Genetic and molecular dissection of naturally occurring variation

Recent progress in plant genome analysis has made it possible to examine the naturally occurring allelic variation underlying complex traits. Many studies have described the genetic mapping of quantitative trait loci for several kinds of complex phenotypic traits. Some researchers have taken up the challenge of performing the molecular cloning of genes at these loci, and examples of cloning have recently been reported. Naturally occurring allelic variation could be a new resource for the functional analysis of plant genes.     

Isolation and characterization of naturally occurring cyanogenic compounds

The literature dealing with the detection, isolation, purification and characterization of cyanogenic glycosides has been integrated with spectral and chemical data as well as other techniques from our laboratory to establish a method for the positive identification of glycosides of this type. The compounds are arranged into biosynthetically related groups (those derived from l-phenylalanine; l-tyrosine; l-leucine, l-valine; l-isoleucine; those with cyclopentene rings and pseudocyanogenic glycosides) and features of each of the above procedures are critically reviewed and spectral data for each group presented (IR, MS, UV and NMR). The NMR spectra of TMS ethers of cyanogenic glycosides have proven especially useful in chemical structure determination. This information is sufficient to permit identification of any of the 26 known glycosides as well as certain uncharacterized ones.     

Thermodynamic characterization of naturally occurring RNA tetraloops

Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem–loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters ΔH°, ΔS°, ΔG°_37, and T_M for each stem–loop were determined. These new experimental values, on average, are 0.7 kcal/mol different from the values predicted for these tetraloops using the model proposed by Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Biochemistry 45: 1400–1407. The data for the 24 tetraloops reported here were then combined with the data for 28 tetraloops that were published previously. A new model, independent of terminal mismatch data, was derived to predict the free energy contribution of previously unmeasured tetraloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.4 kcal/mol. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem–loops containing tetraloops and, furthermore, should allow for improved prediction of secondary structure from sequence. It was also shown that tetraloops within the sequence 5′-GCCNNNNGGC-3′ are, on average, 0.6 kcal/mol more stable than the same tetraloop within the sequence 5′-GGCNNNNGCC-3′. More systemic studies are required to determine the full extent of non-nearest-neighbor effects on tetraloop stability.     

Functional characterization of nine novel naturally occurring human melanocortin-3 receptor mutations

The melanocortin-3 receptor (MC3R) is a member of family A rhodopsin-like G protein-coupled receptors. Mouse genetic studies suggested that MC3R and the related MC4R are non-redundant regulators of energy homeostasis. Lack of Mc3r leads to higher feed efficiency and fat mass. However, until now only a few MC3R mutations have been identified in humans and the role of MC3R in the pathogenesis of obesity was unclear. In the present study, we performed detailed functional studies on nine naturally occurring MC3R mutations recently reported. We found that all nine mutants had decreased cell surface expression. A260V, M275T, and L297V had decreased total expression whereas the other six mutants had normal total expression. Mutants S69C and T280S exhibited significant defects in ligand binding and signaling. The dramatic defects of T280S might be partially caused by decreased cell surface expression. In addition, we found mutants M134I and M275T had decreased maximal binding but displayed similar signaling properties as wild-type MC3R. All the other mutants had normal binding and signaling activities. Co-expression studies showed that all mutants except L297V did not affect wild-type MC3R signaling. Multiple mutations at T280 demonstrated the necessity of Thr for cell surface expression, ligand binding, and signaling. In summary, we provided detailed data of these novel human MC3R mutations leading to a better understanding of structure-function relationship of MC3R and the role of MC3R mutation in obesity.     

Structural characterization of naturally occurring RNA single mismatches

RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence–structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.     

Detection and characterization of naturally occurring plasmids in Bacillus licheniformis

Twenty-two Bacillus licheniformis strains, freshly isolated from pasture-land, were studied for the presence of plasmid DNA. Among these strains, 14 were shown to harbor one or more plasmids of different size. Southern-hybridization experiments showed a high homology between all plasmids investigated and a 2.2-kb PvuII/HindIII fragment of pBL1, a B. licheniformis plasmid previously isolated. Three fragments of pBL1, including the 2.2-kb PvuII/HindIII region, were cloned into pJH101 vector. The resulting chimeras were able to transform Bacillus subtilis. The fragment with high homology probably contains the region with the replicative functions of plasmids from B. licheniformis species.     

Genetic characterization of naturally occurring Rhizobium meliloti populations and their potential to form effective symbioses with lucerne

Genetic characterization by Randomly Amplified Polymorphic DNA (RAPD) fingerprinting was employed to study the status of Rhizobium meliloti populations inhabiting nodules of lucerne. Rhizobium strains were isolated from nodules harvested from plants growing in inoculated or uninoculated experimental plots, uninoculated commercial fields and from lucerne grown in pots containing soils of different origin. Dry matter analyses were recorded and rhizobia were assessed for relative genetic diversity between treatments. Inoculated and uninoculated soils did not differ in terms of dry matter production, and lucerne grew, and was adequately nodulated, in soils with no history of lucerne cultivation. These findings, and the demonstration that there is a rich genetic diversity of Rh. meliloti in these soils, show that it is not always necessary to apply a standard commercial inoculant.     

Genetic factors infuencing mouse type-C RNA virus induction by naturally occurring B cell mitogens.

The present studies demonstrate that xenotropic type C virus is efficiently released in response to lipopolysaccharide by spleen cells of a wide variety of inbred mouse strains. Lipopolysaccharide-mediated virus release primarily involves B lymphocytes and is in part genetically determined. Virus release can also be efficiently stimulated by other naturally occurring B cell mitogens, including Nocardia water soluble mitogen, and PPD. The evidence indicates that these agents act synergistically with halogeneated pyrimidines, but not with each other, to cause virus release. These results indicate that B cell mitogens act to release virus by a mechanism that differs from that of halogenated pyrimidines.     

Biophysical characterization of naturally occurring titin M10 mutations

The giant proteins titin and obscurin are important for sarcomeric organization, stretch response, and sarcomerogenesis in myofibrils. The extreme C-terminus of titin (the M10 domain) binds to the N-terminus of obscurin (the Ig1 domain) in the M-band. The high-resolution structure of human M10 has been solved, along with M10 bound to one of its two known molecular targets, the Ig1 domain of obscurin-like. Multiple M10 mutations are linked to limb-girdle muscular dystrophy type 2J (LGMD2J) and tibial muscular dystrophy (TMD). The effect of the M10 mutations on protein structure and function has not been thoroughly characterized. We have engineered all four of the naturally occurring human M10 missense mutants and biophysically characterized them in vitro. Two of the four mutated constructs are severely misfolded, and cannot bind to the obscurin Ig1 domain. One mutation, H66P, is folded at room temperature but unfolds at 37°C, rendering it binding incompetent. The I57N mutation shows no significant structural, dynamic, or binding differences from the wild-type domain. We suggest that this mutation is not directly responsible for muscle wasting disease, but is instead merely a silent mutation found in symptomatic patients. Understanding the biophysical basis of muscle wasting disease can help streamline potential future treatments.     

Thermodynamic characterization of single mismatches found in naturally occurring RNA

Many naturally occurring RNA structures contain single mismatches. However, the algorithms currently used to predict RNA structure from sequence rely on a minimal set of data for single mismatches, most of which occur rather infrequently in nature. As a result, several approximations and assumptions are used to predict the stability of RNA duplexes containing the most common single mismatches. Therefore, the relative frequency of single mismatches was determined by compiling and searching a database of 955 RNA secondary structures. Thermodynamic parameters for duplex formation, derived from optical melting experiments, are reported for 28 oligoribonucleotides containing frequently occurring single mismatches. These data were then combined with previous data to construct a dataset of 64 single mismatches, including the 30 most common in the database. Because of this increase in experimental thermodynamic parameters for single mismatches that occur frequently in nature, more accurate free energy calculations have resulted. To improve the prediction of the thermodynamic parameters for duplexes containing single mismatches that have not been experimentally measured, single mismatch-specific nearest neighbor parameters were derived. The free energy of an RNA duplex containing a single mismatch that has not been thermodynamically characterized can be calculated by: DeltaG degrees 37,single mismatch = DeltaG degrees 37,mismatch nt + DeltaG degrees 37,mismatch-NN interaction + DeltaG degrees 37,AU/GU. Here, DeltaG degrees 37,mismatch is -0.4, -2.1, and -0.3 kcal/mol for A.G, G.G, and U.U mismatches, respectively; DeltaG degrees 37,mismatch-NN interaction is 0.7, -0.5, 0.4, -0.4, and -1.0 kcal/mol for 5'YRR3'/3'RRY5', 5'RYY3'/3'YYR5', 5'YYR3'/3'RYY5', 5'YRY3'/3'RYR5', and 5'RRY3'/3'YYR5' mismatch-nearest neighbor combinations, respectively, when A and G are categorized as purines (R) and C and U are categorized as pyrimidines (Y); and DeltaG degrees 37,AU/GU is a penalty of 1.2 kcal/mol for replacing a G-C base pair with either an A-U or G-U base pair. Similar predictive models were also derived for DeltaH degrees single mismatch and DeltaS degrees single mismatch. These new predictive models, in conjunction with the reported thermodynamics for frequently occurring single mismatches, should allow for more accurate calculations of the free energy of RNA duplexes containing single mismatches and, furthermore, allow for improved prediction of secondary structure from sequence.     

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence.     

Purification and characterization of the naturally occurring allelic variants of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster

The naturally occurring electrophoretic variants of sn-glycerol-3-phosphate dehydrogenase and a heterodimeric form of the enzyme resulting from a genetic cross of two variant strains of Drosophila were purified to homogeneity by a combination of DEAE-cellulose chromatography and 8-(6-aminohexyl)-amino-ATP-Sepharose affinity chromatography. Each purified protein was compared with respect to a number of physicochemical and kinetic properties. All forms of the enzyme were found to be similar, except for pI differences associated with the electrophoretic variation observed.     

Genetic and immunological characterization of the 14-3-3xi molecule from Schistosoma bovis

Currently available candidate vaccines against schistosomiasis elicit only partial protection. In addition, the type of immune response that could lead to the highest level of protection against schistosomes has not yet been described. Thus, efforts should be made in both the identification of novel proteins essential for the parasite cycle and in the modulation of immune responses against these novel candidates through the combined use of immunomodulatory molecules. Several parasites have 14-3-3 proteins, and these proteins are known to play a key role in parasite biology. In the present work, we report the isolation and characterization of a new 14-3-3 gene from Schistosoma bovis and offer new information regarding the genetic structure of the gene. In addition, we have produced the corresponding recombinant protein. Finally, we describe the immune responses elicited by this protein when combined with 4 different immunomodulators in immunized mice.     

Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently classified into six genotypes and an increasing number of subtypes. Most likely, this heterogeneity is caused by genetic drift; evidence for recombination is scarce. To study the molecular heterogeneity of HCV in Vietnam, we analyzed 58 HCV RNA-positive sera from Vietnamese blood donors by sequence analysis of the CORE and NS5B regions. Phylogenetic analyses revealed the presence of genotype 1 (38%), genotype 2 (10.3%), and genotype 6 viruses (51.7%). All samples showed concordant results except for two (D3 and D54). Sample D54 was a mixed infection of genotype 2i and 6h viruses. Whole-genome analysis and bootscan analysis of sample D3, on the other hand, revealed a recombinant virus with genotype 2i and genotype 6p sequences at the 5' and 3' ends, respectively. The crossover point was located between nucleotide positions 3405 to 3464 (numbering according to prototype strain HCV-H, M67463) at the NS2/NS3 junction. The identification of this naturally occurring recombinant virus strengthens the concept that recombination may play a role in HCV epidemiology and evolution. Furthermore, the location of the recombination breakpoint may be relevant for constructing infectious chimeric viruses.     

Antidromic dorsal root impulses during naturally occurring locomotion in rats

Antidromic dorsal root activity during naturally occurring locomotion (swimming and treadmill walking) was investigated during experiments on white rats. The activity observed consisted of phaselinked and tonic components of antidromic action potentials (APP). A strong correlation was found between intensity of AAP and that of afferent input during actual locomotion; AAP correlated less well with degree of electromyographic activity. Possible sources of the initiation of antidromic activity and the part played in spinal reflex control by presynaptic depolarization are discussed.A. A. Bogomolets Institute of Physiology, Academy of Sciences of the Ukrainian SSR, Kiev. Translated from Neirofiziologiya, Vol. 20, No. 5, pp. 579–585, September–October, 1988.     

A naturally occurring polyclonal B cell activator of normal and autoantibody responses

Previous studies from this laboratory have demonstrated the presence of a suppressor molecule in B/W spleen cultures. Now we present evidence suggesting the existence of a polyclonal B cell activator (sPBA) spontaneously released by B/W splenocytes. Large sPBA (120,000 to 160,000 daltons) was separable from splenic inhibitory factor(s) (less than 10,000 daltons) by ultrafiltration. Reconstitution experiments demonstrated these two molecules had antagonistic effects on splenocyte mitotic events. sPBA is directly mitogenic for T cell-depleted, B cell-enriched cultures. Furthermore, sPBA augments antibody responses in the presence of antigen, or stimulates antibody responses in the absence of antigen. sPBA appears to stimulate IgG as well as IgM antibody production. sPBA stimulates significant in vivo anti-ssDNA responses in preautoimmune B/W but not DBA mice. Physiochemical studies suggest sPBA is a DNA protein complex. sPBA activity is completely lost by heating to 56 degrees C for 30 min. sPBA activity is precipitated at pH 7.8 to 8.0. Furthermore, sPBA preparations do not display significant endotoxin levels or IL 1 and IL 2 activity.