Biology subjects

Yuan, J.

Publications and source records attributed to Yuan, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

An axonemal intron splicing program sustains Plasmodium male development

Differentiation of male gametocyte into flagellated fertile male gamete relies on the axoneme assembly, a major component of male development for mosquito transmission of malaria parasite. RNA-binding protein (RBP)-mediated post-transcription regulation plays important roles in eukaryotic sexual development, including the Plasmodium female development. However, the role of RBP in defining the Plasmodium male transcriptome and its function in the male gametogenesis remain elusive. Here, we screened the gender expression of the genome-wide RBPs and identified an undescribed male-specific RBP gene Rbpm1 in the Plasmodium. RBPm1 is localized in the nucleus of male gametocytes. RBPm1-deficient parasites fail to assemble the axoneme for male gametogenesis and thus mosquito transmission. RBPm1 interacts with spliceosome E complex and regulates splicing initiation of certain introns in a group of 26 axonemal genes. RBPm1 deficiency results in intron retention and protein loss of these axonemal genes. Intron deletion restores axonemal proteins expression and partially rectifies axonemal defects in RBPm1-null gametocytes. Further splicing assays in both reporter and endogenous genes exhibit stringent recognition of the axonemal introns by RBPm1. Therefore, the splicing activator RBPm1 and its target introns constitute an axonemal intron splicing program in the post-transcription regulation essential for Plasmodium male development.

microbiology↗

bioRxiv2023

Central pore-opening structure and gating of the mechanosensitive PIEZO1 channel

PIEZO1 is a mechanically activated cation channel that undergoes force-induced activation and inactivation to control diverse physiological processes1-4. However, the distinct functional states and gating transitions remain structurally undefined. In response to changes in membrane forces, PIEZO1 transitions from a curved to a flattened shape, which might lead to opening and subsequent inactivation of the ion-conducting pore5,6. Here we employed a PIEZO1 mutant to capture various conformational states including an intermediate state with an opened central pore, allowing us to reveal the gating dynamics of this multiple-gate system. Upon transition from the curved to the partially flattened intermediate state, the trimeric cap undergoes a downward and rotational motion to open the lateral cap-gate, while the loop that connects the cap to the pore-lining inner helix acts as a spring-linker, switching from an extended to a compressed state. Along with the partial flattening of the peripheral blades, these conformational changes collectively dilate the cap-gate, spring-gate and the hydrophobic transmembrane-gate, leading to ion permeation through the transmembrane pore. Upon inactivation, while the blades remain flattened, the cap and spring-linker return to an up and extended state. Molecular dynamics simulations verify the ion-permeating pathway and the distinct ion-conducting states of the assigned close, intermediate, open, and inactivated structures. Mutagenesis and electrophysiological characterizations reveal that domains and residues involved in conformational dynamics of the cap and spring-linker are critical for mechanical activation of PIEZO1. Together, these studies have structurally defined the distinct functional states and the curvature-based activation and inactivation mechanisms of PIEZO1.

neuroscience↗

bioRxiv2023

Potassium-mediated bacterial chemotactic response

Bacteria in biofilms secrete potassium ions to attract free swimming cells. However, the basis of chemotaxis to potassium remains poorly understood. Here, using a microfluidic device, we found that Escherichia coli can rapidly accumulate in regions of high potassium concentration on the order of millimoles. Using a bead assay, we measured the dynamic response of individual flagellar motors to stepwise changes in potassium concentration, finding that the response resulted from the chemotaxis signaling pathway instead of the motor response to changes in the proton motive force (PMF). To characterize the chemotactic response to potassium, we exposed the bacteria to a range of potassium concentrations and measured the dose-response curve and adaptation kinetics via a FRET assay, finding that the chemotaxis pathway exhibited a sensitive response and fast adaptation to potassium. We further found that the two major chemoreceptors Tar and Tsr respond differently to potassium. Tar receptors exhibit a biphasic response, whereas Tsr receptors respond to potassium as an attractant. These different responses were consistent with the responses of the two receptors to intracellular pH changes. Therefore, bacteria may sense the change in potassium concentration by sensing the change in intracellular pH. The sensitive response and fast adaptation allow bacteria to sense and localize small changes in potassium concentration. As the ratio of the two major chemoreceptors changes with bacterial growth stages, the differential responses of Tar and Tsr receptors to potassium suggest that cells at different growth stages respond differently to potassium and may have different requirements for potassium.

biophysics↗

bioRxiv2023

Monitoring integrated stress response in live Drosophila

Cells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, our understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder our ability to track and manipulate the ISR in vivo. To overcome these limitations, we have successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables us to label Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff - a characteristic feature of the ISR and viral infections. Through this methodology, we have unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of our reporter, we have engineered ISR-null eIF2S50A mutant flies for stress response analysis. Our results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms.

developmental biology↗

bioRxiv2023

Systems engineering of Saccharomyces cerevisiae for synthesis and accumulation of vanillin

Vanillin represents one of the most widely used flavoring agents in the world. However, microbial synthesis of vanillin is hindered by the host native metabolism that could rapidly degrade vanillin to the byproducts. Here, we report that the industrial workhorse Saccharomyces cerevisiae was engineered by systematic deletion of oxidoreductases to improve the vanillin accumulation. Subsequently, we harnessed the reduced aromatic aldehyde reduction (RARE) yeast platform for de novo synthesis of vanillin from glucose. We investigated multiple coenzyme-A free pathways to improve vanillin production in yeast. The vanillin productivity in yeast was further enhanced by systems engineering to optimize the supply of cofactors (NADPH and S-adenosylmethionine) together with metabolic reconfiguration of yeast central metabolism. The final yeast strain with overall 24 genetic modifications produced 365.55 {+/-} 7.42 mg L-1 under shake-flasks, which represents the highest vanillin titer from glucose achieved to date. Taken together, our work lays a foundation for the future implementation of vanillin production from glucose in budding yeast. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/545388v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@19c47dcorg.highwire.dtl.DTLVardef@131eb80org.highwire.dtl.DTLVardef@5c5a8forg.highwire.dtl.DTLVardef@13d6485_HPS_FORMAT_FIGEXP M_FIG TOC C_FIG

bioengineering↗

bioRxiv2023

Rotten to the core - a neurofunctional signature of subjective core disgust generalizes to socio-moral contexts

While disgust originates in the hard-wired mammalian distaste response, the conscious experience of disgust in humans strongly depends on subjective appraisal and may even extend to sociomoral contexts. In a series of studies, we combined functional magnetic resonance imaging (fMRI) with machine-learning based predictive modeling to establish a comprehensive neurobiological model of subjective disgust. The developed neurofunctional signature accurately predicted momentary self-reported subjective disgust across discovery (n=78) and pre-registered validation (n=30) cohorts and generalized across core disgust (n=34 and n=26), gustatory distaste (n=30), and sociomoral (unfair offers; n=43) contexts. Disgust experience was encoded in distributed cortical and subcortical systems, and exhibited distinct and shared neural representations with subjective fear or negative affect in interoceptive-emotional awareness and conscious appraisal systems while the signatures most accurately predicted the respective target experience. We provide an accurate fMRI-signature for disgust with a high potential to resolve ongoing evolutionary debates.

neuroscience↗

bioRxiv2023

Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis

We present the DRAGEN somatic pipeline for calling small somatic variants from tumor samples, with or without paired normal samples. The DRAGEN somatic variant caller offers 1) a flexible architecture that can be used on a wide array of somatic use cases; 2) built-in noise models enabling robustness against various sources of noise artifacts (mapping, genome context, or sample specific); 3) performance of joint analysis of tumor and normal samples in the case of a tumor-normal workflow yielding improved accuracy; 4) benefits from FPGA acceleration for efficient run time. We demonstrate the speed and accuracy of the DRAGEN tumor-normal pipeline across a range of whole genome sequencing (WGS) datasets and compare against third party tools such as Mutect2/GATK4 [1] and Strelka2 [2]. DRAGEN secondary analysis outperforms all other tools with its ability to complete a 110x/40x T/N whole-genome analysis in less than two hours. It offers exceptional accuracy, with higher sensitivity and precision than third party tools. We also show that the DRAGEN T/N workflow supports analysis of liquid and late-stage solid tumors by tolerating tumor-in-normal (TiN) contamination.

bioinformatics↗

bioRxiv2023

Phytochrome higher order mutants reveal a complex set of light responses in the moss Physcomitrium patens

O_LIPhytochromes are photoreceptors enabling plants to respond to various light conditions. Independent gene duplication events resulted in small phytochrome gene families in mosses, ferns, and seed plants. This phytochrome diversity is hypothesised to be critical for sensing and adapting to different light conditions, but experimental evidence for this idea is lacking for mosses and ferns. C_LIO_LIThe model moss species Physcomitrium patens contains seven phytochromes grouped into three clades, PHY1/3, PHY2/4, and PHY5. Here, we used CRISPR/Cas9 generated single and higher order mutants to investigate their role in light-regulation of protonema and gametophore growth, protonema branching, and induction of gametophores. C_LIO_LIWe found both specific and partially overlapping roles for the three clades of moss phytochromes in regulating these responses in different light conditions, and we identified a mechanism for sensing simulated canopy shade different from the mechanism in seed plants. PHY1/3 clade phytochromes act as primary far-red light receptors, while PHY5 clade phytochromes are the primary red light receptors. PHY2/4 clade phytochromes have functions in both red and far-red light. C_LIO_LISimilar to seed plants, gene duplication events in the phytochrome lineage in mosses were followed by functional diversification into red and far-red light sensing phytochromes. C_LI

plant biology↗

bioRxiv2023

EB1 decoration of microtubule lattice facilitates spindle-kinetochore lateral attachment in Plasmodium male gametogenesis

Faithful chromosome segregation of 8 duplicated haploid genomes into 8 daughter male gametes is essential for male gametogenesis and mosquito transmission of Plasmodium. Plasmodium evolves the endomitosis for this multinucleated cell division. However, the mechanism underlying the spindle-kinetochore attachment remains elusive. End-binding proteins (EBs) are the conserved microtubule (MT) plus-end binding proteins and play an important role in regulating MT plus-end dynamics. Here we report that Plasmodium EB1 is a unique orthologue distinct from the canonical eukaryotic EB1. Both in vitro and in vivo assays revealed that Plasmodium EB1 lost MT plus-end tracking but gained MT-lattice affinity. This MT-binding feature of EB1 is contributed by both the CH domain and the linker region. EB1-deficient parasites produce male gametocytes that develop to the anucleated male gametes, leading to defective mosquito transmission of parasite. EB1 is localized at the nucleoplasm of male gametocytes. Upon gametogenesis, EB1 decorates the full-length of spindle MTs and regulates spindle structure. The kinetochores attach to spindle MTs laterally throughout three rounds of endomitosis and this attachment is EB1-dependent. Consequently, impaired spindle-kinetochore attachment was observed in EB1-deficient parasites. These results indicate that a parasite-specific EB1 with MT-lattice affinity has evolved to fulfill the spindle-kinetochore lateral attachment in male gametogenesis.

microbiology↗

bioRxiv2022

The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensing

A large number of small membrane proteins have been discovered in bacteria, but their mechanism of action has remained mostly elusive. Here, we investigate the mechanism of a physiologically important small protein, MgrB, which represses the activity of the sensor kinase PhoQ and is widely distributed among enterobacteria. The PhoQ/PhoP two-component system is a master regulator of the bacterial virulence program and interacts with MgrB to modulate bacterial virulence, fitness, and drug resistance. A combination of crosslinking approaches with functional assays and protein dynamic simulations revealed structural rearrangements due to interactions between MgrB and PhoQ near the membrane/periplasm interface and along the transmembrane helices. These interactions induce the movement of the PhoQ catalytic domain and the repression of its activity. Without MgrB, PhoQ appears to be much less sensitive to antimicrobial peptides, including the commonly used C18G. In the presence of MgrB, C18G promotes MgrB to dissociate from PhoQ, thus activating PhoQ via derepression. Our findings reveal the inhibitory mechanism of the small protein MgrB and uncover its importance in antimicrobial peptide sensing. Significance StatementSmall proteins have high prevalence, vast diversity, and primarily regulatory functions in biological processes across all domains of life. However, their mechanisms of action remain largely elusive. In this study, we investigate the mechanism of the small protein, MgrB. It interacts with the sensor kinase PhoQ, rearranges its conformation, represses its kinase activity, and regulates bacterial response to environmental changes. In particular for antimicrobial peptides, MgrB is required for bacteria to have a selective response to this host-exclusive stimulus. Our findings underline the importance of a small protein in bacterial fitness and drug resistance and provide a molecular basis for engineering novel peptide-based regulators.

microbiology↗

bioRxiv2022

Harnessing photosynthetic bacterium for light-powered biocatalysis

The traditional whole-cell biocatalysis typically utilizes the heterotrophic microbes as the biocatalyst, which requires carbohydrates to power the cofactor (ATP, NAD(P)H) regeneration. In this study, we sought to harness purple non-sulfur photosynthetic bacterium (PNSB) as the biocatalyst to achieve light-driven cofactor regeneration for cascade biocatalysis. We substantially improved the performance of PNSB-based biocatalysis by using a highly active and conditional expression system, blocking the side-reactions, controlling the feeding strategy, and attenuating the light shading effect. We found that 50 mM ferulic acid could be completely converted to vanillyl alcohol in the recombinant strain, reaching 7.7 g/L vanillyl alcohol. In addition, >99.9% conversion of p-coumaric acid to p-hydroxybenzoic alcohol (6.21 g/L) was similarly achieved under light-anaerobic conditions. Moreover, we examined the isoprenol utilization pathway (IUP) for pinene synthesis and 13.81 mM pinene (1.88 g/L) with 92.1% conversion rate from isoprenol was obtained. Taken together, these results suggested that PNSB could be a promising host for light-powered biotransformation, which offers an efficient approach for synthesizing value-added chemicals in a green and sustainable manner.

synthetic biology↗

bioRxiv2022

eEF2 improves dense connective tissue repair and healing outcome by regulating cellular death, autophagy, apoptosis, proliferation and migration

Outcomes following human dense connective tissue (DCT) repair are often variable and suboptimal, resulting in compromised function and development of chronic painful degenerative diseases. Moreover, biomarkers and mechanisms that guide good clinical outcomes after DCT injuries are mostly unknown. Here, we characterize the proteomic landscape of DCT repair following human tendon rupture and its association with long-term patient-reported outcome. Moreover, the regulatory mechanisms of relevant biomarkers were assessed partly by gene silencing experiments. A Mass-Spectrometry based proteomic approach quantified a large number (769) of proteins, including 51 differentially expressed proteins among 20 good versus 20 poor outcome patients. A novel biomarker, elongation factor-2 (eEF2) was identified as being strongly prognostic of the 1-year clinical outcome. Further bioinformatic and experimental investigation revealed that eEF2 positively regulated autophagy, cell proliferation and migration, as well as reduced cell death and apoptosis, leading to improved DCT repair and outcomes. Findings of eEF2 as novel prognostic biomarker could pave the way for new targeted treatments to improve healing outcomes after DCT injuries.

cell biology↗

bioRxiv2022

Accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features

The three-dimensional (3D) genome organization influences diverse nuclear processes. Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and Hi-C are powerful methods to study the 3D genome organization. However, ChIA-PET and Hi-C experiments are expensive, time-consuming, require tens to hundreds of millions of cells, and are challenging to optimize and analyze. Predicting ChIA-PET/Hi-C data using cheaper ChIP-Seq data and other easily obtainable features could be a useful alternative. It is well-established that the cohesin protein complex is a key determinant of 3D genome organization. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks (DNN), random forest, and gradient boosting, respectively, to predict cohesin-mediated chromatin interaction strength between any two loci in the genome. Comprehensive tests on four cell lines show that the predictions of ChIPr correlate well with the original ChIA-PET data at the peak-level resolution and bin sizes of 25 and 5 Kbp. In addition, ChIPr can accurately capture most of the cell-type-dependent loops identified by ChIA-PET and Hi-C data. Rigorous feature testing indicated that genomic distance and RAD21 (a cohesin component) ChIP-Seq signals are the most important inputs for ChIPr in determining chromatin interaction strength. The standard ChIPr model requires three experimental inputs: ChIP-Seq signals for RAD21, H3K27ac (enhancer/active chromatin mark) and H3K27me3 (inactive chromatin mark). The minimal ChIPr model performs comparably and requires a single experimental input: ChIP-Seq signals for RAD21. Integrative analysis revealed novel insights into the role of CTCF motif, its orientation, and CTCF binding on the prevalence and strength of cohesin-mediated chromatin interactions. These studies outline the general features of genome folding and open new avenues to analyze spatial genome organization in specimens with limited cell numbers.

genomics↗

bioRxiv2022

Using deep convolutional neural networks to test why human face recognition works the way it does

Human face recognition is highly accurate, and exhibits a number of distinctive and well documented behavioral "signatures" such as the use of a characteristic representational space, the disproportionate performance cost when stimuli are presented upside down, and the drop in accuracy for faces from races the participant is less familiar with. These and other phenomena have long been taken as evidence that face recognition is "special". But why does human face perception exhibit these properties in the first place? Here we use deep convolutional neural networks (CNNs) to test the hypothesis that all of these signatures of human face perception result from optimization for the task of face recognition. Indeed, as predicted by this hypothesis, these phenomena are all found in CNNs trained on face recognition, but not in CNNs trained on object recognition, even when additionally trained to detect faces while matching the amount of face experience. To test whether these signatures are in principle specific to faces, we optimized a CNN on car discrimination and tested it on upright and inverted car images. As for face perception, the car-trained network showed a drop in performance for inverted versus upright cars. Similarly, CNNs trained only on inverted faces produce an inverted inversion effect. These findings show that the behavioral signatures of human face perception reflect and are well explained as the result of optimization for the task of face recognition, and that the nature of the computations underlying this task may not be so "special" after all. Significance StatementFor decades, cognitive scientists have collected and characterized behavioral signatures of face recognition. Here we move beyond the mere curation of behavioral phenomena to asking why the human face system works the way it does. We find that many classic signatures of human face perception emerge spontaneously in CNNs trained on face discrimination, but not in CNNs trained on object classification (or on both object classification and face detection), suggesting that these long-documented properties of the human face perception system reflect optimizations for face recognition per se, not by-products of a generic visual categorization system. This work further illustrates how CNN models can be synergistically linked to classic behavioral findings in vision research, thereby providing psychological insights into human perception.

neuroscience↗

bioRxiv2022

Germline determinants of the prostate tumor genome

A persons germline genome strongly influences their risk of developing cancer. Yet the molecular mechanisms linking the host genome to the specific somatic molecular phenotypes of individual cancers are largely unknown. We quantified the relationships between germline polymorphisms and somatic mutational features in prostate cancer. Across 1,991 prostate tumors, we identified 23 co-occurring germline and somatic events in close 2D or 3D spatial genomic proximity, affecting 10 cancer driver genes. These driver quantitative trait loci (dQTLs) overlap active regulatory regions, and shape the tumor epigenome, transcriptome and proteome. Some dQTLs are active in multiple cancer types, and information content analyses imply hundreds of undiscovered dQTLs. Specific dQTLs explain at least 16.7% ancestry-biases in rates of TMPRSS2-ERG gene fusions and 67.3% of ancestry-biases in rates of FOXA1 point mutations. These data reveal extensive influences of common germline variation on somatic mutational landscapes.

cancer biology↗

bioRxiv2022

Enhanced protein synthesis is a defining requirement for neonatal B cell development

The LIN28B RNA binding protein exhibits a ontogenically restricted expression pattern and is a key molecular regulator of fetal and neonatal B lymphopoiesis. It enhances the positive selection of CD5+ immature B cells early in life through amplifying the CD19/PI3K/c-MYC pathway and is sufficient to reinitiate self-reactive B-1a cell output when ectopically expressed in the adult. In this study, interactome analysis in primary B cell precursors showed direct binding by LIN28B to numerous ribosomal protein transcripts, consistent with a regulatory role in cellular protein synthesis. Induction of LIN28B expression in the adult setting is sufficient to promote enhanced protein synthesis during the small Pre-B and immature B cell stages, but not during the Pro-B cell stage. This stage dependent effect was dictated by IL-7 mediated signaling, which masked the impact of LIN28B through an overpowering stimulation on the c-MYC / protein synthesis axis in Pro-B cells. Importantly, elevated protein synthesis was a distinguishing feature between neonatal and adult B cell development that was critically supported by endogenous Lin28b expression early in life. Finally, we used a ribosomal hypomorphic mouse model to demonstrate that subdued protein synthesis is specifically detrimental for neonatal B lymphopoiesis and the output of B-1a cells, without affecting B cell development in the adult. Taken together, we identify elevated protein synthesis as a defining requirement for early-life B cell development that critically depends on Lin28b. Our findings offer new mechanistic insights into the layered formation of the complex adult B cell repertoire.

immunology↗

bioRxiv2022

Differential bending stiffness of the bacterial flagellar hook under counterclockwise and clockwise rotations

The bacterial hook, as a universal joint coupling rotation of the flagellar motor and the filament, is an important component of the flagellum that propels the bacteria to swim. The mechanical properties of the hook are essential for the flagellum to achieve normal functions. In multi-flagellated bacteria such as Escherichia coli, the hook must be compliant so that it can bend for the filaments to form a coherently rotating bundle to generate the thrust when the motor rotates counterclockwise (CCW), yet it also must be rigid so that the bundle can disrupt for the bacteria to tumble to change swimming direction when the motor rotates clockwise (CW). Here, by combining an elastic rod model with high-resolution bead assay to accurately measure the bending stiffness of the hook under CCW or CW rotation in vivo, we elucidate how the hook accomplishes this dual functionality: the hook stiffens under CW rotation, with bending stiffness under CW rotation twice as large as that under CCW rotation. This enables a robust run-and-tumble swimming motility for multi-flagellated bacteria.

biophysics↗

bioRxiv2022

CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter

Candidatus Accumulibacter is a key genus of polyphosphate-accumulating organisms (PAOs) found in laboratory- and full-scale wastewater treatment systems, mediating enhanced biological phosphorus removal (EBPR). However, little is known about their ability to resist phage infection. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in diverse Ca. Accumulibacter taxa (43 in total, including 10 newly recovered genomes). Fourty complete CRISPR loci were identified in 28 genomes, falling into 6 subtypes. The occurrence and distribution of CRISPR-Cas systems did not follow a vertical evolutionary relationship. Phylogenetic analyses of the cas genes and direct repeats (DRs) suggested that the CRISPR-Cas systems were likely acquired via horizontal gene transfer, with acquisition rates higher than those of speciation, rendering different Ca. Accumulibacter distinct adaptivity to phage predations. 2448 spacers were identified, 67 of them matched to known phages. Major differences were observed among the numbers of spacers for different Ca. Accumulibacter, showing unique phages that could be resisted by different members. A comparison of the spacers in genomes having the same cas gene but from distinct geographical locations indicated that habitat isolation may have resulted in the acquisition of different spacers by different Ca. Accumulibacter. Metagenomic analysis allowed the identification of 26 viral contigs (18 are Caudovirales members) in 6 metagenomic datasets from three lab-scale enrichment reactors, matching to 73 spacers in 10 Ca. Accumulibacter genomes in these reactors, showing the specific immunity of these Ca. Accumulibacter. Metatranscriptomic analyses showed the activity of the CRISPR-Cas system under both anaerobic and aerobic conditions. Extra efforts were made to identify prophages in Ca. Accumulibacter genomes. In total, 133 prophage regions were identified. Twenty-seven of them were classified as potentially active prophages. Three prophages (all are Caudovirales members, in DS2011, SCELSE-7IIH and SCELSE-5IIH, respectively) are readily activable. Differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to their distinct responses under phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages with combined experimental and bioinformatic methods in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.

bioinformatics↗