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Although major genetic networks controlling early liver specification and morphogenesis are known, the mechanisms responsible for postnatal hepatic maturation are poorly understood. Here we employ global analyses of the mouse liver transcriptome to demonstrate that postnatal remodelling of the liver is accompanied by large-scale transcriptional and post-transcriptional transitions that are cell-type-specific and temporally coordinated. Combining detailed expression analyses with gain- and loss-of-function studies, we identify epithelial splicing regulatory protein 2 (ESRP2) as a conserved regulatory factor that controls the neonatal-to-adult switch of ∼20% of splice isoforms in mouse and human hepatocytes. The normal shift in splicing coincides tightly with dramatic postnatal induction of ESRP2 in hepatocytes. We further demonstrate that forced expression of ESRP2 in immature mouse and human hepatocytes is sufficient to drive a reciprocal shift in splicing and causes various physiological abnormalities. These findings define a direct role for ESRP2 in the generation of conserved repertoires of adult splice isoforms that facilitate terminal differentiation and maturation of hepatocytes.

Myotonic Dystrophy type 1 (DM1), the most prevalent adult onset muscular dystrophy, is a trinucleotide repeat expansion disease caused by CTG expansion in the 3 0 -UTR of DMPK gene. This expansion results in the expression of toxic gain-of-function RNA that forms ribonuclear foci and disrupts normal activities of RNA-binding proteins belonging to the MBNL and CELF families. Changes in alternative splicing, translation, localization, and mRNA stability due to sequestration of MBNL proteins and up-regulation of CELF1 are key to DM1 pathology. However, recent discoveries indicate that pathogenic mechanisms of DM1 involves many other factors as well, including repeat associated translation, activation of PKC-dependent signaling pathway, aberrant polyadenylation, and microRNA deregulation. Expression of the toxic repeat RNA culminates in the developmental remodeling of the transcriptome, which produces fetal isoforms of proteins that are unable to fulfill the physiological requirements of adult tissues. This review will describe advances in the understanding of DM1 pathogenesis as well as current therapeutic developments for DM1. Developmental Dynamics 244:377-390, 2015. V C 2014 Wiley Periodicals, Inc.

The continued increase in the size of the protein sequence databases as a result of advances in genome sequencing technology is overwhelming the ability to perform experimental characterization of function. Consequently, functions are assigned to the vast majority of proteins via automated, homology-based methods, with the result that as many as 50% are incorrectly annotated or unannotated (e100060520011109PLoS Comput. Biol.20095). This manuscript describes a study of the d-mannonate dehydratase (ManD) subgroup of the enolase superfamily (ENS) to investigate how function diverges as sequence diverges. Previously, one member of the subgroup had been experimentally characterized as ManD [dehydration of d-mannonate to 2-keto-3-deoxy-d-mannonate (equivalently, 2-keto-3-deoxy-d-gluconate)]. In this study, 42 additional members were characterized to sample sequence–function space in the ManD subgroup. These were found to differ in both catalytic efficiency and substrate specificity: (1) high efficiency (kcat/KM = 103 to 104 M–1 s–1) for dehydration of d-mannonate, (2) low efficiency (kcat/KM = 101 to 102 M–1 s–1) for dehydration of d-mannonate and/or D-gluconate, and 3) no-activity with either d-mannonate or d-gluconate (or any other acid sugar tested). Thus, the ManD subgroup is not isofunctional and includes d-gluconate dehydratases (GlcDs) that are divergent from the GlcDs that have been characterized in the mandelate racemase subgroup of the ENS (Lamble et al. 15474024FEBS Lett.2004576133136) (Ahmed et al. 15869466Biochem. J.2005390529540). These observations signal caution for functional assignment based on sequence homology and lay the foundation for the studies of the physiological functions of the GlcDs and the promiscuous ManDs/GlcDs.

A novel lead compound for inhibition of the antibacterial drug target, glutamate racemase, is optimized for both ligand efficiency and lipophilic efficiency. A previously developed hybrid MD-docking and scoring scheme, FERM-SMD, is utilized to predict relative potencies of potential derivatives prior to chemical synthesis. This scheme was successful in distinguishing between high and low affinity binders with minimal experimental structural information, saving time and resources in the process. In vitro potency is increased approximately 4-fold against glutamate racemase from the model organism, B. subtilis. Lead derivatives show 2- to 4-fold increased antimicrobial potency over the parent scaffold. In addition, specificity toward B. subtilis, over E. coli and S. aureus, show dependency on the chemical substituent added to the parent scaffold. Finally, insight is gained into the capacity for these compounds to reach the target enzyme in vivo using a bacterial cell wall lysis assay. The result of this study is a novel small molecule inhibitor of GR with the following characteristics: Ki = 2.5 μM, LE = 0.45 kcal/mol/atom, LiPE = 6.0, MIC50 = 260 μg/mL against B. subtilis, EC50,lysis = 520 μg/mL against B. subtilis