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271.
Bacterial ribosomal protein L11 is post-translationally trimethylated at multiple residues by a single methyltransferase, PrmA. Here, we describe four structures of PrmA from the extreme thermophile Thermus thermophilus. Two apo-PrmA structures at 1.59 and 2.3 A resolution and a third with bound cofactor S-adenosyl-L-methionine at 1.75 A each exhibit distinct relative positions of the substrate recognition and catalytic domains, revealing how PrmA can position the L11 substrate for multiple, consecutive side-chain methylation reactions. The fourth structure, the PrmA-L11 enzyme-substrate complex at 2.4 A resolution, illustrates the highly specific interaction of the N-terminal domain with its substrate and places Lys39 in the PrmA active site. The presence of a unique flexible loop in the cofactor-binding site suggests how exchange of AdoMet with the reaction product S-adenosyl-L-homocysteine can occur without necessitating the dissociation of PrmA from L11. Finally, the mode of interaction of PrmA with L11 explains its observed preference for L11 as substrate before its assembly into the 50S ribosomal subunit. 相似文献
272.
The Ciona intestinalis genome harbors three insulin-like genes: INS-L1, -L2 and -L3. Conserved synteny between the Ciona-human genomes predicts that Ciona INS-Ls are orthologous to the vertebrate insulin-relaxin family, but this relation cannot be inferred from molecular phylogeny. A conserved protein core with six cysteines; typical arrangement of B-, C- and A-protein domains; pro-protein maturation mode; and putative insulin receptor-binding sites were identified in Ciona INS-L proteins. ESTs used to assemble exonic sequences of INS-Ls combined with qRT-PCR analysis provided evidence that the predicted genes are expressed in the developing and adult Ciona. Our results support that Ciona INS-L1 is orthologous to the vertebrate insulin-like/relaxin genes, INS-L2 to insulin genes and INS-L3 to IGF genes. Our analysis also implies that the insulin-like/relaxin ancestor switched receptor type from tyrosine kinase- to GPCR-type, whereas insulin-IGF subfamily retained the tyrosine kinase-type of receptor. We propose that this receptor-switch occurred after the time when urochordates branched from the common chordate lineage, but before the two genome-duplications at the root of the vertebrates. 相似文献
273.
Jimann Shin Arun Padmanabhan Eric D. de Groh Jeong-Soo Lee Sam Haidar Suzanne Dahlberg Feng Guo Shuning He Marc A. Wolman Michael Granato Nathan D. Lawson Scot A. Wolfe Seok-Hyung Kim Lilianna Solnica-Krezel John P. Kanki Keith L. Ligon Jonathan A. Epstein A. Thomas Look 《Disease models & mechanisms》2012,5(6):881-894
274.
Emma ?hrman Pilar Lorenzo Kristin Holmgren Alan J. Grodzinsky Leif E. Dahlberg Tore Saxne Dick Heineg?rd Patrik ?nnerfjord 《The Journal of biological chemistry》2014,289(30):20908-20916
To identify patients at risk for progressive joint damage, there is a need for early diagnostic tools to detect molecular events leading to cartilage destruction. Isolation and characterization of distinct cartilage oligomeric matrix protein (COMP) fragments derived from cartilage and released into synovial fluid will allow discrimination between different pathological conditions and monitoring of disease progression. Early detection of disease and processes in the tissue as well as an understanding of the pathologic mechanisms will also open the way for novel treatment strategies. Disease-specific COMP fragments were isolated by affinity chromatography of synovial fluids from patients with rheumatoid arthritis, osteoarthritis, or acute trauma. Enriched COMP fragments were separated by SDS-PAGE followed by in-gel digestion and mass spectrometric identification and characterization. Using the enzymes trypsin, chymotrypsin, and Asp-N for the digestions, an extensive analysis of the enriched fragments could be accomplished. Twelve different neoepitopes were identified and characterized within the enriched COMP fragments. For one of the neoepitopes, Ser77, an inhibition ELISA was developed. This ELISA quantifies COMP fragments clearly distinguishable from total COMP. Furthermore, fragments containing the neoepitope Ser77 were released into the culture medium of cytokine (TNF-α and IL-6/soluble IL-6 receptor)-stimulated human cartilage explants. The identified neoepitopes provide a complement to the currently available commercial assays for cartilage markers. Through neoepitope assays, tools to pinpoint disease progression, evaluation methods for therapy, and means to elucidate disease mechanisms will be provided. 相似文献
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277.
In this study, we explore how Sphagnum mosses and Scots pine, Pinus sylvestris , interact on different spatial and temporal scales in a boreal bog ecosystem. We were particularly interested in relationships between the occurrence of Sphagnum- dominated habitats and the occurrence of Scots pines of different age and size.
Juvenile and adult pines occurred in different habitats. While juveniles mainly occurred in Sphagnum- dominated habitats, predominantly with Sphagnum rubellum , adult pines were found in habitats dominated by lichens, or with a sparse vegetation cover. Examination of surface peat cores sampled close to adult pines revealed that almost all pines (97%) had established in a Sphagnum -dominated environment and that the habitat had changed since pine establishment. Scots pine is thus capable of changing and exterminating the Sphagnum -dominated environment preferred for germination and establishment. Pines impede Sphagnum growth and peat accumulation significantly once they have reached a stem diameter of approximately 20 mm. It takes from 30 to 90 yr for a pine to reach that size.
Our results show the importance of interactions between Scots pine and Sphagnum mosses in bog ecosystems. We conclude that interactions between trees and Sphagnum mosses are important driving forces behind the vegetation change that has characterised boreal bogs during the Holocene. 相似文献
Juvenile and adult pines occurred in different habitats. While juveniles mainly occurred in Sphagnum- dominated habitats, predominantly with Sphagnum rubellum , adult pines were found in habitats dominated by lichens, or with a sparse vegetation cover. Examination of surface peat cores sampled close to adult pines revealed that almost all pines (97%) had established in a Sphagnum -dominated environment and that the habitat had changed since pine establishment. Scots pine is thus capable of changing and exterminating the Sphagnum -dominated environment preferred for germination and establishment. Pines impede Sphagnum growth and peat accumulation significantly once they have reached a stem diameter of approximately 20 mm. It takes from 30 to 90 yr for a pine to reach that size.
Our results show the importance of interactions between Scots pine and Sphagnum mosses in bog ecosystems. We conclude that interactions between trees and Sphagnum mosses are important driving forces behind the vegetation change that has characterised boreal bogs during the Holocene. 相似文献
278.
Kapralou S Fabbretti A Garulli C Spurio R Gualerzi CO Dahlberg AE Pon CL 《Molecular microbiology》2008,70(6):1368-1377
Bacterial translation initiation factor IF1 is homologous to archaeal aIF1A and eukaryal eIF1A, which form a complex with their homologous IF2-like factors (aIF5B and eIF5B respectively) during initiation of protein synthesis. A similar IF1-IF2 interaction is assumed to occur in all bacteria and supported by cross-linking data and stabilization of the 30S-IF2 interaction by IF1. Here we compare Escherichia coli IF1 with thermophilic factors from Bacillus stearothermophilus and Thermus thermophilus. All three IF1s are structurally similar and functionally interchangeable in vivo and in vitro. However, the thermophilic factors do not stimulate ribosomal binding of IF2DeltaN, regardless of 30S subunits and IF2 origin. We conclude that an IF1-IF2 interaction is not universally conserved and is not essential for cell survival. 相似文献
279.
Henrik Stranneheim Martin Engvall Karin Naess Nicole Lesko Pontus Larsson Mats Dahlberg Robin Andeer Anna Wredenberg Chris Freyer Michela Barbaro Helene Bruhn Tesfail Emahazion M?ns Magnusson Rolf Wibom Rolf H Zetterstr?m Valtteri Wirta Ulrika von D?beln Anna Wedell 《BMC genomics》2014,15(1)
Background
Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group of monogenic disorders with highly variable clinical presentation, often with acute, nonspecific initial symptoms. In many cases irreversible damage can be reduced by initiation of specific treatment, provided that a correct molecular diagnosis can be rapidly obtained. MPS thus has the potential to significantly improve both diagnostics and outcome for affected patients in this highly specialized area of medicine.Results
We have developed a conceptually novel approach for acute MPS, by analysing pulsed whole genome sequence data in real time, using automated analysis combined with data reduction and parallelization. We applied this novel methodology to an in-house developed customized work flow enabling clinical-grade analysis of all IEM with a known genetic basis, represented by a database containing 474 disease genes which is continuously updated. As proof-of-concept, two patients were retrospectively analysed in whom diagnostics had previously been performed by conventional methods. The correct disease-causing mutations were identified and presented to the clinical team after 15 and 18 hours from start of sequencing, respectively. With this information available, correct treatment would have been possible significantly sooner, likely improving outcome.Conclusions
We have adapted MPS to fit into the dynamic, multidisciplinary work-flow of acute metabolic medicine. As the extent of irreversible damage in patients with IEM often correlates with timing and accuracy of management in early, critical disease stages, our novel methodology is predicted to improve patient outcome. All procedures have been designed such that they can be implemented in any technical setting and to any genetic disease area. The strategy conforms to international guidelines for clinical MPS, as only validated disease genes are investigated and as clinical specialists take responsibility for translation of results. As follow-up in patients without any known IEM, filters can be lifted and the full genome investigated, after genetic counselling and informed consent.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1090) contains supplementary material, which is available to authorized users. 相似文献280.