Salmonella enterica serovar Typhimurium possesses a stimulon of genes that are differentially regulated in response to conditions of low fluid shear force that increase bacterial virulence and alter other phenotypes. In this study, we show that a previously uncharacterized member of this stimulon, ydcI or STM1625, encodes a highly conserved DNA binding protein with related homologs present in a range of Gram-negative bacterial genera. Gene expression analysis shows that ydcI is expressed in different bacterial genera and is involved in its autoregulation in S. Typhimurium. We demonstrate that purified YdcI protein specifically binds a DNA probe consisting of its own promoter sequence. We constructed an S. Typhimurium ⌬ydcI mutant strain and show that this strain is more sensitive to both organic and inorganic acid stress than is an isogenic WT strain, and this defect is complemented in trans. Moreover, our data indicate that ydcI is part of the rpoS regulon related to stress resistance. The S. Typhimurium ⌬ydcI mutant was able to invade cultured cells to the same degree as the WT strain, but a strain in which ydcI expression is induced invaded cells at a level 2.8 times higher than that of the WT. In addition, induction of ydcI expression in S. Typhimurium resulted in the formation of a biofilm in stationary-phase cultures. These data indicate the ydcI gene encodes a conserved DNA binding protein involved with aspects of prokaryotic biology related to stress resistance and possibly virulence.Bacterial growth environments characterized by low fluid shear force have been shown to induce a multitude of phenotypic responses, including altered acid, oxidative, thermal, and osmotic stress resistance (7,33,36,41,(52)(53)(54)(55), increased biofilm formation (6, 33, 52), altered protein secretion (14, 15), altered cell surface lipid and polysaccharide profiles (6, 7, 55), and increased survival in cellular and animal hosts (39,(52)(53)(54). Notably, the virulence of Salmonella enterica serovar Typhimurium is increased by low fluid shear growth conditions as measured using murine infection assays and tissue culture models (39,(52)(53)(54). Low fluid shear force (defined here as approximately Ͻ0.01 to 0.2 dynes/cm 2 ) is characterized by a lowturbulence, low-agitation environment, as opposed to high fluid shear (defined here as approximately from 5 to Ͼ50 dynes/cm 2 ) where liquid moves with higher velocity over the cellular surface (3-5, 21, 23, 25, 36). Low fluid shear growth environments include spaceflight, ground-based suspension culture models such as the rotating-wall vessel (RWV) bioreactor, and the spaces between cellular microvilli, the last of which is encountered by numerous pathogens during the natural course of infection (21,23,25,30,40,41). Previous work has shown that bacteria grown in low fluid shear environments induce a molecular response which includes genome-wide changes in gene expression (the low fluid shear stimulon) (6,7,39,48,52,53,55). Since growth under low fluid shear conditions is able to ind...

Our findings identify Slit-Robo as a significant pathway in human heart development and CHD.

USP9X is an X-chromosome gene that escapes X-inactivation. Loss or compromised function of USP9X leads to neurodevelopmental disorders in males and females. While males are impacted primarily by hemizygous partial loss-of-function missense variants, in females de novo heterozygous complete loss-of-function mutations predominate, and give rise to the clinically recognisable USP9X-female syndrome. Here we provide evidence of the contribution of USP9X missense and small in-frame deletion variants in USP9X-female syndrome also. We scrutinise the pathogenicity of eleven such variants, ten of which were novel. Combined application of variant prediction algorithms, protein structure modelling, and assessment under clinically relevant guidelines universally support their pathogenicity. The core phenotype of this cohort overlapped with previous descriptions of USP9X-female syndrome, but exposed heightened variability. Aggregate phenotypic information of 35 currently known females with predicted pathogenic variation in USP9X reaffirms the clinically recognisable USP9X-female syndrome, and highlights major differences when compared to USP9X-male associated neurodevelopmental disorders.

The majority of patients with spinal muscular atrophy (SMA) identified to date harbor a biallelic exonic deletion of SMN1. However, there have been reports of SMA-like disorders that are independent of SMN1, including those due to pathogenic variants in the glycyl-tRNA synthetase gene (GARS1). We report three unrelated patients with de novo variants in GARS1 that are associated with infantile-onset SMA (iSMA).Patients were ascertained during inpatient hospital evaluations for complications of neuropathy. Evaluations were completed as indicated for clinical care and management and informed consent for publication was obtained. One newly identified, disease-associated GARS1 variant, identified in two out of three patients, was analyzed by functional studies in yeast complementation assays. Genomic analyses by exome and/or gene panel and SMN1 copy number analysis of three patients identified two previously undescribed de novo missense variants in GARS1 and excluded Rebecca Markovitz and Rajarshi Ghosh as co-first authors.

The iprA gene (formerly known as yaiV or STM0374) is located in a two-gene operon in the Salmonella enterica serovar Typhimurium genome and is associated with altered expression during spaceflight and rotating-wall-vessel culture conditions that increase virulence. However, iprA is uncharacterized in the literature. In this report, we present the first targeted characterization of this gene, which revealed that iprA is highly conserved across Enterobacteriaceae. We found that S. Typhimurium, Escherichia coli, and Enterobacter cloacae ⌬iprA mutant strains display a multi-log-fold increase in oxidative stress resistance that is complemented using a plasmid-borne wild-type (WT) copy of the S. Typhimurium iprA gene. This observation was also associated with increased catalase activity, increased S. Typhimurium survival in macrophages, and partial dependence on the katE gene and full dependence on the rpoS gene. Our results indicate that IprA protein activity is sensitive to deletion of the N-and C-terminal 10 amino acids, while a region that includes amino acids 56 to 80 is dispensable for activity. RNA sequencing (RNA-Seq) analysis revealed several genes altered in expression in the S. Typhimurium ⌬iprA mutant strain compared to the WT, including those involved in fimbria formation, spvABCD-mediated virulence, ethanolamine utilization, the phosphotransferase system (PTS) transport, and flagellin phase switching from FlgB to FliC (likely a stochastic event) and several genes of hypothetical or putative function. IMPORTANCEOverall, this work reveals that the conserved iprA gene measurably influences bacterial biology and highlights the pool of currently uncharacterized genes that are conserved across bacterial genomes. These genes represent potentially useful targets for bacterial engineering, vaccine design, and other possible applications.M any large-scale genomic studies, virulence factor identification assays, and whole-genome expression analyses have revealed bacterial genes that are uncharacterized but are associated with gene expression changes in different environments that can affect virulence and stress survival (see references 1-8 and several others). These studies reveal a pool of genes that are not understood or characterized but whose importance is highlighted due to how they were identified and, in some cases, to high conservation across bacterial genomes. The iprA gene (previously known as yaiV or STM0374) is located in a two-gene operon in the Salmonella enterica serovar Typhimurium genome and has been observed to display altered expression during spaceflight and under rotating-wall-vessel (RWV) culture conditions, which increase virulence (6, 7). In these studies, microarray analysis revealed that S. Typhimurium iprA was upregulated in cultures inoculated and grown during spaceflight (compared to identically grown ground controls) and in cultures grown under low-fluid-shear RWV conditions (compared to RWV controls in which low-fluid-shear conditions were disrupted) (6, 7). Interestingly, bot...