Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria

Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (k_cat/K_M), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics     

Primary coronary intervention for ST-elevation myocardial infarction in Indonesia and the Netherlands: a comparison

Background. Although the beneficial effects of primary percutaneous coronary intervention (PCI) for ST-elevation myocardial infarction (STEMI) have been demonstrated in a number of trials, most studies were conducted in Western countries. Experience, logistics and patient characteristics may differ in other parts of the world. Methods. Consecutive patients treated with primary PCI in Cinere Hospital, Jakarta, Indonesia, between January 2008 and October 2008 were compared with those treated in the Isala Clinics, Zwolle, the Netherlands. Results. During the study period, a total of 596 patients were treated by primary PCI, 568 in Zwolle and 28 in Jakarta. Patients in Indonesia were younger (54 vs 63 years), more often had diabetes (36 vs. 12%) and high lipids and were more often smokers (68 vs. 31%). Time delay between symptom onset and admission was longer in Indonesia. Patients from Indonesia more often had signs of heart failure at admission. The time between admission and balloon inflation was longer in Indonesia. At angiography, patients from Indonesia more often had multivessel disease. There was no difference in the percentage of restoration of TIMI 3 flow by primary PCI between the two hospitals. Conclusion. Patients with STEMI in Indonesia have a higher risk profile compared with those in the Netherlands, according to prevalence of coronary risk factors, signs of heart failure, multivessel disease and patient delay. Time delay between admission and balloon inflation was much longer in Indonesia, because of both logistic and financial reasons. (Neth Heart J 2009;17:418–21.)     

Efficient hydrogen production from the lignocellulosic energy crop Miscanthus by the extreme thermophilic bacteria Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana

Background  

The production of hydrogen from biomass by fermentation is one of the routes that can contribute to a future sustainable hydrogen economy. Lignocellulosic biomass is an attractive feedstock because of its abundance, low production costs and high polysaccharide content.     

Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding

The absence of a functional ATP Binding Cassette (ABC) protein called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) from apical membranes of epithelial cells is responsible for cystic fibrosis (CF). Over 90% of CF patients carry at least one mutant allele with deletion of phenylalanine at position 508 located in the N-terminal nucleotide binding domain (NBD1). Biochemical and cell biological studies show that the DeltaF508 mutant exhibits inefficient biosynthetic maturation and susceptibility to degradation probably due to misfolding of NBD1 and the resultant misassembly of other domains. However, little is known about the direct effect of the Phe508 deletion on the NBD1 folding, which is essential for rational design strategies of cystic fibrosis treatment. Here we show that the deletion of Phe508 alters the folding dynamics and kinetics of NBD1, thus possibly affecting the assembly of the complete CFTR. Using molecular dynamics simulations, we find that meta-stable intermediate states appearing on wild type and mutant folding pathways are populated differently and that their kinetic accessibilities are distinct. The structural basis of the increased misfolding propensity of the DeltaF508 NBD1 mutant is the perturbation of interactions in residue pairs Q493/P574 and F575/F578 found in loop S7-H6. As a proof-of-principle that the S7-H6 loop conformation can modulate the folding kinetics of NBD1, we virtually design rescue mutations in the identified critical interactions to force the S7-H6 loop into the wild type conformation. Two redesigned NBD1-DeltaF508 variants exhibited significantly higher folding probabilities than the original NBD1-DeltaF508, thereby partially rescuing folding ability of the NBD1-DeltaF508 mutant. We propose that these observed defects in folding kinetics of mutant NBD1 may also be modulated by structures separate from the 508 site. The identified structural determinants of increased misfolding propensity of NBD1-DeltaF508 are essential information in correcting this pathogenic mutant.     

A morphological and genetic analysis of the European bitterling species complex

Bitterling fishes lay their eggs on the gills of living freshwater mussels and are valuable models in behavioural and evolutionary ecology. We used morphological and genetic data to resolve the taxonomic relationships of bitterling in Europe. Previous studies have suggested the European bitterling is either a single species with a wide but discontinuous geographic distribution, or a complex of species. Morphometric and meristic data identified differences between three putative species; with a clear distinction between the eastern Asian Rhodeus sericeus, western European bitterling Rhodeus amarus, and colchian bitterling, Rhodeus colchicus. Polymorphism in the mitochondrial DNA control region was predominantly due to insertion/deletion events, making phylogenetic inference difficult, but the single haplotype found in R. sericeus populations was detected at low frequency (one of 24 individuals) in R. amarus and R. colchicus populations. Eight control region haplotypes were found in R. amarus populations, which were distinct from the two haplotypes in a R. colchicus population. Cytochrome b data produced a phylogeny with strongly‐supported differentiation between a clade of two R. sericeus haplotypes and a clade of six R. amarus/colchicus haplotypes. The star‐like topology of the R. amarus/colchicus haplotypes in a minimum spanning network suggested a rapid radiation in this clade. Our results are consistent with an hypothesis of relatively ancient divergence of R. sericeus from R. amarus/colchicus and more recent and rapid differentiation between R. amarus and R. colchicus. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 337–347.     

Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies

Introduction

Early degeneration of the intervertebral disc (IVD) involves a change in cellular differentiation from notochordal cells (NCs) in the nucleus pulposus (NP) to chondrocyte-like cells (CLCs). The purpose of this study was to investigate the gene expression profiles involved in this process using NP tissue from non-chondrodystrophic and chondrodystrophic dogs, a species with naturally occurring IVD degeneration.

Methods

Dual channel DNA microarrays were used to compare 1) healthy NP tissue containing only NCs (NC-rich), 2) NP tissue with a mixed population of NCs and CLCs (Mixed), and 3) NP tissue containing solely CLCs (CLC-rich) in both non-chondrodystrophic and chondrodystrophic dogs. Based on previous reports and the findings of the microarray analyses, canonical Wnt signaling was further evaluated using qPCR of relevant Wnt target genes. We hypothesized that caveolin-1, a regulator of Wnt signaling that showed significant changes in gene expression in the microarray analyses, played a significant role in early IVD degeneration. Caveolin-1 expression was investigated in IVD tissue sections and in cultured NCs. To investigate the significance of Caveolin-1 in IVD health and degeneration, the NP of 3-month-old Caveolin-1 knock-out mice was histopathologically evaluated and compared with the NP of wild-type mice of the same age.

Results

Early IVD degeneration involved significant changes in numerous pathways, including Wnt/β-catenin signaling. With regard to Wnt/β-catenin signaling, axin2 gene expression was significantly higher in chondrodystrophic dogs compared with non-chondrodystrophic dogs. IVD degeneration involved significant down-regulation of axin2 gene expression. IVD degeneration involved significant down-regulation in Caveolin-1 gene and protein expression. NCs showed abundant caveolin-1 expression in vivo and in vitro, whereas CLCs did not. The NP of wild-type mice was rich in viable NCs, whereas the NP of Caveolin-1 knock-out mice contained chondroid-like matrix with mainly apoptotic, small, rounded cells.

Conclusions

Early IVD degeneration involves down-regulation of canonical Wnt signaling and Caveolin-1 expression, which appears to be essential to the physiology and preservation of NCs. Therefore, Caveolin-1 may be regarded an exciting target for developing strategies for IVD regeneration.     

Pathologies of non‐marine bivalve shells from the Late Triassic of Poland

Gorzelak, P., Nied?wiedzki, G. & Skawina, A. 2010: Pathologies of non‐marine bivalve shells from the Late Triassic of Poland. Lethaia, Vol. 43, pp. 285–289. Shells of Late Triassic non‐marine bivalves from Lisowice (Lipie ?l?skie clay pit, southern Poland), which co‐occur with remains of several vertebrate taxa (mammal‐like reptiles, carnivorous dinosaurs, pterosaurs, temnospondyl amphibians, hybodont sharks, dipnoan and ganoid fish), bear evidence of pathologies. Distribution, dimension and shape of some of these injuries (radiate tooth marks) closely match the dental morphology of lungfish (here probably represented by the genus Ceratodus). Thus, we interpret these pathologies as evidence of unsuccessful predatory attack on bivalves by this fish. This interpretation is also consistent with modern examples of such behaviour among lungfish. The feasibility that other culprits caused other pathologies (shell scarring and wedges) on the bivalves analysed is also discussed. Discovery of these traces constitutes important evidence of predator–prey interaction, which provides ‘fingerprints’ of trophic structure within this Late Triassic freshwater ecosystem. □Freshwater bivalves, lungfish, pathologies, predation, Triassic.     

Protein folding: then and now

Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.