Biology subjects

Abby, S. S.

Publications and source records attributed to Abby, S. S..

13 recordsLinked to original sources

bioRxiv2026

Isoprenoid quinone profiling in complex biological samples using a novel semi-quantitative HPLC-MS/MS method

Isoprenoid quinones are ubiquitous redox lipids that mediate electron transfer in various cellular processes across all domains of life. These molecules also serve as taxonomic and metabolic markers, facilitating the characterisation of microbial communities. However, their structural diversity and extreme hydrophobicity are challenging for comprehensive detection and quantification in complex biological matrices. In this study, we present a semi-quantitative HPLC-MS/MS method that enables the sensitive analysis of the widest range of quinones reported to date. Using a 16-quinone standard mixture, we optimised separation within a 14-minute HPLC gradient and achieved femtomole-level sensitivity in targeted analyses. When applied to sewage sludges sampled weekly over three weeks, our method detected 57 distinct quinones, revealing stage-specific quinone profiles that reflect shifts in bacterial communities during wastewater treatment. This rapid and sensitive workflow provides a robust tool for accurate quinone profiling in complex samples, opening avenues for the discovery of novel quinones through untargeted approaches. By pushing the boundaries of quinone profiling, our method holds significant promise for advancing microbial ecology, environmental monitoring, and biotechnological applications. HighlightsO_LIuHPLC-Orbitrap method for the semi-quantitative profiling of isoprenoid quinones C_LIO_LIAnalysis of the widest range of isoprenoid quinones to date C_LIO_LIFemtomole-level sensitivity in just 14 minutes of chromatographic separation C_LIO_LIDetection of 57 quinones in complex wastewater sludge matrices C_LIO_LIMost comprehensive set of quinone standards including purified microbial quinones C_LI

biochemistry↗

bioRxiv2026

UbiB proteins mediate an ATP-dependent decarboxylation step in bacterial ubiquinone biosynthesis

Polyisoprenoid quinones such as ubiquinone (UQ) play an essential role in cellular physiology, acting as membrane-bound electron and proton carriers in respiratory chains and other biological processes across all domains of life. In Escherichia coli, the canonical UQ biosynthesis pathway is well characterized. It involves twelve proteins (UbiA-UbiK and UbiX), most of which catalyzing one of the eight modifications of the aromatic ring derived from 4-hydroxybenzoic acid (4-HB), while others (UbiB, UbiJ, UbiK) act as accessory factors ensuring efficient UQ production. Following prenylation by UbiA and subsequent decarboxylation by the UbiX/UbiD system, the final six reactions are catalyzed within a soluble Ubi-complex. UbiB, an atypical protein kinase-like enzyme, was proposed to extract decarboxylated intermediates from the membrane and mediate their delivery to the Ubi-complex. In this study, we demonstrate the existence of an alternative decarboxylation system in E. coli, as UQ biosynthesis can proceed in the absence of the UbiX/UbiD system. Our results show that this alternative decarboxylation activity depends on UbiB and requires its ATPase activity. Bioinformatic analyses further revealed that approximately 27% of Pseudomonadota species lack UbiX/UbiD homologs, and we found that UbiB proteins from two such species enhance the alternative decarboxylation activity when expressed in E. coli. In addition, we identified conserved residues in UbiB that are specifically required for decarboxylation but dispensable for the delivery of UQ intermediates to the Ubi-complex. Taken together, our findings support a model in which UbiB acts as an ATP-dependent decarboxylase, thereby broadening the functional scope of this poorly characterized protein. ImportancePolyisoprenoid quinones, including ubiquinone (UQ, also known as coenzyme Q), are essential electron and proton carriers in respiratory chains across all domains of life. After prenylation and decarboxylation, the final six steps of UQ biosynthesis are carried out by a soluble Ubi-complex. The only decarboxylation system currently identified in the UQ pathway, the UbiX/UbiD system, is absent from numerous bacterial genomes, and no isofunctional enzymes have been described to date. UbiB, an atypical protein kinase-like enzyme, has been proposed to mediate the extraction of UQ precursors from the membrane, thereby rendering them accessible to the soluble Ubi-complex. Here, we show that UbiB proteins fulfill an additional function in bacteria. Specifically, they contribute to the decarboxylation of UQ precursors through a mechanism that remains unknown but depends on ATP hydrolysis. Given that UbiB is conserved in all UQ-producing bacteria, it may represent a widespread decarboxylation system within this essential metabolic pathway.

biochemistry↗

bioRxiv2026

COCOA-Tree: Phylogenetic visualization and comparative analysis of coevolving residues

The evolutionary co-occurrence of amino acid changes between protein residues underlies key structural and functional properties of protein families. Building on these coevolutionary patterns, methods have been developed to identify groups of residues associated with enzyme functionalities, such as Statistical Coupling Analysis (SCA) or Specificity-Determining Position (SDP) methods. These methods and their variations differ in the metrics used to quantify coevolution, residues weighting schemes, and corrections introduced to mitigate noise and phylogenetic biases. Yet, systematic comparisons across methods are rarely performed, and the evolutionary origins of the coevolutionary patterns highlighted by each approach are seldom addressed, limiting our ability to disentangle functional from phylogenetic contributions. To address these issues, we introduce COCOA-Tree, a Python library for SCA-like dimensionality-reduction analyses. COCOA-Tree supports custom metrics and enables visualization of coevolutionary patterns on phylogenetic trees. We also provide guidance to map results onto 3D structures in PyMOL. Using COCOA-Tree, we reanalyze published datasets and uncover previously unnoticed evolutionary properties of groups of coevolving residues detected by SCA, known as sectors. In particular, in the well-studied S1A serine protease family, we show that two of the three known sectors exhibit qualitatively distinct levels of sequence conservation depending on the enzymatic functions and on the phylogenetic clades to which the proteins belong. We further show that different coevolution metrics often identify qualitatively distinct groups of coevolving residues, although they yield consistent results for mildly conserved residues. Finally, as an example of the versatility of COCOA-Tree, we provide an example of visualizing pairs of residues detected by Direct Coupling Analysis (DCA) methods on a phylogenetic tree, highlighting a rich diversity of co-evolutionary patterns. Overall, we expect COCOA-Tree to help identify residues that control protein function and thereby improve our capacity for functional engineering and our understanding of the principles governing protein evolution. COCOA-Tree website: https://tree-timc.github.io/cocoatree

bioinformatics↗

bioRxiv2025

Global distribution of isoprenoid quinones across Bacteria

Isoprenoid quinones represent a class of redox lipids involved in many critical cellular functions, including ATP synthesis through electron transport chains. They thus occupy a pivotal role in the bioenergetics of all three domains of life. The diversity of quinone types observed across microbial taxa has long supported their use as chemotaxonomic markers in microbial systematics. More recently, variations in quinone repertoires have been linked to metabolic adaptations and a novel quinone was discovered. Despite a revived interest in the role of quinones, a unified perspective on the distribution of quinones in Bacteria is currently lacking. In this study, quinone biosynthetic pathways were systematically annotated in 26,264 high quality genomes of bacterial species, and specific information on quinones produced by over 6,000 bacterial species was extracted by text mining the abstracts of thousands of articles. The results were mapped onto a phylogenetic tree, providing the most comprehensive overview of quinone distribution in Bacteria to date. This enabled us to highlight the surprisingly dynamic evolutionary history of the two menaquinone-producing pathways. Moreover, the identification and experimental validation of a deeply branching ubiquinone pathway in Desulfobacterota represents the first occurrence of such a pathway outside the Pseudomonadota and provides insights into the nature of the ancestral UQ pathway. The updated compendium of bacterial quinones is a valuable resource to facilitate the prediction of quinone structural features from genomic data, to establish correlations between quinone structures and cellular traits, and to explore the evolution of quinone repertoires in connection with the diversification of microbial metabolisms.

microbiology↗

bioRxiv2025

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes

Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive changes. These antagonistic properties make their overall impact on prokaryotic evolution difficult to grasp. Here, we address this challenge by leveraging the framework of transposon ecology to analyze IS occurrences across and within 30,499 prokaryotic genomes. Combining phylogenomics with multi-scale genomic analysis, quantitative ecology, and mathematical modeling, we provide evidence that although genomes generally provide sufficient resources for IS coexistence, universal mechanisms shape their occurrence and chromosomal distribution across genomes. These include: (i) the preferential localization of ISs within highly variable and GC-heterogeneous chromosomal regions of genomic plasticity (RGPs), which act as the primary reservoir of IS niches; (ii) a linear scaling between IS abundance and niche size, with an average of 5.4 additional accessible insertion sites per IS; (iii) a dependence of IS occurrence on the presence of other ISs, suggesting a form of group behavior; (iv) the accumulation of AT-rich sequences in both coding and non-coding regions up to 100 kb surrounding ISs, indicative of ecological isolation; and (v) the spatial partitioning of mobile genetic elements around ISs, reminiscent of ecological niche differentiation. Besides these general principles, we also uncover niche specificities associated with particular IS families, hinting at regulatory mechanisms that modulate IS activity. Altogether, this comprehensive transposon ecology approach offers new insights and avenues for understanding IS-host interactions and genome evolution, moving beyond traditional host-centric perspectives.

genomics↗

bioRxiv2024

A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism

The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic respiration and photosynthesis. The diversification of quinones, from low redox potential in anaerobes to HPQs in aerobes, is assumed to have followed Earths surface oxygenation [~]2.3 billion years ago. However, the evolutionary origins of HPQs remain unresolved. Here, we characterize the structure and biosynthetic pathway of a novel ancestral HPQ, methyl-plastoquinone, that is unique to bacteria of the phylum Nitrospirota. Methyl-plastoquinone is structurally related to the two previously known HPQs, plastoquinone from Cyanobacteriota/chloroplasts and ubiquinone from Pseudomonadota/mitochondria, respectively. We demonstrate a common origin of the three HPQ biosynthetic pathways that predates the emergence of Nitrospirota, Cyanobacteriota, and Pseudomonadota. An ancestral HPQ biosynthetic pathway evolved [≥] 3.4 billion years ago in an extinct lineage and was laterally transferred to these three phyla [~]2.5-3.2 billion years ago. We show that Cyanobacteriota and Pseudomonadota were ancestrally aerobic and thus propose that aerobic metabolism using HPQs significantly predates Earths surface oxygenation. Two of the three HPQ pathways were later obtained by eukaryotes through endosymbiosis forming chloroplasts and mitochondria, enabling their rise to dominance in modern oxic ecosystems. Significance statementOxygenic photosynthesis and aerobic respiration by bacteria and eukaryotes rely on respiratory quinones with high redox potential that facilitate membrane-bound electron transport. These quinones are integral to aerobic metabolism and therefore the evolution of aerobic metabolism and quinone biosynthesis must be intertwined. Only two types of high redox potential quinones have been described in bacteria and eukaryotes. Here, we describe the structure and biosynthetic pathway of a third type, methyl-plastoquinone, that is exclusive to bacteria of the phylum Nitrospirota. We then use phylogenetic analysis to show that the three high redox potential quinones have a single evolutionary origin and are much older than previously considered, predating the Great Oxygenation Event, when significant amounts of O2 first accumulated in the atmosphere.

microbiology↗

bioRxiv2023

Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2.

Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using the MacSyFinder program. This flexible computational tool uses the knowledge gathered from experimental studies to identify homologous systems in genome data. It can be used with a set of pre-defined MacSyFinder models--"TXSScan", to identify all major secretion systems of diderm bacteria (i.e., with inner and LPS-containing outer membranes) as well as evolutionarily related cell appendages (pili and flagella). For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. Finally, it checks if the clusters genetic content and genomic organization satisfy the constraints of the model. TXSScan models can be altered in the command line or customized to search for variants of known secretion systems. Models can also be built from scratch to identify novel systems. In this chapter, we describe a complete pipeline of analysis, starting from i) the integration of information from a reference set of experimentally studied systems, ii) the identification of conserved proteins and the construction of their HMM protein profiles, iii) the definition and optimization of "macsy-models", and iv) their use and online distribution as tools to search genomic data for secretion systems of interest. MacSyFinder is available here: https://github.com/gem-pasteur/macsyfinder, and MacSyFinder models here: https://github.com/macsy-models.

microbiology↗

bioRxiv2022

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.

bioinformatics↗

bioRxiv2020

Ancestral reconstructions decipher major adaptations of ammonia oxidizing archaea upon radiation into moderate terrestrial and marine environments

Unlike all other archaeal lineages, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaea are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here we reconstructed the genomic content and growth temperature of the ancestor of all AOA as well as the ancestors of the marine and soil lineages based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (I) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (II) an expansion of regulatory capacities in transcription and central metabolic functions and (III) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.

microbiology↗

bioRxiv2020

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored inhabitants, that seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Ca. Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of gene repair systems that may allow to overcome challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy limiting and high-pressure environment.

microbiology↗

bioRxiv2019

In situ growth of anammox bacteria in subseafloor sediments

The deep biosphere buried in marine sediments was estimated to host an equal number of microbes as found in the above oceans 1. It has been debated if these cells are alive and active 2, and their per cell energy availability does not seem to allow for net population growth 3. Here, we report the growth of anammox bacteria in [~]80,000 year old subsurface sediments indicated by their four orders of magnitude abundance increase in the nitrate-ammonia transition zone (NATZ). Their growth coincides with a local increase in anammox power supply. The genome of the dominant anammox bacterium from the NATZ was reconstructed and showed an increased index of replication confirming in situ active growth. The genome belongs to a new Scalindua species so far exclusively found in marine environments, which has the genetic capacity of urea and cyanate utilization and is enriched in genes allowing it to cope with external environmental stressors, such as energy limitation. Our results suggest that specific microbial groups are not only able to survive over geological timescales, but also thrive in the deep subsurface when encountering favorable conditions.

microbiology↗

bioRxiv2019

Diversification of the type IV filament super-family into machines for adhesion, secretion, DNA transformation and motility

Processes of molecular innovation require tinkering and co-option of existing genes. How this occurs in terms of molecular evolution at long evolutionary scales remains poorly understood. Here, we analyse the natural history of a vast group of membrane-associated molecular systems in Bacteria and Archaea - type IV filament super-family (TFF-SF) - that diversified in systems involved in flagellar or twitching motility, adhesion, protein secretion, and DNA natural transformation. We identified such systems in all phyla of the two domains of life, and their phylogeny suggests that they may have been present in the last universal common ancestor. From there, two lineages, a Bacterial and an Archaeal, diversified by multiple gene duplications of the ATPases, gene fission of the integral membrane platform, and accretion of novel components. Surprisingly, we find that the Tad systems originated from the inter-kingdom transfer from Archaea to Bacteria of a system resembling the Epd pilus. The phylogeny and content of ancestral systems suggest that initial bacterial pili were engaged in cell motility and/or DNA transformation. In contrast, specialized protein secretion systems arose much later, and several independent times, in natural history. All these processes of functional diversification were accompanied by genetic rearrangements with implications for genetic regulation and horizontal gene transfer: systems encoded in fewer loci were more frequently exchanged between taxa. Overall, the evolutionary history of the TFF-SF by itself provides an impressive catalogue of the variety of molecular mechanisms involved in the origins of novel functions by tinkering and co-option of cellular machineries.

evolutionary biology↗

bioRxiv2017

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome

Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first cultivated thermophilic representative with a sequenced genome, which allows to search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been cultivated from a hot spring in Ischia, Italy. It grows optimally at 68{degrees}C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 25h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase, genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

microbiology↗