Biology subjects

Monk, J.

Publications and source records attributed to Monk, J..

At least 19 recordsLinked to original sources

bioRxiv2026

DISRUPTION OF A DNA REPAIR PROTEIN PROMOTES ANTIBIOTIC RESISTANCE IN ACINETOBACTER BAUMANNII

Acinetobacter baumannii is a high priority Gram negative opportunistic pathogen known for its high rates of multidrug resistance (MDR). Minocycline (MIN), a tetracycline class antibiotic, is one of the most effective antibiotics for treating A. baumannii infections in patients. Unfortunately, MIN resistance is spreading internationally and has begun to emerge in the United States. While efflux pumps are correlated with MIN resistant A. baumannii, clinical data suggests alternative mechanisms of MIN resistance. To explore the genetic basis for MIN resistance in A. baumannii we employed a machine learning model to predict genetic resistance correlates from clinical isolates. Mutations in ruvB, a DNA repair protein, were strongly correlated with MIN resistant clinical strains of A. baumannii .Consistent with the prediction, tn26 insertion in ruvB in A. baumannii strain AB5075, and deletion of ruvB in strain ATCC 19606, increased MIN minimum inhibitory concentrations to a level that exceeds the MIN resistance breakpoint. RuvB complexes with RuvA and RuvC to resolve Holliday junctions during recombination. However, only ruvB mutants showed the resistance phenotype; neither ruvA nor ruvC mutants were MIN resistant, suggesting loss of the activity of the complex was not the basis for resistance. We observed ruvB mutants produced increased biomass during planktonic growth relative to the other two ruv mutants. Upon examination, the ruvB::tn26 mutant had a 451% increase in biomass and 360% thicker biofilms relative to wildtype. We determined the disruption of ruvB lead to thicker biofilms and enriched in extracellular DNA (eDNA), and DNase I treatment collapsed the enhanced biofilm phenotype and markedly reduced tetracycline class MICs. FLAG-RuvA accumulated within the biofilm matrix in the absence of RuvB, supporting a model in which RuvA contributes to stabilization of eDNA-rich structures. In a murine pneumonia model, ruvB disruption did not significantly alter survival or pulmonary burden in untreated infection but reduced bacterial dissemination and increased minocycline resistance. Together, these findings reveal an unexpected connection between Holliday junction processing, eDNA-rich biofilm architecture, and antibiotic resistance in A. baumannii.

microbiology↗

bioRxiv2026

Pangenomic decomposition reveals lineage-specific immune-evasion and virulence architectures in group A Streptococcus

Streptococcus pyogenes (group A Streptococcus, GAS) causes over 700 million infections annually and has resurged globally as a cause of invasive disease. However, the genomic basis by which distinct GAS lineages produce diverse clinical phenotypes remains incompletely understood. Here, we analyzed 399 quality-controlled complete genomes spanning 103 emm types and 27 countries and applied non-negative matrix factorization (NMF) to decompose the GAS pangenome into co-inherited gene modules capturing both clonal lineages and mobile elements. This framework revealed that the deepest division in the accessory genome is not defined by emm type, but by a 27-gene Sda-1-encoding prophage linked to the hypervirulent M1T1 pandemic clone. This NET-degrading module unites emm1, emm12, and emm77 lineages, including fixation in emm77/ST63, extending its distribution beyond classically invasive lineages. Across lineages, virulence determinants segregate into distinct combinations, indicating that invasive disease arises through convergent but mechanistically distinct programs. Consistent with this, highly invasive ST52-emm28 lacks Sda1 and deploys an alternative repertoire. The decomposition also resolves a gene module corresponding to the emm-pattern D regulon associated with skin tropism, linking accessory genome structure to host niche adaptation. We further identify three sequence-divergent speC paralogs on independent prophages. These findings define modular GAS virulence architectures and establish NMF-based pangenome analysis as a framework for genomic surveillance beyond single-locus typing. ImportanceGroup A Streptococcus causes diseases ranging from strep throat to life-threatening flesh-eating infections, with severe cases increasing in recent years and no vaccine currently available. The species is conventionally classified by its M protein gene, but this single-locus system does not capture the extensive genomic diversity driven by prophages that transfer toxin and immune-evasion genes between bacterial lineages. Here, we applied unsupervised machine learning to decompose the pangenome of nearly 400 complete genomes into modules of co-inherited genes. We find that the deepest division among lineages is determined by a prophage carrying a gene that enables evasion of neutrophil extracellular traps, and identify this module at fixation in a lineage not previously known to carry it. We also show that a key toxin gene exists as three independently evolved variants on distinct prophages, and that invasive lineages deploy distinct combinations of virulence factors. This framework enables genomic surveillance based on virulence architecture rather than single-gene typing.

microbiology↗

bioRxiv2026

Functional brain network correlates of pubertal timing and depressive symptoms in preadolescence

BACKGROUNDVariation in pubertal maturation relative to same-age, same-sex peers (pubertal timing) has been linked to increased risk for depressive symptoms during adolescence. This developmental period is also characterized by substantial reorganization of functional brain networks. However, how pubertal timing relates to resting-state functional connectivity (rsFC) changes and depression risk remains unclear. METHODSWe examined pubertal timing and rsFC associations in preadolescents aged 9-11 years from the Adolescent Brain Cognitive Development (ABCD) Study. Pubertal timing was estimated using a puberty age gap approach based on parent-reported physical development. Linear mixed-effects and Bayesian multilevel models were used to assess cross-sectional and longitudinal associations between pubertal timing and rsFC across large-scale functional brain networks. We also tested whether rsFC differences explained associations between pubertal timing and later depressive symptoms. RESULTSEarlier pubertal timing was associated with heterogeneous rsFC patterns, with stronger and more widespread effects in females. In females, earlier pubertal timing was associated with rsFC increases and decreases across sensory-motor and association networks, whereas in males, associations were more limited and localized to sensorimotor and cerebellar systems. Longitudinally, earlier pubertal timing in females predicted reductions in rsFC at the 2-year follow-up, with no significant associations in males. rsFC differences did not explain the pubertal timing and later depressive symptoms association. CONCLUSIONSPubertal timing is associated with sex-specific patterns of brain functional connectivity during early adolescence, with greater heterogeneity and broader network involvement in females. These findings suggest that pubertal maturation contributes to early reorganization of functional brain networks, although these changes did not explain subsequent depressive symptoms.

neuroscience↗

bioRxiv2026

The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

Enterococci are Gram-positive opportunistic pathogens responsible for a wide range of nosocomial infections. One enterococcocal species, Enterococcus faecium, is steadily increasing in prevalence and has been listed among major multidrug-resistant ESKAPE pathogens. To gain systems-level insights into its metabolism and support discovery of potential therapeutic targets, we constructed iDR478, a comprehensive manually curated genome-scale metabolic model (GEM) to serve as a digital twin for E. faecium TX0016 (strain DO). The reconstruction was based on extensive homology searches and literature evidence, and further refined and gap-filled through experimental validation. Phenotypic profiling using Biolog microarrays enabled assessment of carbon source utilization, while amino acid leave-out growth assays allowed the evaluation of auxotrophies. The final refined model accurately predicted 100% of amino acid auxotrophies and 85% of growth on sole carbon sources. Discrepancies between model predictions and experimental phenotypes identified specific knowledge gaps across metabolic pathways, including unresolved carbon source utilization phenotypes, e.g., psicose, sorbitol, and palatinose utilization. Those gaps will guide future experimental characterization. Additionally, we conducted gene essentiality analysis to evaluate the predictive capacity of iDR478. Since no experimental gene essentiality data are currently available for E. faecium, model predictions were compared against Tn-seq experimental results from E. faecalis MMH594. Under simulated unconstrained uptake conditions, iDR478 achieved 84.2% concordance with the experimental essentiality results of E. faecalis MMH594. iDR478 thus provides a framework for studying E. faecium, offers insights into its metabolic network, and serves as a source for guiding future research and identification of therapeutic targets.

systems biology↗

bioRxiv2026

Parallel processing chains span cytoarchitectures to organize association cortex

Task fMRI1 and electrophysiology2 have revealed distributed, linked cortical patches with shared category preferences (e.g., faces, objects, places)1,3-5, smaller than cytoarchitectonic areas. Resting-state functional connectivity (RSFC) similarly showed that somato-cognitive action network (SCAN) nodes interleave with effectors (foot, hand, mouth), subdividing the precentral gyrus6. Here, using multiple precision functional mapping (PFM) modalities (RSFC, task, lags), we discovered that most of association cortex is organized like face processing and SCAN, with small, discrete patches interconnected into chains. Such patch-chains densely tile prefrontal cortex but are largely absent from primary cortex. Cortico-striatal connectivity is organized such that patches of the same chain connect to the same striatal location. Within chains, infra-slow fMRI signals are ordered in time. RSFC-defined chains align with task fMRI localizers (e.g., visual, motor, pain). Chains are absent at birth and emerge in the first year of life, suggesting their formation is at least partially experience-driven. Cytoarchitectonic areas are subdivided by patches, and patches in the same chain are distributed across different cytoarchitectures. Chains represent parallel ordered processing streams that are separated by information domain and behavioral goals, not cytoarchitectonics. Functional subdivision of architectonics into smaller patches, interlinked to form cross-architecture chains, enable greater parallelization and flexible specialization of processing.

neuroscience↗

bioRxiv2026

A Clinically Silent Resistance Phenotype That Promotes Acinetobacter baumannii Survival During Colistin Therapy

Acinetobacter baumannii is a major cause of multidrug-resistant nosocomial infections, particularly ventilator-associated pneumonia, for which therapeutic options are increasingly limited. Colistin, a polymyxin antibiotic, is a drug of last resort for A. baumannii, boasting high susceptibility rates. Yet, despite relatively low rates of breakpoint-defined colistin resistance, clinical outcomes are highly variable, and the bacterial strategies that enable survival during colistin therapy remain poorly understood. Here, we integrate supervised machine-learning-guided genomic prioritization with functional, physiological, and in vivo analyses to interrogate the genetic basis of colistin response in A. baumannii. Machine-learning analysis of clinical isolates identified candidate loci associated with colistin survival, many of which did not alter minimum inhibitory concentration (MIC) when disrupted. Instead, growth-dynamic assays uncovered a subset of mutants capable of maintaining fitness upon inhibitory colistin exposure despite classification as susceptible via standardized antibiotic susceptibility testing. We define this phenotype as clinically silent resistance (CSR), a genetically encoded, MIC-independent survival state. Using a murine pneumonia model, we further demonstrate that CSR mutants thrive during colistin therapy in vivo. Together, these findings reveal a hidden layer of colistin survival that is not captured by standard susceptibility testing and highlight fundamental limitations of breakpoint-centric paradigms for predicting treatment outcomes in A. baumannii.

microbiology↗

bioRxiv2025

Patterns of brain-wide associations reflect socioeconomics

Previous brain-wide association studies (BWAS) cross-sectionally linked a specific behavioral trait, most commonly IQ or psychopathology, to variation in brain function or structure. Here, we expanded the focus of BWAS from effect sizes to interpretability and generalizability by mapping 649 variables to brain function and structure. We compared the resultant BWAS maps to other types of brain data to annotate the BWAS patterns. Socioeconomic status (SES) -- not IQ or psychopathology -- showed the strongest associations with both resting-state functional connectivity (RSFC) and cortical thickness in the Adolescent Brain Cognitive Development (ABCD) Study. A principal exposome brain pattern, anchored to sensory and motor cortex, captured 34% of the variance across all BWAS maps. This exposome pattern was strongly correlated with the SES and IQ BWAS maps and non-BWAS maps of sleep (EEG), norepinephrine (PET), and stimulants (drug trial), but not cognitive activation maps (task fMRI). Adjusting for SES, reduced brain-IQ associations by 40%. Brain with IQ associations did not generalize, as they could no longer be detected in subsamples drawn from only higher SES backgrounds, while brain with SES associations remained strong in higher-IQ-only subsamples. These findings reveal SES as the principal axis of population-level brain variation, possibly stemming from the sleep deprivation and heightened stress associated with lower SES, since socioeconomics can only indirectly affect the brain.

neuroscience↗

bioRxiv2025

Stimulant medications affect arousal and reward, not attention

Prescription stimulants such as methylphenidate are being used by an increasing portion of the population, primarily children. These potent norepinephrine and dopamine reuptake inhibitors promote wakefulness, suppress appetite, enhance physical performance, and are purported to increase attentional abilities. Prior functional magnetic resonance imaging (fMRI) studies have yielded conflicting results about the effects of stimulants on the brains attention, action/motor, and salience regions that are difficult to reconcile with their proposed attentional effects. Here, we utilized resting-state fMRI (rs-fMRI) data from the large Adolescent Brain Cognitive Development (ABCD) Study to understand the effects of stimulants on brain functional connectivity (FC) in children (n = 11,875; 8-11 years old) using network level analysis (NLA). We validated these brain-wide association study (BWAS) findings in a controlled, precision imaging drug trial (PIDT) with highly-sampled (165-210 minutes) healthy adults receiving high-dose methylphenidate (Ritalin, 40 mg). In both studies, stimulants were associated with altered FC in action and motor regions, matching patterns of norepinephrine transporter expression. Connectivity was also changed in the salience (SAL) and parietal memory networks (PMN), which are important for reward-motivated learning and closely linked to dopamine, but not the brains attention systems (e.g. dorsal attention network, DAN). Stimulant-related differences in FC closely matched the rs-fMRI pattern of getting enough sleep, as well as EEG- and respiration-derived brain maps of arousal. Taking stimulants rescued the effects of sleep deprivation on brain connectivity and school grades. The combined noradrenergic and dopaminergic effects of stimulants may drive brain organization towards a more wakeful and rewarded configuration, explaining improved task effort and persistence without direct effects on attention networks.

neuroscience↗

bioRxiv2024

Brain functional connectivity, but not neuroanatomy, captures the interrelationship between sex and gender in preadolescents

Understanding sex differences in the adolescent brain is crucial, as these differences are linked to neurological and psychiatric conditions that vary between males and females. Predicting sex from adolescent brain data may offer valuable insights into how these variations shape neurodevelopment. Recently, attention has shifted toward exploring socially-identified gender, distinct from sex assigned at birth, recognizing its additional explanatory power. This study evaluates whether resting-state functional connectivity (rsFC) or cortical thickness more effectively predicts sex and sex/gender alignment (the congruence between sex and gender) and investigates their interrelationship in preadolescents. Using data from the Adolescent Brain Cognitive Development (ABCD) Study, we employed machine learning to predict both sex (assigned at birth) and sex/gender alignment from rsFC and cortical thickness. rsFC predicted sex with significantly higher accuracy (86%) than cortical thickness (75%) and combining both did not improve the rsFC models accuracy. Brain regions most effective in predicting sex belonged to association (default mode, dorsal attention, and parietal memory) and visual (visual and medial visual) networks. The rsFC sex classifier trained on sex/gender aligned youth was significantly more effective in classifying unseen youth with sex/gender alignment than in classifying unseen youth with sex/gender unalignment. In females, the degree to which their brains rsFC matched a sex profile (female or male), was positively associated with the degree of sex/gender alignment. Lastly, neither rsFC nor cortical thickness predicted sex/gender alignment. These findings highlight rsFCs predictive power in capturing the relationship between sex and gender and the complexity of the interplay between sex, gender, and the brains functional connectivity and neuroanatomy.

neuroscience↗

bioRxiv2024

The brainstem's red nucleus was evolutionarily upgraded to support goal-directed action

The red nucleus is a large brainstem structure that coordinates limb movement for locomotion in quadrupedal animals (Basile et al., 2021). The humans red nucleus has a different pattern of anatomical connectivity compared to quadrupeds, suggesting a unique purpose (Hatschek, 1907). Previously the function of the human red nucleus remained unclear at least partly due to methodological limitations with brainstem functional neuroimaging (Sclocco et al., 2018). Here, we used our most advanced resting-state functional connectivity (RSFC) based precision functional mapping (PFM) in highly sampled individuals (n = 5) and large group-averaged datasets (combined N [~] 45,000), to precisely examine red nucleus functional connectivity. Notably, red nucleus functional connectivity to motor-effector networks (somatomotor hand, foot, and mouth) was minimal. Instead, red nucleus functional connectivity along the central sulcus was specific to regions of the recently discovered somato-cognitive action network (SCAN; (Gordon et al., 2023)). Outside of primary motor cortex, red nucleus connectivity was strongest to the cingulo-opercular (CON) and salience networks, involved in action/cognitive control (Dosenbach et al., 2007; Newbold et al., 2021) and reward/motivated behavior (Seeley, 2019), respectively. Functional connectivity to these two networks was organized into discrete dorsal-medial and ventral-lateral zones. Red nucleus functional connectivity to the thalamus recapitulated known structural connectivity of the dento-rubral thalamic tract (DRTT) and could prove clinically useful in functionally targeting the ventral intermediate (VIM) nucleus. In total, our results indicate that far from being a motor structure, the red nucleus is better understood as a brainstem nucleus for implementing goal-directed behavior, integrating behavioral valence and action plans.

neuroscience↗

bioRxiv2023

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

The Staphylococcus aureus clonal complex 8 (CC8) is made up of several subtypes with varying levels of clinical burden; from community-associated methicillin resistant S. aureus (CA-MRSA) USA300 strains to hospital-associated (HA-MRSA) USA500 strains and ancestral methicillin susceptible (MSSA) strains. This phenotypic distribution within a single clonal complex makes CC8 an ideal clade to study the emergence of mutations important for antibiotic resistance and community spread. Gene level analysis comparing USA300 against MSSA and HA-MRSA strains have revealed key horizontally acquired genes important for its rapid spread in the community. However, efforts to define the contributions of point mutations and indels have been confounded by strong linkage disequilibrium resulting from clonal propagation. To break down this confounding effect, we combined genetic association testing with a model of the transcriptional regulatory network (TRN) to find candidate mutations that may have led to changes in gene regulation. First, we used a De Bruijn graph genome-wide association study (DBGWAS) to enrich mutations unique to the USA300 lineages within CC8. Next, we reconstructed the TRN by using Independent Component Analysis on 670 RNA sequencing samples from USA300 and non-USA300 CC8 strains which predicted several genes with strain-specific altered expression patterns. Examination of the regulatory region of one of the genes enriched by both approaches, isdH, revealed a 38 base pair deletion containing a Fur binding site and a conserved Single Nucleotide Polymorphism (SNP) which likely led to the altered expression levels in USA300 strains. Taken together, our results demonstrate the utility of reconstructed TRNs to address the limits of genetic approaches when studying emerging pathogenic strains.

systems biology↗

bioRxiv2023

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

Hydrogen sulfide (H2S), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress. This mitigation of oxidative stress was suggested to be an important survival mechanism to achieve antimicrobial resistance (AMR) in many pathogenic bacteria. CyuR (known as DecR or YbaO) is a recently characterized Cys-dependent transcription regulator, responsible for the activation of the cyuAP operon and generation of hydrogen sulfide from Cys. Despite its potential importance, the regulatory network of CyuR remains poorly understood. In this study, we investigated the roles of the CyuR regulon in a Cys-dependent AMR mechanism in E. coli strains. We found: 1) Cys metabolism has a significant role in AMR and its effect is conserved in many E. coli strains, including clinical isolates; 2) CyuR negatively controls the expression of mdlAB encoding a transporter that exports antibiotics such as cefazolin and vancomycin; 3) CyuR binds to a DNA sequence motif GAAwAAATTGTxGxxATTTsyCC in the absence of Cys, confirmed by an in vitro binding assay; and 4) CyuR may regulate 25 additional genes as suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings expanded the understanding of the biological roles of CyuR relevant to antibiotic resistance associated with Cys.

systems biology↗

bioRxiv2022

Motion Impact Score for Detecting Spurious Brain-Behavior Associations

Between-participant differences in head motion introduce systematic bias to resting state fMRI brain-wide association studies (BWAS) that is not completely removed by denoising algorithms. Researchers who study traits, or phenotypes associated with in-scanner head motion (e.g. psychiatric disorders) need to know if trait-functional connectivity (FC) effects are biased by residual motion artifact in order to avoid reporting false positive results. We devised an adaptable method, Split Half Analysis of Motion Associated Networks (SHAMAN), to assign a motion impact score to specific trait-FC effects. The SHAMAN approach distinguishes between motion artifact causing overestimation or underestimation of trait-FC effects. SHAMAN was > 95% specific at sample sizes of n = 100 and above. SHAMAN was powered to detect motion overestimation scores 80% of the time at sample sizes of n = 5,000 but could detect motion underestimation scores only 50% of the time at n = 5000, making it most useful for researchers seeking to avoid overestimating trait-FC effects in large BWAS. We computed motion impact scores for trait-FC effect with 45 demographic, biophysical, cognitive, and personality traits from n = 7,270 participants in the Adolescent Brain Cognitive Development (ABCD) Study. After standard denoising with ABCD-BIDS and without motion censoring, 42% (19/45) of traits had significant (p < 0.05) motion overestimation scores and 38% (17/45) of traits had significant motion underestimation scores. Censoring at framewise displacement (FD) < 0.2 mm reduced the proportion of traits with significant motion overestimation scores from 42% to 2% (1/45) but did not decrease the number of traits with significant motion underestimation scores.

neuroscience↗

bioRxiv2022

A mind-body interface alternates with effector-specific regions in motor cortex

Primary motor cortex (M1) has been thought to form a continuous somatotopic homunculus extending down precentral gyrus from foot to face representations1,2. The motor homunculus has remained a textbook pillar of functional neuroanatomy, despite evidence for concentric functional zones3 and maps of complex actions4. Using our highest precision functional magnetic resonance imaging (fMRI) data and methods, we discovered that the classic homunculus is interrupted by regions with sharpy distinct connectivity, structure, and function, alternating with effector-specific (foot, hand, mouth) areas. These inter-effector regions exhibit decreased cortical thickness and strong functional connectivity to each other, and to prefrontal, insular, and subcortical regions of the Cingulo-opercular network (CON), critical for executive action5 and physiological control6, arousal7, and processing of errors8 and pain9. This interdigitation of action control-linked and motor effector regions was independently verified in the three largest fMRI datasets. Macaque and pediatric (newborn, infant, child) precision fMRI revealed potential cross-species analogues and developmental precursors of the inter-effector system. An extensive battery of motor and action fMRI tasks documented concentric somatotopies for each effector, separated by the CON-linked inter-effector regions. The inter-effector regions lacked movement specificity and co-activated during action planning (coordination of hands and feet), and axial body movement (e.g., abdomen, eyebrows). These results, together with prior work demonstrating stimulation-evoked complex actions4 and connectivity to internal organs (e.g., adrenal medulla)10, suggest that M1 is punctuated by an integrative system for implementing whole-body action plans. Thus, two parallel systems intertwine in motor cortex to form an integrate-isolate pattern: effector-specific regions (foot, hand, mouth) for isolating fine motor control, and a mind-body interface (MBI) for the integrative whole-organism coordination of goals, physiology, and body movement.

neuroscience↗

bioRxiv2022

Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

Inexpensive DNA sequencing has led to a rapidly increasing number of whole genome sequences in the public domain. Natural sequence variation can now be assessed across a large number of sequenced strains of a bacterial species, resulting in the definition of the wild-type alleleome (the collection of alleles for every gene found in the species). Concurrently, laboratory evolution emerged as a new approach to address biological questions and to develop new phenotypic traits, and a large number of laboratory acquired mutations can be found in databases. The availability of this large-scale sequence variation data now allows for a detailed comparison of mutations fixed in natural versus laboratory evolutions. Such comparison shows that laboratory-acquired mutations are rarely found in the wild-type alleleome of Escherichia coli. The E. coli alleleome is highly conserved as most of the sequence variation is concentrated in about 2% of the coding region. We find that there are typically two alternate amino acids coded for in the variable locations, and switches between the two are found in the data sets. Finally, we find that adaptive laboratory mutations, unlike wild-type mutations, do not utilize the redundancy built into the genetic code: they are less likely to be synonymous and rely on changing a single nucleotide in a codon. However, the uniqueness of mutations fixed in laboratory evolutions bodes well for synthetic biology by revealing novel exploitable sequence space untouched by natural evolution.

bioengineering↗

bioRxiv2021

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates the dhaKLM operon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs. IMPORTANCEThe reconstruction of the transcriptional regulatory network (TRN) is important for gram-negative bacteria such as E. coli. LysR-type TFs are abundant in Enterobacteria, but many LTF functions still remain unknown. Here we report putative functions of uncharacterized TFs based on multi-omics data related to L-threonine, L-glutamate, and putrescine utilization. Amino acids (AAs) and polyamines are important sources of nitrogen for many microorganisms, but the increase in one amino acid or putrescine concentration in a minimal medium also induces stress. Although polyamine metabolism has been studied, the TRN that controls the putrescine (Ptr) and AA utilization at minimal medium conditions are still poorly understood. The function of previously uncharacterized transcriptional regulators YbdO, YgfI, and YneJ (PtrR) were identified in Escherichia coli. PtrR is important for Ptr and L-glutamate utilization, while YgfI transcriptional regulation was found to be important for growth on L-threonine and glycerol as a carbon source.

systems biology↗

bioRxiv2021

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa which are found in a variety of niches, and are an important cause of opportunistic healthcare-associated infections in humans. Due to increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulphur and phosphorus substrates. Models were curated and their accuracy assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions on growth in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.

microbiology↗

bioRxiv2020

Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation in E. coli

Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states. Comparative analysis of a regulon and its target genes between different strains of the same species is lacking. Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. Using ChIP-exo experiments, we performed a comprehensive study of Fur binding sites in nine Escherichia coli strains with different lifestyles. 79 of the 431 target genes (18%) found belong to Fur core regulon, comprising genes involved in ion transport and metabolism, energy production and conversion, and amino acid metabolism and transport. 179 of the target genes (42%) comprise the accessory regulon, most of which were related to cell wall structure and biogenesis, and virulence factor pathways. The remaining target genes (173 or 40%) were in the unique regulon, with gene functions that were largely unknown. Furthermore, deletion of the fur gene led to distinct phenotypes in growth, motility, antibiotic resistance, and the change of siderophore production. These results provide a more complete understanding of how Fur regulates a set of target genes with surprising variation in closely related bacteria.

systems biology↗