaptive. C_LIO_LIGenome assemblies or GenBank records used as representative reference sequences are listed in Table 1 and acknowledged in each record in the database. C_LI O_TBL View this table: org.highwire.dtl.DTLVardef@1d32ff1org.highwire.dtl.DTLVardef@1f0af8borg.highwire.dtl.DTLVardef@94f185org.highwire.dtl.DTLVardef@7c8b7aorg.highwire.dtl.DTLVardef@a93255_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONInformation on A. baumannii OCL reference sequences used to populate the updated OCL database for Kaptive v 2.0.5 C_TABLECAPTION C_TBL

microbiology↗

bioRxiv2022

An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus

2.Several novel non-antibiotic therapeutics for the critical priority bacterial pathogen, Acinetobacter baumannii, rely on specificity to the cell-surface capsular polysaccharide (CPS). Hence, prediction of CPS type deduced from genes in whole genome sequence data underpins the development and application of these therapies. In this study, we provide a comprehensive update to the A. baumannii K locus reference sequence database for CPS typing (available in Kaptive v. 2.0.1) to include 145 new KL, providing a total of 237 KL reference sequences. The database was also reconfigured for compatibility with the updated Kaptive v. 2.0.0 code that enables prediction of K type from special logic parameters defined by detected combinations of KL and additional genes outside the K locus. Validation of the database against 8994 publicly available A. baumannii genome assemblies from NCBI databases identified the specific KL in 73.45% of genomes with perfect, very high or high confidence. Poor sequence quality or the presence of insertion sequences were the main reasons for lower confidence levels. Overall, 17 KL were overrepresented in available genomes, with KL2 the most common followed by the related KL3 and KL22. Substantial variation in gene content of the central portion of the K locus, that usually includes genes specific to the CPS type, included 34 distinct groups of genes for synthesis of various complex sugars and >400 genes for forming linkages between sugars or adding non-sugar substituents. A repertoire of 681 gene types were found across the 237 KL, with 88.4% found in <5% of KL. 3. Significance as a BioResource to the communityNew therapies that target the bacterial polysaccharide capsule (CPS) show promise as effective tools to curb the high mortality rates associated with extensively resistant A. baumannii; one of the worlds most troublesome Gram-negative pathogens. As important information about the CPS structure produced by an isolate can be extracted from Whole Genome Sequences (WGS), simple bioinformatic tools and definitive sequence databases are needed to facilitate robust prediction of CPS type from WGS data. Here, we provide a comprehensive update to the international CPS sequence typing database for A. baumannii, increasing the utility of this resource for prediction of CPS type from WGS to assist with clinical surveillance, and/or the design and application of CPS-targeted therapies. This study is expected to further inform epidemiological tracking efforts, as well as the design of therapeutics targeting the CPS, enhancing global efforts to identify, trace and treat infections caused by this pathogen. 4. Data summaryO_LIThe updated A. baumannii KL reference sequence database including 241 fully annotated gene clusters is available for download under Kaptive v. 2.0.1 at https://github.com/katholt/Kaptive. C_LIO_LIGenome assemblies, short read data, or GenBank records used as representative reference sequence for each K locus are listed in Supplementary Table S1, and are referenced within each entry in the A. baumannii KL reference sequence database. C_LI The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

genomics↗

bioRxiv2019

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

Multiply antibiotic resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of the 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for the 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardised nomenclature. These databases are compatible with Kaptive, a tool for in silico typing of bacterial surface polysaccharide loci, and their utility was validated using a) >630 assembled A. baumannii draft genomes for which the KL and OCL regions had been previously typed manually, and b) 3386 A. baumannii genome assemblies downloaded from NCBI. Among the previously typed genomes, Kaptive was able to confidently assign KL and OCL types with 100% accuracy. Among the genomes retrieved from NCBI, Kaptive detected known KL and OCL in 87% and 90% of genomes, respectively indicating that the majority of common KL and OCL types are captured within the databases; 13 KL were not detected in any public genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multi-locus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally-distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available at https://github.com/katholt/Kaptive and will be updated as further locus types become available. Data Summary1. Databases including fully annotated gene cluster sequences for A. baumannii K loci and OC loci are available for download at https://github.com/katholt/Kaptive 2. The Kaptive software, which can be used to screen new genomes against the K and O locus database is available at https://github.com/katholt/Kaptive (command-line code) and http://kaptive.holtlab.net/ (interactive web service). 3. Details of the Kaptive search results validating in silico serotyping of K and O loci using our approach are provided as supplementary files, Dataset 1 (92 KL reference sequences and 12 OCL reference sequences), Dataset 2 (642 genomes assembled from reads available in NCBI SRA) and Dataset 3 (3415 genome assemblies downloaded from NCBI GenBank). Impact statementThe ability to identify and track closely related isolates is key to understanding, and ultimately controlling, the spread of multiply antibiotic resistant A. baumannii causing difficult to treat infections, which are an urgent public health threat. Extensive variation in the KL and OCL gene clusters responsible for biosynthesis of capsule and the outer core of lipooligosaccharide, respectively, are potentially highly informative epidemiological markers. However, clear, well-documented identification of each variant and simple-to-use tools and procedures are needed to reliably identify them in genome sequence data. Here, we present curated databases compatible with the available web-based and command-line Kaptive tool to make KL and OCL typing readily accessible to assist epidemiological surveillance of this species. As many bacteriophage recognise specific properties of the capsule and attach to it, capsule typing is also important in assessing the potential of specific phage for therapy on a case by case basis.

microbiology↗