Ulf-Peter Guenther - Academia.edu (original) (raw)

Papers by Ulf-Peter Guenther

Research paper thumbnail of Effect of pre‐tRNA 5’ leader sequence variation on the thermodynamic coupling and shared molecular recognition between RNA and protein components of RNase P

Research paper thumbnail of A novel Q378X mutation exists in the transmembrane transporter protein ABCC6 and its pseudogene: implications for mutation analysis in pseudoxanthoma elasticum

Journal of Molecular Medicine, 2001

Pseudoxanthoma elasticum (PXE) is an inherited disorder of the elastic tissue with characteristic... more Pseudoxanthoma elasticum (PXE) is an inherited disorder of the elastic tissue with characteristic progressive calcification of elastic fibers in skin, eye, and the cardiovascular system. Recently mutations in the ABCC6 gene, encoding a transmembrane transporter protein, were identified as cause of the disease. Surprisingly, sequence and RFLP analysis for exon 9 with primers corresponding to flanking intronic sequence in diseased and haplotype negative members from all of our families and in a control population revealed either a homozygous or heterozygous state for the Q378X (1132C→T) nonsense mutation in all individuals. With the publication of the genomic structure of the PXE locus we had identified the starting point of a large genom

Research paper thumbnail of doi:10.1093/nar/gkq1002 The RNA helicase database

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www.rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based sear...

Research paper thumbnail of Distress Type 1 (SMARD1) The Natural Course of Infantile Spinal Muscular Atrophy With Respiratory

BACKGROUND: Only scarce information is available on the long-termoutcome and the natural course o... more BACKGROUND: Only scarce information is available on the long-termoutcome and the natural course of children with infantile spinalmuscular atrophy with respiratory distress type 1 (SMARD1) due tomutations in the IGHMBP2 gene.OBJECTIVE: To describe the natural disease course, to systematicallyquantify the residual capacities of children with SMARD1 who surviveonpermanentmechanicalrespiration,andtoidentifymarkerspredict-ing the disease outcome at the time of manifestation.METHODS: We conducted a longitudinal study of 11 infantile SMARD1patients over a mean observational period of 7.8 (SD 3.2) years.Disease-specific features were continuously assessed by using asemiquantitative scoring system. Additionally, we analyzed the residualenzymatic activity of 6 IGHMBP2 mutants in our patients.RESULTS:Afteraninitialrapiddeclineoftheclinicalscoreuntiltheageof 2 years, residual capabilities reached a plateau or even improved.The overall clinical outcome was markedly heterogeneous, but clinicalscor...

Research paper thumbnail of The RNA helicase database

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www.rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehen-sive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organ-isms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based se...

Research paper thumbnail of A heterozygous genomic rearrangement in a patient with juvenile spinal muscle atrophy with respiratory distress type 1 (SMARD1)

Research paper thumbnail of Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

Research paper thumbnail of A helicase links upstream ORFs and RNA structure

Research paper thumbnail of The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs

Nature, 2018

The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue D... more The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by a range of viruses. How Ded1p and its orthologues engage RNAs during the initiation of translation is unknown. Here we show, by integrating transcriptome-wide analyses of translation, RNA structure and Ded1p-RNA binding, that the effects of Ded1p on the initiation of translation are connected to near-cognate initiation codons in 5' untranslated regions. Ded1p associates with the translation pre-initiation complex at the mRNA entry channel and repressing the activity of Ded1p leads to the accumulation of RNA structure in 5' untranslated regions, the initiation of translation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main open reading frames. T...

Research paper thumbnail of Coupling between the DEAD-box RNA helicases Ded1p and eIF4A

eLife, Jan 5, 2016

Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p.... more Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p. Here we show that S. cerevisiae eIF4A and Ded1p directly interact with each other and simultaneously with the scaffolding protein eIF4G. We delineate a comprehensive thermodynamic framework for the interactions between Ded1p, eIF4A, eIF4G, RNA and ATP, which indicates that eIF4A, with and without eIF4G, acts as modulator for activity and substrate preferences of Ded1p, which is the RNA remodeling unit in all complexes. Our results reveal and characterize an unexpected interdependence between the two RNA helicases and eIF4G, and suggest that Ded1p is an integral part of eIF4F, the complex comprising eIF4G, eIF4A, and eIF4E.

Research paper thumbnail of The Natural Course of Infantile Spinal Muscular Atrophy With Respiratory Distress Type 1 (SMARD1)

Research paper thumbnail of A New Mutation of IGHMBP2 Gene

Pediatric Neurology, 2006

Research paper thumbnail of The RNA helicase database

Nucleic Acids Research, 2011

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www .rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based searches of the database.

Research paper thumbnail of Hidden specificity in an apparently nonspecific RNA-binding protein

Nature, 2013

Nucleic acid binding proteins are generally viewed as either specific or non-specific, depending ... more Nucleic acid binding proteins are generally viewed as either specific or non-specific, depending on characteristics of their binding sites in DNA or RNA 1,2. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with defined signatures in sequence, structure, or both 1-4. Proteins that bind to sites devoid of defined sequence or structure signatures are considered non-specific 1,2,5. Substrate binding by these proteins is poorly understood, and it is not known to what extent seemingly non-specific proteins discriminate between different binding sites, aside from those sequestered by nucleic acid structures 6. Here, we systematically examine substrate binding by the apparently non-specific RNA-binding protein C5, and find clear discrimination between different binding site variants. C5 is the protein subunit of the tRNA processing ribonucleoprotein enzyme RNase P from E. coli. The protein binds 5′ leaders of precursor tRNAs at a site without sequence or structure signatures. We measure functional binding of C5 to all possible sequence variants in its substrate binding site, using a high-throughput sequencing kinetics approach (HiTS-Kin) that simultaneously follows processing of thousands of RNA species. C5 binds different substrate variants with affinities varying by orders of magnitude. The distribution of functional affinities of C5 for all substrate variants strikingly resembles affinity distributions of highly specific nucleic acid binding proteins. Unlike these specific proteins, C5 does not bind its physiological RNA targets with the highest affinity, but with affinities near the median of the distribution, a region not associated with a sequence signature. We delineate defined rules governing substrate recognition by C5, which reveal specificity that is hidden in cellular substrates for RNase P. Our findings suggest that Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Research paper thumbnail of Helicase Multitasking in Ribosome Assembly

Molecular Cell, 2009

In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RN... more In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RNA helicase Prp43 on preribosomal RNA. The target regions suggest distinct functions of Prp43 in ribosome biogenesis.

Research paper thumbnail of Single nucleotide polymorphism map of five long-QT genes

Journal of Molecular Medicine, 2005

We screened a white population for single nucleotide polymorphisms (SNPs) in five long QT syndrom... more We screened a white population for single nucleotide polymorphisms (SNPs) in five long QT syndrome genes, namely, KCNQ1 (LQT1), HERG (LQT2), SCN5A (LQT3), KCNE1 (LQT5), and KCNE2 (LQT6). We found 35 SNPs, 10 of which have not been previously described. Ten SNPs were in KCNE1, six in HERG, eight in KCNQ1, four in KCNE2, and seven in SCN5A. Four SNPs were associated with QTc interval in our 141 subjects, one in KCNE1, one in KCNE2, and two in SCN5A. Two of these SNPs have not been described. We conclude that these five long QT syndrome genes contain common variants, some of which are associated with QTc interval in normal persons. We suggest that analysis of these SNPs in a much larger cohort would enable establishment of common haplotypes that are associated with QTc. These haplotypes could facilitate prediction of arrhythmia risk in the general population

Research paper thumbnail of Clinical variability in distal spinal muscular atrophy type 1 (DSMA1): determination of steady-state IGHMBP2 protein levels in five patients with infantile and juvenile disease

Journal of Molecular Medicine, 2009

Distal spinal muscular atrophy type 1 (DSMA1) is caused by mutations in the immunoglobulin μ-bind... more Distal spinal muscular atrophy type 1 (DSMA1) is caused by mutations in the immunoglobulin μ-binding protein 2 (IGHMBP2) gene. Patients with DSMA1 present between 6 weeks and 6 months of age with progressive muscle weakness and respiratory failure due to diaphragmatic palsy. Contrary to this "classic" infantile disease, we have previously described a DSMA1 patient with juvenile disease onset. In this paper, we present (1) a second juvenile case and (2) the first study of DSMA1 on protein level in patients with infantile (n=3) as well as juvenile (n=2) disease onset observing elevated residual steady-state IGHMBP2 protein levels in the patients with late onset DSMA1 as compared to those with classic DSMA1. Mutation screening in IGHMBP2 revealed two patients compound heterozygous for a novel missense mutation (c.1478C→T; p.T493I) and

Research paper thumbnail of Spinal Muscular Atrophy With Respiratory Distress Type 1 (SMARD1)

Journal of Child Neurology, 2007

Autosomal recessive spinal muscular atrophy with respiratory distress type 1 (SMARD1), recently r... more Autosomal recessive spinal muscular atrophy with respiratory distress type 1 (SMARD1), recently referred to as distal spinal muscular atrophy 1 (DSMA1; MIM#604320) and also known as distal hereditary motor neuropathy type 6 (dHMN6 or HMN6), results from mutations in the IGHMBP2 gene on chromosome 11q13.3 encoding the immunoglobulin µ-binding protein 2. In contrast to the infantile spinal muscular atrophy type 1 (SMA1; Werdnig-Hoffmann disease) with weakness predominantly of proximal muscles and bell-shaped thorax deformities due to intercostal muscle atrophy, infants with distal spinal muscular atrophy 1 usually present with distal muscle weakness, foot deformities, and sudden respiratory failure due to diaphragmatic paralysis that often requires urgent intubation. In this article, the authors review the clinical, neuropathological, and genetic aspects of distal spinal muscular atrophy 1 and discuss differential diagnoses.

Research paper thumbnail of Clinical and mutational profile in spinal muscular atrophy with respiratory distress (SMARD): defining novel phenotypes through hierarchical cluster analysis

Human Mutation, 2007

Communicated by Garry Cutting Autosomal recessive spinal muscular atrophy with respiratory distre... more Communicated by Garry Cutting Autosomal recessive spinal muscular atrophy with respiratory distress (SMARD) is a heterogeneous disorder. Mutations in the immunoglobulin l-binding protein gene (IGHMBP2) lead to SMARD1, but clinical criteria that delineate SMARD1 from other SMARD syndromes are not well established. Here we present a retrospective clinical and genetic study to determine the criteria that would predict the presence or absence of IGHMBP2 mutations. From 141 patients with respiratory distress and a spinal muscular atrophy phenotype we recorded the clinical features through a questionnaire and sequenced the entire coding region of IGHMBP2. In 47 (33%) patients we identified IGHMBP2 mutations, 14 of which were not described before. Clinical features and combinations thereof associated with the presence of IGHMBP2 mutations were discovered through hierarchical cluster analysis. This method detects common traits not evident at first sight by grouping items according to their similarity. The combination of ''manifestation of respiratory failure between 6 weeks and 6 months'' AND (''presence of diaphragmatic eventration'' OR ''preterm birth'') predicted the presence of IGHMBP2 mutations with 98% sensitivity and 92% specificity. Non-SMARD1 patients fell into two different symptom clusters, mainly separated by the age at respiratory failure and the presence of multiple congenital contractures. The 14 novel IGHMBP2 mutations comprised missense, frameshift, splice-site, and nonsense mutations. All missense mutations altered conserved residues within or adjacent to the putative DNA helicase domain. The c.123513A4G splice-site mutation did not entirely suppress correct splicing and we found a residual wild-type IGHMBP2 mRNA steady-state level of 24.476.9%, which was, however, not sufficient to avert SMARD1 in this patient.

Research paper thumbnail of IGHMBP2 is a ribosome-associated helicase inactive in the neuromuscular disorder distal SMA type 1 (DSMA1)

Human Molecular Genetics, 2009

Distal spinal muscular atrophy type 1 (DSMA1) is an autosomal recessive disease that is clinicall... more Distal spinal muscular atrophy type 1 (DSMA1) is an autosomal recessive disease that is clinically characterized by distal limb weakness and respiratory distress. In this disease, the degeneration of α-motoneurons is caused by mutations in the immunoglobulin μ-binding protein 2 (IGHMBP2). This protein has been implicated in DNA replication, pre-mRNA splicing and transcription, but its precise function in all these processes has remained elusive. We have purified catalytically active recombinant IGHMBP2, which has enabled us to assess its enzymatic properties and to identify its cellular targets. Our data reveal that IGHMBP2 is an ATPdependent 5'→3' helicase, which unwinds RNA and DNA duplices in vitro. Importantly, this helicase localizes predominantly to the cytoplasm of neuronal and non-neuronal cells and associates with ribosomes. DSMA1-causing amino acid substitutions in IGHMBP2 do not affect ribosome binding yet severely impair ATPase and helicase activity. We propose that IGHMBP2 is functionally linked to translation, and that mutations in its helicase domain interfere with this function in DSMA1 patients.

Research paper thumbnail of Effect of pre‐tRNA 5’ leader sequence variation on the thermodynamic coupling and shared molecular recognition between RNA and protein components of RNase P

Research paper thumbnail of A novel Q378X mutation exists in the transmembrane transporter protein ABCC6 and its pseudogene: implications for mutation analysis in pseudoxanthoma elasticum

Journal of Molecular Medicine, 2001

Pseudoxanthoma elasticum (PXE) is an inherited disorder of the elastic tissue with characteristic... more Pseudoxanthoma elasticum (PXE) is an inherited disorder of the elastic tissue with characteristic progressive calcification of elastic fibers in skin, eye, and the cardiovascular system. Recently mutations in the ABCC6 gene, encoding a transmembrane transporter protein, were identified as cause of the disease. Surprisingly, sequence and RFLP analysis for exon 9 with primers corresponding to flanking intronic sequence in diseased and haplotype negative members from all of our families and in a control population revealed either a homozygous or heterozygous state for the Q378X (1132C→T) nonsense mutation in all individuals. With the publication of the genomic structure of the PXE locus we had identified the starting point of a large genom

Research paper thumbnail of doi:10.1093/nar/gkq1002 The RNA helicase database

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www.rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based sear...

Research paper thumbnail of Distress Type 1 (SMARD1) The Natural Course of Infantile Spinal Muscular Atrophy With Respiratory

BACKGROUND: Only scarce information is available on the long-termoutcome and the natural course o... more BACKGROUND: Only scarce information is available on the long-termoutcome and the natural course of children with infantile spinalmuscular atrophy with respiratory distress type 1 (SMARD1) due tomutations in the IGHMBP2 gene.OBJECTIVE: To describe the natural disease course, to systematicallyquantify the residual capacities of children with SMARD1 who surviveonpermanentmechanicalrespiration,andtoidentifymarkerspredict-ing the disease outcome at the time of manifestation.METHODS: We conducted a longitudinal study of 11 infantile SMARD1patients over a mean observational period of 7.8 (SD 3.2) years.Disease-specific features were continuously assessed by using asemiquantitative scoring system. Additionally, we analyzed the residualenzymatic activity of 6 IGHMBP2 mutants in our patients.RESULTS:Afteraninitialrapiddeclineoftheclinicalscoreuntiltheageof 2 years, residual capabilities reached a plateau or even improved.The overall clinical outcome was markedly heterogeneous, but clinicalscor...

Research paper thumbnail of The RNA helicase database

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www.rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehen-sive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organ-isms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based se...

Research paper thumbnail of A heterozygous genomic rearrangement in a patient with juvenile spinal muscle atrophy with respiratory distress type 1 (SMARD1)

Research paper thumbnail of Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

Research paper thumbnail of A helicase links upstream ORFs and RNA structure

Research paper thumbnail of The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs

Nature, 2018

The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue D... more The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian orthologue DDX3 are critical for the initiation of translation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by a range of viruses. How Ded1p and its orthologues engage RNAs during the initiation of translation is unknown. Here we show, by integrating transcriptome-wide analyses of translation, RNA structure and Ded1p-RNA binding, that the effects of Ded1p on the initiation of translation are connected to near-cognate initiation codons in 5' untranslated regions. Ded1p associates with the translation pre-initiation complex at the mRNA entry channel and repressing the activity of Ded1p leads to the accumulation of RNA structure in 5' untranslated regions, the initiation of translation from near-cognate start codons immediately upstream of these structures and decreased protein synthesis from the corresponding main open reading frames. T...

Research paper thumbnail of Coupling between the DEAD-box RNA helicases Ded1p and eIF4A

eLife, Jan 5, 2016

Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p.... more Eukaryotic translation initiation involves two conserved DEAD-box RNA helicases, eIF4A and Ded1p. Here we show that S. cerevisiae eIF4A and Ded1p directly interact with each other and simultaneously with the scaffolding protein eIF4G. We delineate a comprehensive thermodynamic framework for the interactions between Ded1p, eIF4A, eIF4G, RNA and ATP, which indicates that eIF4A, with and without eIF4G, acts as modulator for activity and substrate preferences of Ded1p, which is the RNA remodeling unit in all complexes. Our results reveal and characterize an unexpected interdependence between the two RNA helicases and eIF4G, and suggest that Ded1p is an integral part of eIF4F, the complex comprising eIF4G, eIF4A, and eIF4E.

Research paper thumbnail of The Natural Course of Infantile Spinal Muscular Atrophy With Respiratory Distress Type 1 (SMARD1)

Research paper thumbnail of A New Mutation of IGHMBP2 Gene

Pediatric Neurology, 2006

Research paper thumbnail of The RNA helicase database

Nucleic Acids Research, 2011

RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA met... more RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www .rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based searches of the database.

Research paper thumbnail of Hidden specificity in an apparently nonspecific RNA-binding protein

Nature, 2013

Nucleic acid binding proteins are generally viewed as either specific or non-specific, depending ... more Nucleic acid binding proteins are generally viewed as either specific or non-specific, depending on characteristics of their binding sites in DNA or RNA 1,2. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with defined signatures in sequence, structure, or both 1-4. Proteins that bind to sites devoid of defined sequence or structure signatures are considered non-specific 1,2,5. Substrate binding by these proteins is poorly understood, and it is not known to what extent seemingly non-specific proteins discriminate between different binding sites, aside from those sequestered by nucleic acid structures 6. Here, we systematically examine substrate binding by the apparently non-specific RNA-binding protein C5, and find clear discrimination between different binding site variants. C5 is the protein subunit of the tRNA processing ribonucleoprotein enzyme RNase P from E. coli. The protein binds 5′ leaders of precursor tRNAs at a site without sequence or structure signatures. We measure functional binding of C5 to all possible sequence variants in its substrate binding site, using a high-throughput sequencing kinetics approach (HiTS-Kin) that simultaneously follows processing of thousands of RNA species. C5 binds different substrate variants with affinities varying by orders of magnitude. The distribution of functional affinities of C5 for all substrate variants strikingly resembles affinity distributions of highly specific nucleic acid binding proteins. Unlike these specific proteins, C5 does not bind its physiological RNA targets with the highest affinity, but with affinities near the median of the distribution, a region not associated with a sequence signature. We delineate defined rules governing substrate recognition by C5, which reveal specificity that is hidden in cellular substrates for RNase P. Our findings suggest that Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Research paper thumbnail of Helicase Multitasking in Ribosome Assembly

Molecular Cell, 2009

In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RN... more In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RNA helicase Prp43 on preribosomal RNA. The target regions suggest distinct functions of Prp43 in ribosome biogenesis.

Research paper thumbnail of Single nucleotide polymorphism map of five long-QT genes

Journal of Molecular Medicine, 2005

We screened a white population for single nucleotide polymorphisms (SNPs) in five long QT syndrom... more We screened a white population for single nucleotide polymorphisms (SNPs) in five long QT syndrome genes, namely, KCNQ1 (LQT1), HERG (LQT2), SCN5A (LQT3), KCNE1 (LQT5), and KCNE2 (LQT6). We found 35 SNPs, 10 of which have not been previously described. Ten SNPs were in KCNE1, six in HERG, eight in KCNQ1, four in KCNE2, and seven in SCN5A. Four SNPs were associated with QTc interval in our 141 subjects, one in KCNE1, one in KCNE2, and two in SCN5A. Two of these SNPs have not been described. We conclude that these five long QT syndrome genes contain common variants, some of which are associated with QTc interval in normal persons. We suggest that analysis of these SNPs in a much larger cohort would enable establishment of common haplotypes that are associated with QTc. These haplotypes could facilitate prediction of arrhythmia risk in the general population

Research paper thumbnail of Clinical variability in distal spinal muscular atrophy type 1 (DSMA1): determination of steady-state IGHMBP2 protein levels in five patients with infantile and juvenile disease

Journal of Molecular Medicine, 2009

Distal spinal muscular atrophy type 1 (DSMA1) is caused by mutations in the immunoglobulin μ-bind... more Distal spinal muscular atrophy type 1 (DSMA1) is caused by mutations in the immunoglobulin μ-binding protein 2 (IGHMBP2) gene. Patients with DSMA1 present between 6 weeks and 6 months of age with progressive muscle weakness and respiratory failure due to diaphragmatic palsy. Contrary to this "classic" infantile disease, we have previously described a DSMA1 patient with juvenile disease onset. In this paper, we present (1) a second juvenile case and (2) the first study of DSMA1 on protein level in patients with infantile (n=3) as well as juvenile (n=2) disease onset observing elevated residual steady-state IGHMBP2 protein levels in the patients with late onset DSMA1 as compared to those with classic DSMA1. Mutation screening in IGHMBP2 revealed two patients compound heterozygous for a novel missense mutation (c.1478C→T; p.T493I) and

Research paper thumbnail of Spinal Muscular Atrophy With Respiratory Distress Type 1 (SMARD1)

Journal of Child Neurology, 2007

Autosomal recessive spinal muscular atrophy with respiratory distress type 1 (SMARD1), recently r... more Autosomal recessive spinal muscular atrophy with respiratory distress type 1 (SMARD1), recently referred to as distal spinal muscular atrophy 1 (DSMA1; MIM#604320) and also known as distal hereditary motor neuropathy type 6 (dHMN6 or HMN6), results from mutations in the IGHMBP2 gene on chromosome 11q13.3 encoding the immunoglobulin µ-binding protein 2. In contrast to the infantile spinal muscular atrophy type 1 (SMA1; Werdnig-Hoffmann disease) with weakness predominantly of proximal muscles and bell-shaped thorax deformities due to intercostal muscle atrophy, infants with distal spinal muscular atrophy 1 usually present with distal muscle weakness, foot deformities, and sudden respiratory failure due to diaphragmatic paralysis that often requires urgent intubation. In this article, the authors review the clinical, neuropathological, and genetic aspects of distal spinal muscular atrophy 1 and discuss differential diagnoses.

Research paper thumbnail of Clinical and mutational profile in spinal muscular atrophy with respiratory distress (SMARD): defining novel phenotypes through hierarchical cluster analysis

Human Mutation, 2007

Communicated by Garry Cutting Autosomal recessive spinal muscular atrophy with respiratory distre... more Communicated by Garry Cutting Autosomal recessive spinal muscular atrophy with respiratory distress (SMARD) is a heterogeneous disorder. Mutations in the immunoglobulin l-binding protein gene (IGHMBP2) lead to SMARD1, but clinical criteria that delineate SMARD1 from other SMARD syndromes are not well established. Here we present a retrospective clinical and genetic study to determine the criteria that would predict the presence or absence of IGHMBP2 mutations. From 141 patients with respiratory distress and a spinal muscular atrophy phenotype we recorded the clinical features through a questionnaire and sequenced the entire coding region of IGHMBP2. In 47 (33%) patients we identified IGHMBP2 mutations, 14 of which were not described before. Clinical features and combinations thereof associated with the presence of IGHMBP2 mutations were discovered through hierarchical cluster analysis. This method detects common traits not evident at first sight by grouping items according to their similarity. The combination of ''manifestation of respiratory failure between 6 weeks and 6 months'' AND (''presence of diaphragmatic eventration'' OR ''preterm birth'') predicted the presence of IGHMBP2 mutations with 98% sensitivity and 92% specificity. Non-SMARD1 patients fell into two different symptom clusters, mainly separated by the age at respiratory failure and the presence of multiple congenital contractures. The 14 novel IGHMBP2 mutations comprised missense, frameshift, splice-site, and nonsense mutations. All missense mutations altered conserved residues within or adjacent to the putative DNA helicase domain. The c.123513A4G splice-site mutation did not entirely suppress correct splicing and we found a residual wild-type IGHMBP2 mRNA steady-state level of 24.476.9%, which was, however, not sufficient to avert SMARD1 in this patient.

Research paper thumbnail of IGHMBP2 is a ribosome-associated helicase inactive in the neuromuscular disorder distal SMA type 1 (DSMA1)

Human Molecular Genetics, 2009

Distal spinal muscular atrophy type 1 (DSMA1) is an autosomal recessive disease that is clinicall... more Distal spinal muscular atrophy type 1 (DSMA1) is an autosomal recessive disease that is clinically characterized by distal limb weakness and respiratory distress. In this disease, the degeneration of α-motoneurons is caused by mutations in the immunoglobulin μ-binding protein 2 (IGHMBP2). This protein has been implicated in DNA replication, pre-mRNA splicing and transcription, but its precise function in all these processes has remained elusive. We have purified catalytically active recombinant IGHMBP2, which has enabled us to assess its enzymatic properties and to identify its cellular targets. Our data reveal that IGHMBP2 is an ATPdependent 5'→3' helicase, which unwinds RNA and DNA duplices in vitro. Importantly, this helicase localizes predominantly to the cytoplasm of neuronal and non-neuronal cells and associates with ribosomes. DSMA1-causing amino acid substitutions in IGHMBP2 do not affect ribosome binding yet severely impair ATPase and helicase activity. We propose that IGHMBP2 is functionally linked to translation, and that mutations in its helicase domain interfere with this function in DSMA1 patients.