Identification and characterization of novel human tissue-specific RFX transcription factors

<p>Abstract</p> <p>Background</p> <p>Five regulatory factor X (RFX) transcription factors (TFs)–RFX1-5–have been previously characterized in the human genome, which have been demonstrated to be critical for development and are associated with an expanding list of serious human disease conditions including major histocompatibility (MHC) class II deficiency and ciliaophathies.</p> <p>Results</p> <p>In this study, we have identified two additional RFX genes–RFX6 and RFX7–in the current human genome sequences. Both RFX6 and RFX7 are demonstrated to be winged-helix TFs and have well conserved RFX DNA binding domains (DBDs), which are also found in winged-helix TFs RFX1-5. Phylogenetic analysis suggests that the RFX family in the human genome has undergone at least three gene duplications in evolution and the seven human RFX genes can be clearly categorized into three subgroups: (1) RFX1-3, (2) RFX4 and RFX6, and (3) RFX5 and RFX7. Our functional genomics analysis suggests that RFX6 and RFX7 have distinct expression profiles. RFX6 is expressed almost exclusively in the pancreatic islets, while RFX7 has high ubiquitous expression in nearly all tissues examined, particularly in various brain tissues.</p> <p>Conclusion</p> <p>The identification and further characterization of these two novel RFX genes hold promise for gaining critical insight into development and many disease conditions in mammals, potentially leading to identification of disease genes and biomarkers.</p

Platinum Cyclooctadiene Complexes with Activity against Gram-positive Bacteria

Antimicrobial resistance is a looming health crisis, and it is becoming increasingly clear that organic chemistry alone is not sufficient to continue to provide the world with novel and effective antibiotics. Recently there has been an increased number of reports describing promising antimicrobial properties of metal-containing compounds. Platinum complexes are well known in the field of inorganic medicinal chemistry for their tremendous success as anticancer agents. Here we report on the promising antibacterial properties of platinum cyclooctadiene (COD) complexes. Amongst the 15 compounds studied, the simplest compounds Pt(COD)X$_{2}$ (X=Cl, I, Pt1 and Pt2) showed excellent activity against a panel of Gram-positive bacteria including vancomycin and methicillin resistant Staphylococcus aureus. Additionally, the lead compounds show no toxicity against mammalian cells or haemolytic properties at the highest tested concentrations, indicating that the observed activity is specific against bacteria. Finally, these compounds showed no toxicity against Galleria mellonella at the highest measured concentrations. However, preliminary efficacy studies in the same animal model found no decrease in bacterial load upon treatment with Pt1 and Pt2. Serum exchange studies suggest that these compounds exhibit high serum binding which reduces their bioavailability in vivo, mandating alternative administration routes such as e. g. topical application

MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis

Eight proteins, defects in which are associated with Meckel-Gruber syndrome and nephronophthisis ciliopathies, work together as two functional modules at the transition zone to establish basal body/transition zone connections with the membrane and barricade entry of non-ciliary components into this organelle

Characterization of nematode DAF-19 and human RFX6 transcription factors

Regulatory factor X (RFX) transcription factors play an important role in regulating expression of ciliary genes associated with ciliopathies. However, the annotation of RFX genes may be incomplete and their function is not well understood. Here I describe two novel tissue-specific RFX genes in humans: RFX6 and RFX7. To study RFX genes in the model organism Caenorhabditis elegans, I undertook examining the expression of all four known isoforms of daf-19, the only RFX gene in C. elegans, by using Mos1 mediated Single Copy transgene Insertion (MosSCI) method. I discovered that both daf-19c and daf-19d isoforms are expressed in ciliated neurons and that their promoters are modular. In particular, daf-19c is expressed in all ciliated neurons while daf-19d in all but labial neurons. My analysis helped select suitable promoters for driving expression of RFX6 in ciliated neurons of C. elegans for testing its function in cilia

Delving through electrogenic biofilms: from anodes to cathodes to microbes

The study of electromicrobiology has grown into its own field over the last decades and involves microbially driven redox reactions at electrodes as part of a microbial electrochemical system (MES). The microorganisms known to use electrodes as either electron acceptors; electricigens, or electron donors; electrotrophs, drive the redox reactions within these systems through extracellular electron transfer (EET) processes. These exoelectrogenic microorganisms form biofilms, referred to as electroactive biofilms (EAB), in order to maximize adherence and contact with electrode surfaces and with one another. In this review, we will discuss the key differences between biofilms that utilize the electrode as an electron acceptor or donor, including their mechanisms for electron transfer, structural and functional compositions as well as which species are enriched for in each microenvironment. Lastly, we will discuss the intricacies of interspecies and intraspecies biofilm formation in electrode biofilms and considerations required for future bioengineering efforts

Microbial Fuel Cells, Related Technologies, and Their Applications

Microbial fuel cells present an emerging technology for utilizing the metabolism of microbes to fuel processes including biofuel, energy production, and the bioremediation of environments. The application and design of microbial fuel cells are of interest to a range of disciplines including engineering, material sciences, and microbiology. In addition, these devices present numerous opportunities to improve sustainable practices in different settings, ranging from industrial to domestic. Current research is continuing to further our understanding of how the engineering, design, and microbial aspects of microbial fuel cell systems impact upon their function. As a result, researchers are continuing to expand the range of processes microbial fuel cells can be used for, as well as the efficiency of those applications

Enhanced growth of pilin-deficient Geobacter sulfurreducens mutants in carbon poor and electron donor limiting conditions

Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative limited growth in these conditions. This growth is further impeded for OmcZ-deficient and OmcS-deficient mutants. A PilB-deficient mutant which prevents pilin production but allows for secretion of OmcZ had moderate growth in these conditions, indicating a role for cytochrome localization to enabling survival in the electron donor and carbon-limited conditions. To determine which pathways enhanced growth using formate, Sequential Window Acquisition of all Theoretical Mass Spectra mass spectrometry (SWATH-MS) proteomics of formate adapted PilA-deficient mutants and acetate grown wild type was performed. PilA-deficient mutants had an overall decrease in tricarboxylic acid (TCA) cycle enzymes and significant upregulation of electron transport chain associated proteins including many c-type cytochromes and [NiFe]-hydrogenases. Whole genome sequencing of the mutants shows strong convergent evolution and emergence of genetic subpopulations during adaptation to growth on formate. The results described here suggest a role for membrane constrained c-type cytochromes to the enhancement of survival and growth in electron donor and carbon-limited conditions

Adaptive evolution of Geobacter sulfurreducens in coculture with Pseudomonas aeruginosa

Interactions between microorganisms in mixed communities are highly complex, being either syntrophic, neutral, predatory, or competitive. Evolutionary changes can occur in the interaction dynamics between community members as they adapt to coexistence. Here, we report that the syntrophic interaction between and coculture change in their dynamics over evolutionary time. Specifically, sp. dominance increases with adaptation within the cocultures, as determined through quantitative PCR and fluorescence hybridization. This suggests a transition from syntrophy to competition and demonstrates the rapid adaptive capacity of spp. to dominate in cocultures with Early in coculture establishment, two single-nucleotide variants in the and genes emerged that were strongly selected for throughout coculture evolution with phenazine wild-type and phenazine-deficient mutants. Sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS) proteomics revealed that the variant cooccurred with the upregulation of an adenylate cyclase transporter, CyaE, and a resistance-nodulation-division (RND) efflux pump notably known for antibiotic efflux. To determine whether antibiotic production was driving the increased expression of the multidrug efflux pump, we tested -derived phenazine-1-carboxylic acid (PHZ-1-CA) for its potential to inhibit growth and drive selection of the and genetic variants. Despite its inhibitory properties, PHZ-1-CA did not drive variant selection, indicating that other antibiotics may drive overexpression of the efflux pump and CyaE or that a novel role exists for these proteins in the context of this interaction. and spp. cohabit many of the same environments, where spp. often dominate. Both bacteria are capable of extracellular electron transfer (EET) and play important roles in biogeochemical cycling. Although they recently in 2017 were demonstrated to undergo direct interspecies electron transfer (DIET) with one another, the genetic evolution of this syntrophic interaction has not been examined. Here, we use whole-genome sequencing of the cocultures before and after adaptive evolution to determine whether genetic selection is occurring. We also probe their interaction on a temporal level and determine whether their interaction dynamics change over the course of adaptive evolution. This study brings to light the multifaceted nature of interactions between just two microorganisms within a controlled environment and will aid in improving metabolic models of microbial communities comprising these two bacteria

Correction to: Enhanced growth of pilin-deficient Geobacter sulfurreducens mutants in carbon poor and electron donor limiting conditions (vol 78, pg 618, 2019)

The published version of this article contained an old version of Fig. 2

Deciphering the electric code of geobacter sulfurreducens in cocultures with pseudomonas aeruginosa via SWATH-MS proteomics

Interspecies electron transfer (IET) occurs in many microbial communities, enabling extracellular electron exchange for syntrophic utilization of mixed resources. Various mechanisms of IET have been characterized including direct IET (DIET) and hydrogen IET (HIT) but their evolution throughout syntrophic adaptation has not been investigated through an omics approach. A syntrophic coculture of Geobacter sulfurreducens and Pseudomonas aeruginosa was established and evolved in restricted medium. The medium required cooperative metabolism due to preferential utilization of formate and fumarate by P. aeruginosa and G. sulfurreducens respectively. Pure cultures did not yield significant growth while substantial growth was observed in cocultures. The syntrophy was not reliant on phenazine, since Δphz mutant strain cocultures grew, however appeared to rely on cytochromes as evidenced from the stunted growth G. sulfurreducens ΔomcZ and ΔomcS mutant cocultures. SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) proteomic analysis of initial cocultures revealed upregulation in DIET-associated cytochromes, whereas adapted cocultures revealed upregulation in HybA, a G. sulfurreducens uptake hydrogenase critical to HIT. This suggests DIET plays a critical role in the establishment of syntrophy between G. sulfurreducens and P. aeruginosa but is later consolidated with HIT as the cocultures adapt. This is the first instance to show a temporal distribution of DIET and HIT within the same coculture