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Oligonucleotide-mediated gene modification and its promise for animal agriculture.

One of the great aspirations in modern biology is the ability to utilise the expanding knowledge of the genetic basis of phenotypic diversity through the purposeful tailoring of the mammalian genome. A number of technologies are emerging which have the capacity to modify genes in their chromosomal context. Not surprisingly, the major thrust in this area has come from the evaluation of gene therapy applications to correct mutations implicated in human genetic diseases. The recent development of somatic cell nuclear transfer (SCNT) provides access to these technologies for the purposeful modification of livestock animals. The enormous phenotypic variety existent in contemporary livestock animals has in many cases been linked to quantitative trait loci (QTL) and their underlying point mutations, often referred to as single-nucleotide polymorphisms (SNPs). Thus, the ability for the targeted genetic modification of livestock animals constitutes an attractive opportunity for future agricultural applications. In this review, we will summarize attempts and approaches for oligonucleotide-mediated gene modification (OGM) strategies for the site-specific modification of the genome, with an emphasis on chimeric RNA-DNA oligonucleotides (RDOs) and single-stranded oligonucletides (ssODNs). The potential of this approach for the directed genetic improvement of livestock animals is illustrated through examples, outlining the effects of point mutations on important traits, including meat and milk production, reproductive performance, disease resistance and superior models of human diseases. Current technological hurdles and potential strategies that might remove these barriers in the future are discussed.

Animal Diseases↗

Stepwise modification of lysine residues of glucose oxidase with citraconic anhydride.

Structural properties of modified forms of glucose oxidase made by stepwise specific modification have been investigated. By a single step modification, one of the modified forms resulted in the conversion of native structure of glucose oxidase to molten globule like form [S. Hosseinkhani, B. Ranjbar, H. Naderi-Manesh, M. Nemat-Gorgani, FEBS Lett. 561 (2004) 213-216]. Chemical modification of lysine residues in glucose oxidase was carried out using different concentration of citraconic anhydride. Modification brought about changes in the tertiary structure with some degree of alteration in secondary structure. FTIR, far and near-UV CD spectropolarimetry, intrinsic and extrinsic fluorescence spectroscopy showed structural changes of glucose oxidase in a concentration dependent manner. This was supported by comparative study of secondary and tertiary structure.

Aspergillus niger↗

Non-enzymatic posttranslational modifications of bovine serum albumin by oxo-compounds investigated by chromatographic and electrophoretic methods.

Non-enzymatic posttranslational modifications of bovine serum albumin (BSA) by oxo-compounds, particularly glucose, ribose, glyoxal and glutardialdehyde, have been investigated using a set of modern chromatographic and electrophoretic separation methods. High-performance liquid chromatography (HPLC) alternatively with UV spectrophotometric (diode array) or mass spectrometric (MS) detection, polyacrylamide gel electrophoresis (PAGE) with Coomassie brilliant blue staining detection, and capillary zone electrophoresis (CZE) with UV spectrophotometric detection have been employed for the investigation of the chemical and structural changes of BSA caused by its reaction with the above oxo-compounds exhibiting different degree of reactivity. The extent of modifications was found to be dependent on the nature of the oxo-compound used and progressed in the glucose<ribose<glyoxal<glutaraldehyde order. With the aid of HPLC/UV/MS and CZE/UV tryptic peptide mapping and amino acid analysis of both unmodified and modified BSA it was revealed that the mildest modification resulted from the reaction of BSA with glucose, in this case presumably only monofunctional derivatives have arisen, whereas the most intensive modifications were found after BSA reaction with glutardialdehyde, which resulted in high degree of both inter- and intra-molecular cross-linking, due to which no unmodified peptides were detected after tryptic cleavage of BSA modified by this agent.

Aldehydes↗

The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA.

Post-transcriptional modifications were mapped in domains II, IV and V of 23S RNA from the archaeon Haloarcula marismortui. The RNA was investigated by two primer extension techniques using reverse transcriptase and three mass spectrometry techniques. One primer extension technique utilized decreasing concentrations of deoxynucleotide triphosphates to detect 2'-O-ribose methylations and other polymerase blocking modifications. In the other, the rRNA was chemically modified, followed by mild alkaline hydrolysis to map pseudo-uridine groups (Psis). RNA fragments for mass spectrometry were isolated from 23S rRNA by site-directed RNase H or mung bean nuclease digestion followed by gel purification. Modified RNase digestion fragments were identified with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) and the modifications were further studied by tandem MS. Psis suggested by the primer extension technique were verified by specific cyanoethylation and mass spectrometric detection. A total of only five post-transcriptionally methylated nucleotides and three Psis were detected in the three 23S rRNA domains. One of the methylated nucleotides has not been reported while a dispute about the number of Psis is solved. The limited number of modified nucleotides suggests that H. marismortui does not have special needs for extensive rRNA modifications. We have performed detailed investigations on the three-dimensional location and molecular interactions of the modified nucleotides by computer analysis. Our results show that all the modified positions are at regions with RNA-RNA contacts and all except one are at the surface of the subunit and in functionally important regions.

Haloarcula marismortui↗

Effects of lifestyle modifications on C-reactive protein: contribution of weight loss and improved aerobic capacity.

High-sensitivity C-reactive protein (hs-CRP) is associated with an increased risk of cardiovascular disease and the development of type 2 diabetes mellitus. We analyzed the effects of lifestyle modifications including exercise training on hs-CRP in 47 overweight and obese adults. Subjects were divided into a lifestyle modification group (n=23) (exercise and diet instruction) and a control group (n=24) who did not participate in any lifestyle modification. After 3 months, body weight (80.8+/-11.5 to 73.5+/-10.7 kg, P<.01), total cholesterol (217+/-38.4 to 178.0+/-25.6 mg/dL, P<.01), low-density lipoprotein cholesterol (151.3+/-34.9 to 116.7+/-27.8 mg/dL, P<.01), Vo(2)peak (30.3+/-5.1 to 37.1+/-6.9 mL/[kg . min], P<.01), and log hs-CRP (0.75+/-0.4 to 0.56+/-0.3 mg/dL, P=.01) were significantly improved in the lifestyle modification group, but there was no significant improvement in the control group. Changes in log hs-CRP were associated with changes in Vo(2)peak (r=-0.41, P=.004) and changes in weight loss (r=0.42, P=.004). In stepwise multiple regression analysis, weight loss (P=.034) and improved Vo(2)peak (P=.039) were independent predictors of the changes in hs-CRP. When grouped into quartiles according to decreasing weight and increasing Vo(2)peak, levels of changes in log hs-CRP improved across quartiles of weight loss (P<.05) and improved Vo(2)peak (P<.01). Thus, lifestyle changes including regular exercise training in overweight and obese adults decreased hs-CRP, and this was associated with weight loss and improved Vo(2)peak.

Adult↗

Effects of lifestyle modification on metabolic parameters and carotid intima-media thickness in patients with type 2 diabetes mellitus.

The aim of this study was to examine the effects of a 6-month intensive lifestyle modification intervention on metabolic parameters and carotid intima-media thickness (IMT) in patients with type 2 diabetes mellitus. Fifty-eight subjects with type 2 diabetes mellitus were randomly assigned to the intervention group or the control group. The subjects in the intervention group participated in a 16-week intensive lifestyle modification program and subsequent monthly meetings during the 6-month study period. Control subjects received basic dietary education and usual care. Anthropometric data, metabolic parameters, and carotid IMT were examined before the intervention and after 6 months. Lifestyle modification intervention group patients showed a significant reduction in HbA1c (-1.0% +/- 1.3% vs +0.1% +/- 1.2%, P = .002), fasting blood glucose (-1.6 +/- 1.5 vs +0.3 +/- 2.5 mmol/L, P = .001), and 2-hour postprandial plasma glucose (-2.1 +/- 2.5 vs +0.8 +/- 4.4 mmol/L, P = .003) compared with control patients after 6 months. Body weight (-2.0 +/- 2.6 vs +0.2 +/- 1.7 kg, P = .001), body mass index (-0.8 +/- 1.0 vs 0.0 +/- 0.8 kg/m2, P = .003), and systolic blood pressure (-8.2 +/- 15.9 vs +0.4 +/- 14.1 mm Hg, P = .041) were significantly decreased in the intervention group. A significantly reduced carotid mean IMT progression was seen in the intervention group after 6 months (-0.040 +/- 0.136 vs +0.083 +/- 0.167 mm, P = .007). Changes in HbA1c (r = 0.34, P = .028), fasting plasma glucose (r = 0.31, P = .045), and 2-hour postprandial plasma glucose (r = 0.37, P = .015) correlated with the mean carotid IMT change after adjustment for age and sex. In conclusion, a 6-month intensive lifestyle modification intervention in patients with type 2 diabetes mellitus resulted in improved glycemic control and decreased progression of carotid IMT.

Aged↗

Rapid tRNA decay can result from lack of nonessential modifications.

The biological role of many nonessential tRNA modifications outside of the anticodon remains elusive despite their evolutionary conservation. We show here that m7G46 methyltransferase Trm8p/Trm82p acts as a hub of synthetic interactions with several tRNA modification enzymes, resulting in temperature-sensitive growth. Analysis of three double mutants indicates reduced levels of tRNA(Val(AAC)), consistent with a role of the corresponding modifications in maintenance of tRNA levels. Detailed examination of a trm8-delta trm4-delta double mutant demonstrates rapid degradation of preexisting tRNA(Val(AAC)) accompanied by its de-aminoacylation. Multiple copies of tRNA(Val(AAC)) suppress the trm8-delta trm4-delta growth defect, directly implicating this tRNA in the phenotype. These results define a rapid tRNA degradation (RTD) pathway that is independent of the TRF4/RRP6-dependent nuclear surveillance pathway. The degradation of an endogenous tRNA species at a rate typical of mRNA decay demonstrates a critical role of nonessential modifications for tRNA stability and cell survival.

Anticodon↗

Relationship between SUMO-1 modification of caspase-7 and its nuclear localization in human neuronal cells.

The aim of this study was to elucidate the role of SUMO-1 modification in caspase-7 in neuronal cells. We have previously demonstrated that procaspase-2 could be a possible target for SUMO-1 modification. In the present study, we attempted to investigate whether other caspases also interact with Ubc9/SUMO-1. The specific binding of SUMO-1 with caspase-7 was observed in mammalian cells. Deletion mutant analysis revealed that a SUMO-1 modification site may be located in at least N-terminal p20 subunit of caspase-7. Furthermore, SUMO-1-modified caspase-7 appeared as a dot-like structure in nuclear localization. These findings suggest that SUMO-1 modification in caspase-7 may be linked to specific its localization in the nucleus and may therefore contribute to the cleavage of nuclear substrates during neuronal apoptosis.

Blotting, Western↗

Contribution of the kinetics of G protein dissociation to the characteristic modifications of N-type calcium channel activity.

Direct G protein inhibition of N-type calcium channels is recognized by characteristic biophysical modifications. In this study, we quantify and simulate the importance of G protein dissociation on the phenotype of G protein-regulated whole-cell currents. Based on the observation that the voltage-dependence of the time constant of recovery from G protein inhibition is correlated with the voltage-dependence of channel opening, we depict all G protein effects by a simple kinetic scheme. All landmark modifications in calcium currents, except inhibition, can be successfully described using three simple biophysical parameters (extent of block, extent of recovery, and time constant of recovery). Modifications of these parameters by auxiliary beta subunits are at the origin of differences in N-type channel regulation by G proteins. The simulation data illustrate that channel reluctance can occur as the result of an experimental bias linked to the variable extent of G protein dissociation when peak currents are measured at various membrane potentials. To produce alterations in channel kinetics, the two most important parameters are the extents of initial block and recovery. These data emphasize the contribution of the degree and kinetics of G protein dissociation in the modification of N-type currents.

Analgesics, Opioid↗

Modification of tryptophan and tryptophan residues in proteins by reactive nitrogen species.

Formation of 3-nitrotyrosine by the reaction between reactive nitrogen species (RNS) and tyrosine residues in proteins has been analyzed extensively and it is used widely as a biomarker of pathophysiological and physiological conditions mediated by RNS. In contrast, few studies on the nitration of tryptophan have been reported. This review provides an overview of the studies on tryptophan modifications by RNS and points out the possible importance of its modification in pathophysiological and physiological conditions. Free tryptophan can be modified to several nitrated products (1-, 4-, 5-, 6-, and 7-), 1-N-nitroso product, and several oxidized products by reaction with various RNS, depending on the conditions used. Among them, 1-N-nitrosotryptophan and 6-nitrotryptophan (6-NO(2)Trp) have been found as the abundant products in the reaction with peroxynitrite, and 6-NO(2)Trp has been the most abundant product in the reaction with the peroxidase/hydrogen peroxide/nitrite systems. 6-NO(2)Trp has also been observed as the most abundant nitrated product of the reactions between peroxynitrite or myeloperoxidase/hydrogen peroxide/nitrite and tryptophan residues both in human Cu,Zn-superoxide dismutase and in bovine serum albumin, as well as the reaction of peroxynitrite with myoglobin and hemoglobin. Several oxidized products have also been identified in the modified Cu,Zn-SOD. However, no 1-N-nitrosotryptophan and 1-N-nitrotryptophan has been observed in the proteins reacted with peroxynitrite or the myeloperoxidase/H(2)O(2)/nitrite system. The modification of tryptophan residues in proteins may occur at a more limited number of sites in vivo than that of tyrosine residues, since tryptophan residues are more buried inside proteins and exist less frequently in proteins, generally. However, surface-exposed tryptophan residues tend to participate in the interaction with the other molecules, therefore the modification of those tryptophans may result in modulation of the specific interaction of proteins and enzymes with other molecules.

Animals↗

Numerous posttranslational modifications provide opportunities for the intricate regulation of metabolic enzymes at multiple levels.

The metabolic plasticity displayed by plants during normal development, and in response to environmental fluctuations and stressors, is essential for their growth and survival. The capacity to regulate metabolic enzymes intricately arises in part from posttranslational modifications that can affect enzymatic activity, intracellular localization, protein-protein interactions, and stability. Protein phosphorylation and thiol/disulfide redox modulation are important modifications in plants, and it is likely that O-glycosylation and S-nitrosylation will also emerge as important mechanisms. Recent advances in the field of proteomics, in particular the development of novel and specific chemistries for the detection of a diverse number of modifications, are rapidly expanding our awareness of possible modifications and our understanding of the enzymes whose functions are likely to be regulated posttranslationally.

Arabidopsis↗

Selective side-chain modification of cysteine and arginine residues blocks pathogenic activity of HIV-1-Tat functional peptides.

Extracellular Tat protein of HIV-1 activates virus replication in HIV-infected cells and induces a variety of host factors in the uninfected cells, some of which play a critical role in the progression of HIV infection. The cysteine-rich and arginine-rich basic domains represent key components of the HIV-Tat protein for pathogenic effects of the full-length Tat protein and, therefore, could be ideal candidates for the development of a therapeutic AIDS vaccine. The present study describes selective modifications of the side-chain functional groups of cysteine and arginine amino acids of these HIV-Tat peptides to minimize the pathogenic effects of these peptides while maintaining natural peptide linkages. Modification of cysteine by introducing either a methyl or t-butyl group in the free sulfhydryl group and replacing the guanidine group with a urea linkage in the side chain of arginine in the cysteine-rich and arginine-rich Tat peptide sequences completely blocked the ability of these peptides to induce HIV replication, chemokine receptor CCR-5 expression, and NF-kappaB activity in monocytes. Such modifications also inhibited angiogenesis and migration of Kaposi's sarcoma cells normally induced by Tat peptides. Such chemical modifications of the cysteine-rich and arginine-rich peptides did not affect their reactivity with antibodies against the full-length Tat protein. With an estimated 40 million HIV-positive individuals worldwide and approximately 4 million new infections emerging every year, a synthetic subunit HIV-Tat vaccine comprised of functionally inactive Tat domains could provide a safe, effective, and economical therapeutic vaccine to reduce the progression of HIV disease.

Arginine↗

Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics.

Use of minor modification of isotope ratio to code samples for expression proteomics is being investigated. Alteration of (13)C abundance to approximately 2% yields a measurable effect on peptide isotopic distribution and inferred isotope ratio. Elevation of (13)C abundance to 4% leads to extension of isotopic distribution and background peaks across every unit of the mass range. Assessment of isotope ratio measurement variability suggests substantial contributions from natural measurement variability. A better understanding of this variable will allow assessment of the contribution of sequence dependence. Both variables must be understood before meaningful mixing experiments for relative expression proteomics are performed. Subtle modification of isotope ratio ( approximately 1-2% increase in (13)C) had no effect upon either the ability of data-dependent acquisition software or database searching software to trigger tandem mass spectrometry or match MSMS data to peptide sequences. More severe modification of isotope ratio caused a significant drop in performance of both functionalities. Development of software for deconvolution of isotope ratio concomitant with protein identification using LC-MSMS, or any other proteomics strategy, is underway (Isosolv). The identified peptide sequence is then be used to provide elemental composition for accurate isotope ratio decoding and the potential to control for specific amino acid biases should these prove significant. It is suggested that subtle modification of isotope ratio proteomics (SMIRP) offers a convenient approach to in vivo isotope coding of plants and might ultimately be extended to mammals including humans.

Carbon Isotopes↗

Chromosomal histone modification patterns--from conservation to diversity.

The organization of DNA into chromatin regulates expression and maintenance (replication, repair, recombination, segregation) of genetic information in a dynamic manner. The N-terminal tails of the nucleosomal core histones are subjected to post-translational modifications such as acetylation, methylation, phosphorylation, ubiquitination, glycosylation, ADP-ribosylation, carbonylation and sumoylation. These modifications, together with DNA methylation, control the folding of the nucleosomal array into higher order structures and mediate signalling for cellular processes. Although histones and their modifications are highly conserved, recent data show that chromosomal distribution of individual modifications (acetylation, methylation, phosphorylation) can differ along the cell cycle as well as among and between groups of eukaryotes. This implies the possibility of evolutionary divergence in reading the "histone code".

Acetylation↗

Minor modifications in apical dissection of radical retropubic prostatectomy in patients with clinical stage T2 prostate cancer reduce positive surgical margin incidence.

OBJECTIVES: To describe modifications in the apical dissection of radical retropubic prostatectomy (RRP) in men with palpable disease that reduce the incidence of positive apical surgical margins. Positive surgical margins occur in up to 45% of patients undergoing RRP, even in contemporary series. The apex is the most common site of positive margins, and patients with palpable (clinical Stage T2) disease are more likely to have positive surgical margins than patients with nonpalpable (clinical Stage T1c) disease. METHODS: Ninety-five men, 48 to 77 years old (mean age 59.6) with clinical Stage T2 tumors underwent RRP between October 1998 and May 2001. Surgical modifications included identification of the prostatic urethral junction by dissection of the levator ani muscle from the prostate and partial transection of the puboprostatic ligaments; variable division of the membranous urethra 1 to 3 mm distal to the prostatic urethral junction; division of prostatic ischial ligaments before dividing the catheter and posterior membranous urethra; and division of the neurovascular bundle at the urogenital diaphragm before liberating the prostate from the rectum. RESULTS: Positive surgical margins occurred in only 8 (8.4%) of 95 patients, even though tumor extended beyond the prostatic capsule in 55% of cases. Only 2 (2.1%) of the 95 patients had isolated positive apical surgical margins. Urinary continence was not adversely affected by these modifications. CONCLUSIONS: Easily applied modifications in the apical dissection of RRP significantly reduce the incidence of positive apical margins in patients with clinical Stage T2 prostate cancer.

Adenocarcinoma↗

Technical modification of microsurgical varicocelectomy can reduce operating time.

OBJECTIVES: To evaluate the impact of a technical modification of the microsurgical subinguinal varicocelectomy on surgical operating time. METHODS: We introduced a technical modification to the standard microsurgical subinguinal varicocelectomy (division of the spermatic cord package before microsurgical dissection) in January 1999, to simplify the procedure and reduce surgical operating time. We performed a retrospective review of surgical outcomes in 89 men who underwent microsurgical varicocelectomy before modification of the procedure and 76 men who underwent microsurgical varicocelectomy after modification of the procedure. We compared operating times (in minutes), intraoperative findings, improvement in semen parameters, and postoperative complications between the two groups. RESULTS: Overall, 101 men underwent a left and 64 men bilateral microsurgical varicocelectomy. Operating time (mean +/- standard error of the mean) was significantly less for the modified procedure compared with standard microsurgical varicocelectomy (50.2 +/- 1.8 minutes versus 56.5 +/- 1.3 minutes for left-sided procedures and 81.7 +/- 2.6 minutes versus 104.0 +/- 4.0 minutes for bilateral procedures, respectively). No postoperative complications (including recurrence or clinical hydrocele) were identified at 6 weeks postoperatively. Total motile sperm count improved significantly in both groups after surgery. CONCLUSIONS: The modified microsurgical varicocelectomy reduces surgical operating time significantly without compromising outcome.

Humans↗

Glycan moiety modifications of feline alpha1-acid glycoprotein in retrovirus (FIV, FeLV) affected cats.

alpha1-Acid glycoprotein (AGP) is considered one of the major acute phase proteins in cats. In humans, AGP is a heavily glycosylated protein that undergoes several modifications of its glycan moiety during acute and chronic inflammatory pathologies. In this paper we present the feline AGPs (fAGP) glycan moiety modifications in the course of two prevalent feline diseases, the FIV (feline immunodeficiency virus) dependent feline acquired viral immunodeficiency and the feline leukemia virus (FeLV) associated lymphoma. The glycan moiety of fAGP was investigated by means of the binding of its oligosaccharides residues with specific lectins. Four lectins were used: Sambucus nigra agglutinin I and Maackia amurensis agglutinin lectins were used to detect sialic acid residues, Aleuria aurantia lectin was used to detect L-fucose residues and Concanavalin A was used to evaluate the degree of branching. It was found that fAGP undergoes several post-translational modifications of its glycan pattern: in particular the degree of sialylation is increased in FeLV-positive cats diagnosed with lymphoma, while FeLV-positive that did not presented any specific clinical signs cats do not present any increase of expression of sialic acid on the surface. Furthermore, FIV induced a modification of the glycan moiety of fAGP, which however varied widely among individuals. In order to determine the number and the position of oligosaccharide chains, the cDNA sequence of fAGP was also determined. The translation of the mature fAGP coding sequence gave rise to a sequence of 183 residues, with five potential N-glycosylation sites, but also with seven potential phosphorylation sites.

Amino Acid Sequence↗

Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice.

Induction of mouse germ cells occurs from the proximal epiblast at around embryonic day (E) 7.0. These germ cells then migrate to, and enter the gonads at about E10.5 after which they undergo epigenetic reprogramming including erasure of parental imprints. However, the epigenetic properties acquired by nascent germ cells and the potential remodeling of these epigenetic marks in the subsequent migratory period have been largely unexplored. Here we have used immunohistochemistry to examine several genome-wide epigenetic modifications occurring in germ cells from their specification to their colonization of the genital ridges. We show that at around E8.0, germ cells concomitantly and significantly reduce H3-K9 dimethylation and DNA methylation, two major repressive modifications for gene expression. These events are preceded by the transient loss of all the DNA methyltransferases from their nuclei. By contrast, germ cells substantially increase the levels of H3-K27 trimethylation, another repressive modification with more plasticity, at E8.5-9.0 and maintain this state until at least E12.5. H3-K4 methylation and H3-K9 acetylation, modifications associated with transcriptionally permissive/active chromatin, are similar in germ and surrounding somatic cells but germ cells transiently increase these marks sharply upon their entry into the genital ridge. H3-K9 trimethylation, a hallmark of centromeric heterochromatin, is kept relatively constant during the periods examined. We suggest that this orderly and extensive epigenetic reprogramming in premigratory and migratory germ cells might be necessary for their reacquisition of underlying totipotency, for subsequent specific epigenetic remodeling, including the resetting of parental imprints, and for the production of gametes with an appropriate epigenotype for supporting normal development.

Animals↗