Helicase-inactivating mutations as a basis for dominant negative phenotypes

There is ample evidence from studies of both unicellular and multicellular organisms that helicase-inactivating mutations lead to cellular dysfunction and disease phenotypes. In this review, we will discuss the mechanisms underlying the basis for abnormal phenotypes linked to mutations in genes encoding DNA helicases. Recent evidence demonstrates that a clinically relevant patient missense mutation in Fanconi Anemia Complementation Group J exerts detrimental effects on the biochemical activities of the FANC J helicase, and these molecular defects are responsible for aberrant genomic stability and a poor DNA damage response. The ability of FANC J to use the energy from AT P hydrolysis to produce the force required to unwind duplex or G-quadruplex DNA structures or destabilize protein bound to DNA is required for its DNA repair functions in vivo. Strikingly, helicase-inactivating mutations can exert a spectrum of dominant negative phenotypes, indicating that expression of the mutant helicase protein potentially interferes with normal DNA metabolism and has an effect on basic cellular processes such as DNA replication, the DNA damage response and protein trafficking. This review emphasizes that future studies of clinically relevant mutations in helicase genes will be important to understand the molecular pathologies of the associated diseases and their impact on heterozygote carriers.Key words: helicase, dominant negative, dominant lethal, DNA repair, replication, genomic stability, human disease, Fanconi anemia, FANCJ, G-quadruplexClassic genetic complementation studies in E. coli provided some of the first biological evidence that the catalytic DNA unwinding activity performed by helicases is critically important in various aspects of cellular DNA metabolism including replication, DNA repair and recombination.^1,2 Appreciation that the conserved amino acid motifs found in a variety of cellular DNA helicases compose protein domains important for ATP binding and hydrolysis, DNA binding and coupling of ATP hydrolysis to separation of complementary strands in a structured nucleic acid molecule led to new insights for how helicases function mechanistically (reviewed in ref. ^3–5). Advances in understanding the roles of helicases in DNA repair really provided a foundation for future progress in the field. The genetics in bacterial systems gradually led to similar complementation experiments in the unicellular eukaryotic model organisms Sachromyces cerevisiae and Sachromyces pombe.^6–10 In a number of cases, the underlying mechanisms whereby helicases operate to preserve genomic stability were found to be generally conserved between prokaryotes and eukaryotes. Ultimately, genetic analyses of helicase mutants in higher order eukaryotes (e.g., C. elegans,^11–13 Drosophila,¹⁴ Xenopus^15,16) have begun to pave the way for studies of mammalian DNA helicases in cell-based models and mice. As human helicase genetic disorders are continuously being discovered,^17–24 the interest and pace of investigation to understand how helicases preserve the genome continues to accelerate (reviewed in refs. ^25–31).In this review, we will focus on discussing some landmark studies that describe how helicase-inactivating mutations disrupt normal cellular DNA metabolism, with a particular emphasis on dominant negative phenotypes exerted by mutations in helicase genes. This topic deserves special attention since recent evidence from our lab and others suggests that naturally occurring mutations in helicase genes exert deleterious effects even in a wild-type background which provides insight to the molecular-genetic roles of various helicases to maintain genomic stability. We will begin by discussing genetic and biochemical studies of bacterial DNA helicases which provide an excellent foundation for this line of inquiry, and then focus on eukaryotic helicases with a particular emphasis placed on human DNA helicases, mutated in chromosomal instability and DNA repair disorders.     

Polar mutations in membrane proteins as a biophysical basis for disease

Transmembrane (TM) alpha-helices are surrounded by the hydrocarbon chains of the lipid bilayer. The low dielectric constant of this environment makes it extremely unfavorable for a residue with a polar side chain to exist in a non-H-bonded state. Therefore, in combination with a wild-type polar residue partner, a polar TM mutant could generate, in some cases, a non-native H-bond that could impair native protein structure/function-and possibly lead to a disease state. We have examined protein mutation databases and have found many examples of TM-based apolar to polar mutations that are, in fact, a cause of human disease. Here we review the various molecular defects that such mutations can produce, including impeding protein dynamics by side-chain-side-chain interhelical H-bond cross-links; alteration of helical packing through steric hindrance; and disruption of a protein active site. We further note that the reverse case--membrane-embedded polar to apolar mutations--can similarly cause human disease, implying that native interhelical H-bonds can also play pivotal roles in stabilizing native TM domains. As a specific example, we show that the Gly to Arg mutation occurs statistically more frequently in TM domains as compared to its occurrence in soluble domains, suggesting that TM-based G-to-R mutations have a high "phenotypic propensity" for disease. A more complete understanding of how mutations involving polar residues in TM domains of proteins translate into compromised function may aid in the development of novel therapeutics.     

Titin mutations as the molecular basis for dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is a heterogeneous cardiac disease characterized by ventricular dilatation and systolic dysfunction. Recent genetic studies have revealed that mutations in genes for cardiac sarcomere components lead to DCM. The cardiac sarcomere consists of thick and thin filaments and a giant protein, titin. Because one of the loci of familial DCM was mapped to the region of the titin gene, we searched for titin mutations in the patients and identified four possible disease-associated mutations. Two mutations, Val54Met and Ala743Val, were found in the Z-line region of titin and decreased binding affinities of titin to Z-line proteins T-cap/telethonin and alpha-actinin, respectively, in yeast two-hybrid assays. The other two mutations were found in the cardiac-specific N2-B region of titin and one of them was a nonsense mutation, Glu4053ter, presumably encoding for a truncated nonfunctional molecule. These observations suggest that titin mutations may cause DCM in a subset of the patients.     

attG and attC mutations of Agrobacterium tumefaciens are dominant negative mutations that block attachment and virulence

The cryptic plasmid (pAT) of Agrobacterium tumefaciens was not required for virulence or attachment to plant surfaces. However, mutations in the attC and attG genes located on pAT caused the bacteria to become avirulent and non-attaching on tomato, carrot, and Bryophyllum daigremontiana. This was the case whether the mutation was in the copy of the genes located on pAT or whether it was carried in a second copy of the attA-G operon located on a plasmid in cells that contained a wild-type copy of pAT. Thus attC and attG mutations are dominant negative mutations. The mechanism by which these mutations block attachment and virulence is unknown.     

Upslope movements and large scale expansions: the taxonomy and biogeography of the Coenonympha arcania –C. d arwiniana –C. gardetta butterfly species complex

Sibling species groups are suitable models for the understanding of inter‐ and intraspecific processes in taxonomy and biogeography. We analysed 262 individuals from the Alps of the Coenonympha arcania/gardetta species complex by allozyme electrophoresis. These taxa showed high variance amongst populations (F_ST: 0.391) and strong intertaxon genetic differentiation (F_CT: 0.376). Although morphologically similar, Coenonympha gardetta and Coenonympha arcania clearly differ in their genetic characteristics; the morphologically intermediate taxa Coenonympha darwiniana darwiniana and Coenonympha darwiniana macromma are genetically well distinguished from each other and the two other taxa. Coenonympha arcania and C. d. macromma most probably share a common ancestor and evolved by cladogenesis, whereas the taxonomic situation of C. d. darwiniana is still unresolved: This taxon might be the result of hybridization between C. arcania and C. gardetta or it might have a common ancestor together with C. gardetta. We suggest species rank for all four taxa. The distribution of genetic diversity of these populations and the differentiation amongst populations suggest rather different biogeographical scenarios: C. arcania most probably is of Mediterranean origin with postglacial range expansion northwards; C. gardetta survived the last ice age in peripheral refugia of the Alps and has spread all over this high mountain system in the postglacial; C. darwiniana and C. macromma survived the Würm in geographic proximity to their actual distribution areas and only have performed moderate uphill translocations during postglacial warming. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 890–904.     

Amphibians as research models for regenerative medicine

The ability to regenerate bone across a critical size defect would be a marked clinical advance over current methods for dealing with such structural gaps. Here, we briefly review the development of limb bones and the mandible, the regeneration of urodele limbs after amputation, and present evidence that urodele and anuran amphibians represent a valuable research model for the study of segment defect regeneration in both limb bones and mandible.     

Disease-associated mutations in SOD1 are impervious to dominant positive or negative effects

The familial form of amyotrophic lateral sclerosis is caused by mutations in the SOD1 gene encoding the cytosolic antioxidant enzyme Cu,Zn superoxide dismutase. Although there is no clear correlation between disease and dismutating catalytic activity among the various disease-associated SOD1 alleles, all of the known missense mutations significantly alter the half-life of the encoded polypeptides. Using transient transfection studies in mammalian cells, it was demonstrated that a frameshift mutation in SOD1 which results in a truncated polypeptide is similarly destabilized. Using an epitope-tagging strategy to discriminate between mutant and wild-type SOD1 polypeptides, no evidence for dominant effects on polypeptide stability was detected, including that of a positive effect of the wild-type on mutant SOD1 polypeptides or that of a negative effect of mutant on wild-type SOD1 polypeptides. These experiments thus favor a non-catalytic role of mutant forms of SOD1 in disease progression.     

ATM gene mutations result in both recessive and dominant expression phenotypes of genes and microRNAs

The defining characteristic of recessive disorders is the absence of disease in heterozygous carriers of the mutant alleles. However, it has been recognized that recessive carriers may differ from noncarriers in some phenotypes. Here, we studied ataxia telangiectasia (AT), a classical recessive disorder caused by mutations in the ataxia telangiectasia mutated (ATM) gene. We compared the gene and microRNA expression phenotypes of noncarriers, AT carriers who have one copy of the ATM mutations, and AT patients with two copies of ATM mutations. We found that some phenotypes are more similar between noncarriers and AT carriers compared to AT patients, as expected for a recessive disorder. However, for some expression phenotypes, AT carriers are more similar to the patients than to the noncarriers. Analysis of one of these expression phenotypes, TNFSF4 level, allowed us to uncover a regulatory pathway where ATM regulates TNFSF4 expression through MIRN125B (also known as miR-125b or miR125b) [corrected] In AT carriers and AT patients, this pathway is disrupted. As a result, the level of MIRN125B is lower and the level of its target gene, TNFSF4, is higher than in noncarriers. A decreased level of MIRN125B is associated with breast cancer, and an elevated level of TNFSF4 is associated with atherosclerosis. Thus, our findings provide a mechanistic suggestion for the increased risk of breast cancer and heart disease in AT carriers. By integrating molecular and computational analyses of gene and microRNA expression, we show the complex consequences of a human gene mutation.     

Chemiluminometric β-galactosidase detection as a basis for a tetracycline screening test in milk

The observation that tetracyclines inhibit the biosynthesis of β-galactosidase in Escherichia coli to a greater extent than other antibacterials was exploited for the development of a chemiluminometric method to detect residues of this class of antibiotics in milk. The procedure involves the incubation of a milk sample with 10⁷ CFU/ml of an E. coli strain in the presence of IPTG, an inducer of β-galactosidase, and of EGTA, a chelator of calcium ions, followed by a 1000-fold dilution and measurement of the residual enzymatic activity using the chemiluminogenic substrate Galacton. Chemiluminometry proved an essential tool in this procedure because the extensive dilution of the sample, necessary to avoid light quenching by turbidity, results in an insufficient level of β-galactosidase activity to be measurable by colorimetry. This tetracycline galactosidase (TG) test has been validated and compared in the field to existing commercial screening assays for antibiotics. Its detection limit for tetracyclines ranges between 40 and 65 μg/kg, which is below the European maximum residue limit (MRL = 100 μg/kg) in milk. No other antibacterials, at concentrations commonly expected in milk, were found to interfere with the TG test. Strategies to avoid false positive reactions possibly arising from very high somatic cell counts will be reported elsewhere. © 1998 John Wiley & Sons, Ltd.     

New insights into 5q- syndrome as a ribosomopathy

Myelodysplastic Syndromes (MDS) are a heterogeneous group of acquired clonal bone marrow disorders, characterised by ineffective haematopoiesis. The mechanisms underlying many of these blood disorders have remained elusive due to the difficulty in pinpointing specific gene mutations or haploinsufficencies, which can occur within large deleted regions. However, there is an increasing interest in the classification of some of these diseases as ribosomopathies. Indeed, studies have implicated Ribosomal Protein (RP) S14 as a strong candidate for haploinsufficiency in 5q- syndrome, a particular form of MDS. Recently, two novel mouse models have provided evidence for the involvement of both RPS14 and the p53 pathway, and specific miRNAs in 5q- syndrome. In this review we will discuss: 5q- syndrome mouse models, the possible mechanisms underlying this blood disorder with respect to the candidate genes, and comparisons with other ribosomopathies, and the involvement of the p53 pathway in these diseases.     

Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells

The introduction of double stranded RNA (dsRNA) into the cytoplasm of mammalian cells usually leads to a potent antiviral response resulting in the rapid induction of interferon beta (IFNβ).     

Cas9‐mediated mutagenesis of potato starch‐branching enzymes generates a range of tuber starch phenotypes

We investigated whether Cas9‐mediated mutagenesis of starch‐branching enzymes (SBEs) in tetraploid potatoes could generate tuber starches with a range of distinct properties. Constructs containing the Cas9 gene and sgRNAs targeting SBE1, SBE2 or both genes were introduced by Agrobacterium‐mediated transformation or by PEG‐mediated delivery into protoplasts. Outcomes included lines with mutations in all or only some of the homoeoalleles of SBE genes and lines in which homoeoalleles carried several different mutations. DNA delivery into protoplasts resulted in mutants with no detectable Cas9 gene, suggesting the absence of foreign DNA. Selected mutants with starch granule abnormalities had reductions in tuber SBE1 and/or SBE2 protein that were broadly in line with expectations from genotype analysis. Strong reduction in both SBE isoforms created an extreme starch phenotype, as reported previously for low‐SBE potato tubers. HPLC‐SEC and ¹H NMR revealed a decrease in short amylopectin chains, an increase in long chains and a large reduction in branching frequency relative to wild‐type starch. Mutants with strong reductions in SBE2 protein alone had near‐normal amylopectin chain‐length distributions and only small reductions in branching frequency. However, starch granule initiation was enormously increased: cells contained many granules of <4 μm and granules with multiple hila. Thus, large reductions in both SBEs reduce amylopectin branching during granule growth, whereas reduction in SBE2 alone primarily affects numbers of starch granule initiations. Our results demonstrate that Cas9‐mediated mutagenesis of SBE genes has the potential to generate new, potentially valuable starch properties without integration of foreign DNA into the genome.     

Two dominant photomorphogenic mutations of Arabidopsis thaliana identified as suppressor mutations of hy2

By screening suppressor mutants of the hy2 mutation of Arabidopsis thaliana , two dominant photomorphogenic mutants, shy1-1D and shy2-1D , for two genetic loci designated as SHY1 and SHY2 ( s uppressor of hy 2 mutation) have been isolated. Both of these non-allelic, extragenic suppressor mutations of hy2 are located on chromosome 1 of the Arabidopsis genome. Both mutations suppress the elongated hypocotyl phenotype of hy2 by light-independent inhibition of hypocotyl growth as well as by increasing the effectiveness of light inhibition of hypocotyl elongation. The shy1-1D mutation is partially photomorphogenic in darkness with apical hook opening and reduced hypocotyl elongation. The shy2-1D mutant displays highly photomorphogenic characteristics in darkness such as true leaf development, cotyledon expansion, and extremely reduced hypocotyl growth. In regard to hypocotyl elongation, however, the shy2-1D mutation is still light sensitive. Examination of red/far-red light responses shows that the shy1-1D mutation suppresses the hypocotyl elongation of the hy2 mutation effectively in red light but not effectively in far-red light. The shy2-1D suppresses hypocotyl elongation of the hy2 mutation effectively in both red and far-red light. Both mutations can also suppress the early-flowering phenotype of hy2 and have a distinct pleiotropic effect on leaf development such as upward leaf rolling. The data obtained suggest that SHY1 and SHY2 represent a novel class of components involved in the photomorphogenic pathways of Arabidopsis . This is the first report on the identification of dominant mutations in the light signal transduction pathway of plants.     

Impact of BCR-ABL mutations on patients with chronic myeloid leukemia

Therapies that target BCR-ABL in chronic myeloid leukemia, including imatinib, dasatinib and nilotinib, have dramatically improved patient outcome. BCR-ABL mutations, however, contribute to treatment resistance by disrupting drug contact sites or causing conformational changes thus making contact sites inaccessible. Clinical data indicate that developing BCR-ABL mutations during imatinib treatment is predictive for shorter progression-free survival, and that outcomes may depend on mutation type or location. In vitro, dasatinib and nilotinib inhibit most imatinib-resistant BCR-ABL mutations, except for T315I. In clinical studies, other mutations associated with treatment resistance include V299L, T315A, and F317I/L for dasatinib and Y253F/H, E255K/V, and F359C/V for nilotinib. Evaluating patients with clinical signs of resistance for BCR-ABL mutations is an important component of disease monitoring, potentially facilitating selection of subsequent therapy. First-line treatment with dasatinib or nilotinib instead of imatinib may reduce emergence of resistance but novel agents are needed to overcome the problematic T315I mutation.     

Laminin 5 mutations in junctional epidermolysis bullosa: molecular basis of Herlitz vs non-Herlitz phenotypes

Junctional epidermolysis bullosa (JEB) is a group of heritable blistering diseases in which tissue separation occurs within the lamina lucida of the cutaneous basement membrane zone. Clinically, two broad subcategories have been recognized: The Herlitz variant (H-JEB; OMIM 226700) is characterized by early demise of the affected individuals, usually within the first year of life, while non-Herlitz (nH-JEB; OMIM 226650) patients show a milder phenotype with life-long blistering, yet with normal lifespan. In this study, we have examined a cohort of 27 families, 15 with Herlitz and 12 with non-Herlitz JEB, for mutations in the candidate genes, LAMA3, LAMB3, and LAMC2, encoding the subunit polypeptides of laminin 5. The mutation detection strategy consisted of PCR amplification of all exons in these genes, followed by heteroduplex scanning and nucleotide sequencing. We were able to identify pathogenic mutations in both alleles of each proband, the majority of the mutations being in the LAMB3 gene. Examination of the mutation database revealed that most cases with Herlitz JEB harbored premature termination codon (PTC) mutations in both alleles. In non-Herlitz cases, the PTC mutation was frequently associated with a missense mutation or a putative splicing mutation in trans. In three cases with putative splicing mutations, RT-PCR analysis revealed a repertoire of splice variants in-frame, predicting the synthesis of either shortened or lengthened, yet partly functional, polypeptides. These observations would explain the relatively mild phenotype in cases with splicing mutations. Collectively, these findings, together with the global laminin 5 mutation database, contribute to our understanding of the genotype/phenotype correlations explaining the Herlitz vs non-Herlitz phenotypes.     

Truncated TrkB: beyond a dominant negative receptor

BDNF activates trkB receptors to regulate neuronal survival, differentiation, and proliferation. Mutations in the BDNF gene, altered BDNF expression, and altered trkB expression are associated with degenerative and psychiatric disorders. The full-length trkB receptor (trkB.tk(+)) undergoes autophosphorylation to activate intracellular signaling pathways. The truncated trkB receptor (trkB.t1) is abundantly expressed in the brain but lacks the catalytic tyrosine kinase domain. TrkB.t1 is a dominant-negative receptor that inhibits trkB.tk(+) signaling. While this is an important function of trkB.t1, it is only one of its many functions. TrkB.t1 sequesters and translocate BDNF, induces filopodia and neurite outgrowth, stimulates intracellular signaling cascades, regulates Rho GTPase signaling, and modifies cytoskeletal structures. TrkB.t1 is an active signaling molecule with regulatory effects on neurons and astrocytes.