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Alagesan, K.

Publications and source records attributed to Alagesan, K..

13 recordsLinked to original sources

The cost-benefit trade-off of peritrichous flagellation in bacteria

Many bacteria assemble multiple flagella, although building flagella imposes a substantial biosynthetic and energetic cost. We used the peritrichously flagellated model organism Salmonella enterica to quantify how flagellar abundance affects bacterial growth, proteome allocation, and motility. For this, we generated genetically modified strains with inducible or constitutive expression of the flagellar master regulator flhDC, resulting in a panel of strains ranging from nearly non-flagellated to hyperflagellated cells. We found that higher flagellar investment reduced growth rate and redirected proteome allocation, with an expansion of the flagellar sector occurring largely at the expense of the ribosomal sector. Growth analyses of flagellar assembly mutants, combined with cost modeling, suggested that flagellin biosynthesis dominated the energetic burden, whereas motor rotation contributed a smaller additional cost. Despite the associated cost, increased flagellation improved soft-agar spreading, single-cell swimming speed, effective diffusivity, and competitive fitness in spatially structured environments. A coarse-grained proteome-allocation model parametrized from these data reproduced the observed growth penalties, while simulations of navigation in dynamic chemical gradients predicted that motility benefits saturate near a flagellar investment of 3% of proteome mass. Beyond this point, rising biosynthetic costs outweigh diminishing motility gains. In summary, these results support a quantitative cost-benefit model in which heterogeneous, spatially structured environments favor an intermediate number of flagella by balancing motility benefits against the biosynthetic costs of building and operating multiple flagella.

microbiology↗

Microbiota-induced fatty acid synthesis facilitates intestinal infection and immune-mediated damage in Drosophila

The role of the microbiota in facilitating infection is increasingly recognized, though the underlying mechanisms remain under investigation. In this study, we demonstrate that the gut microbiome, particularly Lactiplantibacillus plantarum, promotes enteric infection in Drosophila melanogaster by reshaping host physiology and immune responses. Upon gut colonization, L. plantarum enhances fatty acid (FA) production in the gut. Reducing FA synthesis improves host survival, and pathogen mutants deficient in FA utilization exhibit reduced virulence. FAs support pathogen growth, increase virulence, and enhance resistance to antimicrobial effectors, ultimately facilitating pathogen persistence in the gut. Persisting pathogens consequently overstimulate the immune system, leading to excessive production of antimicrobial peptides (AMPs). Flies lacking AMPs, particularly Metchnikowin and Attacin D mutants, show better survival during infection, implicating AMPs in immunopathology. Our findings identify a mechanism whereby microbiota-induced release of host FAs stimulates pathogen virulence and persistence, ultimately driving AMP-mediated immunopathology.

microbiology↗

A Pore-Forming Toxin Monalysin Contributes to Infection-Induced Suppression of Defecation in Female Drosophila

Pathogen expulsion from the gut via defecation is an important defence strategy against infection. The microbial factors that can subvert this defence reaction remain poorly understood. While many microbes have been found to increase host intestinal peristalsis, Pseudomonas entomophila infection in Drosophila melanogaster leads to infection-induced defecation blockage, particularly in females. Here, we show that this phenotype is driven by a secreted, thermosensitive protein regulated by the GacS/GacA two-component system. Proteomic comparison of the {Delta}gacA mutant, which does not inhibit defecation, and the avirulent {Delta}hfq mutant lacking RNA chaperon Hfq, which still triggers the phenotype, identified pore-forming toxin Monalysin as one of the candidate factors required for inhibiting defecation. Consistently, the Monalysin-deficient mutant was unable to inhibit defecation. Hence, Monalysin besides causing intestinal damage, has a previously unknown role in suppressing defecation and potentially pathogen expulsion. Overall, our study identified a bacterial factor that rapidly reduces defecation frequency, consistent with transient suppression of intestinal transit, thus advancing our understanding of pathogen strategies used to subvert host defences.

microbiology↗

Targeting the translation machinery: The RNase Y specificity factor Y-complex coordinates ribosome degradation

Limiting the synthesis and activity of ribosomes is crucial for adaptation to stresses, such as heat or nutrient starvation. In Bacillus subtilis, this can be achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. Here, we performed a genetic screen to uncover novel factors contributing to the heat shock response of B. subtilis. We identified the Y-complex, which confers specificity to the endonuclease RNase Y, as a critical player during stress conditions, such as heat or transition into stationary phase. This protein complex is required for processing diverse RNAs, notably the maturation of mRNAs encoding proteins involved in translation and metabolism. We further demonstrate that the Y-complex and RNase Y initiate the degradation of rRNAs of mature ribosomes, lowering their abundance. We propose that the Y-complex is a regulatory hub that modulates gene expression, adjusts protein synthesis and resource allocation.

microbiology↗

Sex Differences in Drosophila Intestinal Metabolism Contribute to Sexually Dimorphic Infection Outcome and Alter Gut Pathogen Virulence

Sexual dimorphism in infection outcomes is a pervasive phenomenon, the underlying mechanisms of which remain incompletely understood. Here, utilizing Pseudomonas entomophila intestinal infection in Drosophila, we demonstrated that sex differences in intestinal redox processes contribute to female bias in susceptibility to gut infection. Female inability to overcome excessive pathogen-induced oxidative stress results in defecation blockage, pathogen persistence, and host death. Male flies exhibit increased carbohydrate metabolism and pentose phosphate pathway activity - a key antioxidant defense system. This allows males to withstand oxidative stress-induced defecation blockage and clear the pathogen from the intestine, resulting in survival. Additionally, P. entomophila showed increased expression of several virulence factors, including RNA-binding protein Hfq, in the female gut, contributing to female-biased virulence of P. entomophila. Thus, the effect of the gut metabolic environment on host defenses and pathogen virulence determines the sex differences in intestinal infection outcomes. HighlightsIntestinal transit of gut pathogen contributes to sexually dimorphic susceptibility to Drosophila gut infection. Male bias in PPP favors pathogen clearance and recovery post-infection. P. entomophila reacts differently to female gut environment, where higher levels of Hfq might contribute to virulence/lethality. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/655590v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1d6d36borg.highwire.dtl.DTLVardef@d24f2aorg.highwire.dtl.DTLVardef@14b4ed1org.highwire.dtl.DTLVardef@123b46c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Novel RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria

The ribosome employs a set of highly conserved translation factors to efficiently synthesise proteins. Some translation factors interact with the ribosome in a transient manner and are thus challenging to identify. However, proteins involved in translation can be specifically identified by their interaction with ribosomal RNAs. Using a combination of proteomics approaches, we identified novel RNA binding proteins in the pathogenic bacterium Streptococcus pyogenes. One of these, a universally conserved protein YebC, was shown to transiently interact with 23S rRNA near the peptidyl-transferase centre. Deletion of yebC moderately affected the physiology and virulence of S. pyogenes. We performed ribosome profiling and detected increased pausing at proline-rich amino acid stretches in the absence of functional YebC. Further results obtained with in vivo reporters and in vitro translation system suggest that YebC is a novel translation factor required for efficient translation of proteins with proline-rich motifs.

molecular biology↗

A platform for the recombinant production of Group A Streptococcus glycoconjugate vaccines

Strep A is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydratte biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins within E. coli cells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by NMR spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.

microbiology↗

IMPROVED N- AND O-GLYCOPEPTIDE IDENTIFICATION USING HIGH-FIELD ASYMMETRIC WAVEFORM ION MOBILITY SPECTROMETRY (FAIMS)

AO_SCPLOWBSTRACTC_SCPLOWMass spectrometry is the premier tool for identifying and quantifying site-specific protein glycosylation globally. Analysis of intact glycopeptides often requires an enrichment step, after which the samples remain highly complex and exhibit a broad dynamic range of abundance. Here, we evaluated the analytical benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to nano-liquid chromatography mass spectrometry (nLC-MS) for analyses of intact glycopeptide devoid of any enrichment step. We compared the effects of compensation voltage on the transmission of N- and O-glycopeptides derived from heterogeneous protein mixtures using two FAIMS devices. We comprehensively demonstrate the performance characteristics of the FAIMS device for glycopeptide analysis and recommend optimal electrode temperature and compensation voltage (CV) settings for N- and O-glycopeptide analysis. Under optimal CV settings, FAIMS-assisted gas-phase fractionation in conjunction with chromatographic reverse phase separation resulted in a 31% increase in the detection of both N- and O-glycopeptide compared to control experiments without FAIMS. Overall, our results demonstrate that FAIMS provides an alternative means to access glycopeptides without any enrichment providing an unbiased global glycoproteome landscape. In addition, our work provides the framework to verify difficult-to-identify glycopeptide features.

biochemistry↗

Better together - Relative retention time plus spectral matching improves automated glycan characterization using PGC-nLC-IT-ESI-MS/MS

Porous Graphitized Carbon nano-liquid chromatography tandem mass spectrometry (PGC-nLC-MS/MS) is a glycomics technique with the unique capacity to differentiate isobaric glycans. The lack of suitable software tools integrating chromatography and MS-information delivered by PGC-nLC-MS/MS has been limiting fast and robust glycan identification and quantitation. We report a LC-system-independent strategy called GlycoRRT that combines relative retention time (RRT) and negative ion fragment spectra analyses for isobaric structure-specific glycomics of PGC-nLC-MS/MS data. The GlycoRRT toolset is fully customizable and easily adaptable enabling semi-automated high-throughput structural assignments. The current library contains over 200 entries and their individual meta-data (MS instrumentation, experimental conditions, retention times, fragmentation profiles and glycan structural diagnostic ion features) relevant for reliable data analyses. The GlycoRRT workflow was employed to map the N- and O-glycome in blood group matched human plasma and urine as well as decipher Immunoglobulin (IgG) glycosylation features from 13 different animal species. We have also developed visualization tools to enable a consistent, reliable, and reproducible analysis of large sets of multidimensional PGC-nLC-MS/MS glycomics data. This comprehensive glycan resource provides the glycan map of human and animal species, will serve as a reference in dissecting the role of glycans in host pathogen interaction and zoonotic disease transmission.

biochemistry↗

Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of Glycopeptide Data

Glycoproteome profiling (glycoproteomics) is a powerful yet analytically challenging research tool. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse software aiding the process have appeared, but their relative performance remains untested. Conducted through the HUPO Human Proteome Project - Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates the performance of informatics solutions for system-wide glycopeptide analysis. Mass spectrometry-based glycoproteomics datasets from human serum were shared with all teams. The relative team performance for N- and O-glycopeptide data analysis was comprehensively established and validated through orthogonal performance tests. Excitingly, several high-performance glycoproteomics informatics solutions were identified. While the study illustrated that significant informatics challenges remain, as indicated by a high discordance between annotated glycopeptides, lists of high-confidence (consensus) glycopeptides were compiled from the standardised team reports. Deep analysis of the performance data revealed key performance-associated search variables and led to recommendations for improved "high coverage" and "high accuracy" glycoproteomics search strategies. This study concludes that diverse software for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies, and specifies key variables that may guide future software developments and assist informatics decision-making in glycoproteomics.

biochemistry↗

A novel, ultrasensitive approach for quantitative carbohydrate composition and linkage analysis using LC-ESI ion trap tandem mass spectrometry

Glycan identification and characterisation is essential to correlate glycoconjugate structure to biological function. The structural assignment of carbohydrates is often based on MS composition analyses and knowledge on well-studied glycosylation pathways. Nevertheless, many monosaccharide building blocks are indistinguishable by mass alone and detailed linkage information is also not easily obtained by MS/MS analyses, in particular when organisms are studied where the glycosylation pathways are less well defined. Here, we present a novel, simple and sensitive method using Reversed Phase (RP) - Liquid Chromatography Electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS) for unambiguous identification and linkage determination of monosaccharides including N-acetylneuraminic acids. Sequential permethylation and reductive amination steps are employed prior and after acid hydrolysis to enable separation and differentiation of the various monosaccharides and their respective linkage positions. The well-established, monosaccharide specific methylation patterns allowed for the identification of the various derivatised monosaccharide alditols based on their retention time and tandem mass spectrometry fingerprint. Absolute quantitation can also be accomplished by including a set of internal standards, thus simultaneously providing qualitative and quantitative information on the monosaccharide residues present.

biochemistry↗

Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification

We used a small synthetic glycopeptide library to systematically evaluate the effect of glycosylation site location and glycan size on the efficiency of ETD MS/MS fragmentation and subsequent automated identification. Understanding how the physico-chemical properties of glycopeptides influence glycopeptide fragmentation allows for optimizing fragmentation conditions and software assisted data analyses, which rely on informative fragmentation spectra for subsequent data processing to identify glycopeptides. Often, mis-assignment of glycopeptides occurs due to uncertainties such as failure to produce sufficient peptide backbone fragment ions. Our synthetic glycopeptide library contained glycopeptides differing in glycosylation site position within the peptide as well as glycan size (from the pentasaccharide N-glycan core to fully sialylated, biantennary N-glycans). Different software solutions such as SEQUEST and Amanda were compared for ETD glycopeptide identification. We found that all, glycan size, glycosylation site position within a glycopeptide and individual precursor m/z significantly impacted the number and quality of assignable glycopeptide backbone fragments, and thus the likelihood to be correctly identified in software assisted data analyses.

biochemistry↗

To enrich or not to enrich: Enhancing (glyco)peptide ionization using the CaptiveSpray nanoBooster ™

The CaptiveSpray source ensures a stable spray and excellent nano ESI performance facilitated by a vortex gas that sweeps around the emitter spray tip to support liquid desolvation and focus the Taylor cone. Enriching the vortex gas with dopant solvents provides tremendous opportunities to increase ionization efficiency, in particular for hydrophilic compounds such as glycopeptides. How this CaptiveSpray nanobooster benefits their analysis, however, has to date not been systematically studied.\n\nWe evaluated various dopant solvents such as (i) acetone (ii) acetonitrile (iii) methanol (iv) ethanol and (v) isopropanol for their ability to enhance glycopeptide ionization. Using a synthetic IgG2 glycopeptide as a standard, acetonitrile provided a five-fold increase in signal intensities and resulted in an overall charge state increase compared to conventional CaptiveSpray ionization. This trend remained the same when tryptic IgG (glyco)peptides were analyzed and allowed highly sensitive detection of glycopeptides even without any enrichment. While acetone dopant gas enhanced glycopeptide ionization by doubling glycopeptide signal intensities, all other tested solvents resulted either in ion suppression or adduct formation. This is in agreement with and can be explained by their individual physio-chemical properties of the solvents. Finally, by omitting glycopeptide enrichment steps, we established a bias-free human Immunoglobulin G (IgG) subclass specific glycosylation profile applying the optimized CaptiveSpray nanoBooster nano-LC-ESI-MS/MS analysis conditions.

biochemistry↗