Total RNA suitable for molecular biology analysis

Development of methods based on determining expression of individual genes resulted in the need for large amounts of high quality RNA preparations. It is widely accepted that in intact rRNA the 28S and 18S band ratio must be 2:1. It is not quite clear what is the main cause of lower rRNA bands intensity ratio. It is difficult to isolate RNA with 2:1 28S/18S ratio from RNase-rich and some tumor tissues. At the same time this requirement may be excessive and RNA preparations with lower 28S/18S rRNA ratio may be quite adequate for most techniques of determining gene expression. As demonstrated in this study, the level of a particular RNA may be reliably determined by RT-PCR even in a total RNA that is usually considered as degraded (28S to 18S ratio as low as 0.4), provided that random primer is used in RT. In contrast, the use of the oligo(dT) primer in RT-PCR may lead to underestimation of specific mRNA level in the degraded RNA samples, depending on the distance of amplified fragment from the poly(A) end. A criterion based on average degradation level of a number of reference genes is suggested to discriminate specific RNA degradation from random and unspecific ones.     

Change in the Distribution of Acetylcholinesterase Molecular Forms in Hirschsprung's Disease

Abstract: Density gradient ultracentrifugation shows that two molecular forms of acetylcholinesterase (4S and 10S) can be distinguished in the bowels of both normal subjects and Hirschsprung's disease patients. In this disease, besides the very large elevation of acetylcholinesterase activity, the relative distribution of the heavy and light forms was also changed. In the affected bowel the 10S/4S ratio was 2.5 times higher than the normal value. It is assumed that the accumulation of the 10S form might be a response of the intestine to this pathological state. It is also suggested that the increase in the heavy form is closely connected with the nerve fibre proliferation in the aganglionic megacolon.     

Un nouveau marqueur sérique de la pathologie inflammatoire de l’intestin : la protéine S100A12

S100A12 is a calcium binding protein with pro-inflammatory properties. It is secreted by activated neutrophils and interacts with the multiligand receptor for advanced glycation end products (RAGE), found on macrophages, endothelium and lymphocytes. It is strongly expressed in inflamed intestinal tissues of patients with active Crohn's disease and ulcerative colitis and circulating levels of S100A12 seem to be reliable markers of inflammation in monitoring disease activity. An Elisa-kit is under process by Cisbio international to measure concentrations of S100A12 in serum.     

Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era,an essential GTPase in Escherichia coli

Era is a small GTP-binding protein and essential for cell growth in Escherichia coli. It consists of two domains: N-terminal GTP-binding and C-terminal RNA-binding KH domains. It has been shown to bind to 16S rRNAs and 30S ribosomal subunits in vitro. Here, we report that a precursor of 16S rRNA accumulates in Era-depleted cells. The accumulation of the precursors is also seen in a cold-sensitive mutant, E200K, in which the mutation site is located in the C-terminal domain. The major precursor molecule accumulated seems to be 17S rRNA, containing extra sequences at both 5' and 3' ends of 16S rRNA. Moreover, the amounts of both 30S and 50S ribosomal subunits relative to the amount of 70S monosomes increase in Era-depleted and E200K mutant cells. The C-terminal KH domain has a high structural similarity to the RbfA protein, a cold shock protein that also specifically associates with 30S ribosomal subunits. RbfA is essential for cell growth at low temperature, and a precursor of 16S rRNA accumulates in an rbfA deletion strain. The 16S rRNA precursor seems to be identical in size to that accumulated in Era mutant cells. Surprisingly, the cold-sensitive cell growth of the rbfA deletion cells was partially suppressed by overproduction of the wild-type Era. The C-terminal domain alone was not able to suppress the cold-sensitive phenotype, whereas Era-dE, which has a 10-residue deletion in a putative effector region of the N-terminal domain, functioned as a more efficient suppressor than the wild-type Era. It was found that Era-dE suppressed defective 16S rRNA maturation, resuming a normal polysome profile to reduce highly accumulated free 30S and 50S subunits in the rbfA deletion cells. These results indicate that Era is involved in 16S rRNA maturation and ribosome assembly.     

Transmissible modification induced in Mycobacterium tuberculosis and Mycobacterium bovis in vitro]

A biologically active material (fraction "S") is isolated from cultures of scotochromogenic mycobacteria. Mycobacterium tuberculosis, or Mycobacterium bovis by disrupting the cells, sedimentation through 2.2 M sucrose, and ultrafiltration. The fraction "S" induces the modification of tubercle bacilli into non acid-fast bacteria forming smooth colonies on nutritive glycerol agar within 24-36 h of incubation. Three new phenotypes are thus obtained; two proved to be stable upon subculturing. Frequently the phenomenon occurs with a very large part of the Koch's bacillus population exposed to the inducing agent effect. It can be reproduced with crude preparations of DNA obtained from the fraction "S." It is inhibited by concanavalin A. The observed modification does not correspond to a transfer of characteristics of the inducing agent from the donor mycobacteria; furthermore it can be manifested even in the strain used for the preparation of the fraction "S."     

Spatial organization of template polynucleotides on the ribosome determined by fluorescence methods.

The spatial organization of template polynucleotides on the ribosome and the dynamics of their interaction with 30 S subunits have been studied by fluorescence spectroscopy. The topography of the mRNA in the ribosome has been determined using singlet-singlet energy transfer. This method has allowed us to estimate distances between donors and acceptors of energy which have been linked to the terminal residues of template polynucleotides (poly- and oligo(U) and oligo(A] and 16 S RNA or to SH-groups of ribosomal proteins S1 and S8. The dynamics of mRNA-ribosome interaction have been investigated by the fluorescence stopped-flow technique. It has been shown that the binding to the 30 S subunit of poly(U) with length much shorter (16 nucleotides) than that covered by the ribosome is greatly enhanced by protein S1. However, the final position of oligo(U)16 on the 30 S subunit, which probably includes the ribosomal decoding site, proves to be quite different from that occupied by oligo(U)16 on a free protein S1. Interaction of oligo- and poly(U) with the 30 S subunit occurs in at least two steps: the first one is as fast as the interaction of poly(U) with free S1, whereas the second step represents a first-order reaction. Therefore, the second step may reflect some rearrangement of the template in the ribosome after its primary binding. It is suggested that protein S1 in some cases may fulfill the role of a transient binding site for mRNA in the course of its interaction with the ribosome. The general shape of the template in the mRNA binding region of the ribosome has been studied using various synthetic ribopolynucleotides and has been shown to be similar. It can be represented by a loop(s) or "U-turn(s)". On the basis of estimation of distances from the ends of poly(U) to some well-localized points on the 30 S ribosomal surface, a tentative model of mRNA path through the ribosome is proposed.     

16S rDNA-RFLP分析新疆快生大豆根瘤菌的分类地位

采用１６Ｓ ｒＤＮＡ－ＲＦＬＰ技术,对自新疆土壤中捕捉的３４株快生大豆根瘤菌及相关已知种的模式菌株进行了比较分析。从酶切图谱类型和在结果表明,所有新分离的菌株与Ｓ．ｘｉｎｊｉａｎｇｅｎｓｉｓ的图谱类型基本一致,而与Ｓ．ｆｒｅｄｉｉ的图谱类型有明显差异,与Ｓ．ｍｅｌｉｌｏｔｉ,Ｓ．ｓａｈｅｌｉ,Ｓ．ｍｅｄｉｃａｅ,Ｓ．ｔｅｒａｎｇａ也不相同。３４株新分离的菌株全部与Ｓ．ｘｉｎｇｊｉａｎｇｅｎｓｉｓｉ     

Characterization and classification of virus particles associated with hepatitis A. I. Size, density, and sedimentation.

Virus-like particles were purified from stools of patients in an epidemic of hepatitis A in Germany. When reference MS-1 chimpanzee pre-inoculation and convalescent sera were used, the close serological relationship of the purified particles to well-known isolates of hepatitis A could be established. On the other hand, the physicochemical characteristics of the particles were determined in parallel to the characteristics of a marker parvovirus (LuIII) and a marker picornavirus (poliovirus type 2). It could be shown that the majority of the hepatitis A-associated particles band at 1.34 g/ml in CsCl and, like poliovirus, sediment at about 160S. In addition, a distinct hepatitis A antigen was observed, which banded at 1.305 g/ml and sedimented between 50 and 90S. A further component accumulated in the density range of between 1.38 and 1.44 g/ml. However, it seemed to be rather labile. Upon reisolation from CsCl and sedimentation in sucrose, it resolved into a 160S, a 90 to 100S, and a 50S form. The size of the 160S particles (27 to 29 nm) could be readily distinguished from that of the parvovirus (22 to 24 nm). It is concluded, therefore, that hepatitis A-associated virus particles are more likely to be classified with the picornaviruses than with the parvoviruses.     

Initiation of mammalian protein synthesis. The multiple functions of the initiation factor eIF-3

The protein synthesis initiation factor eIF-3 (a multicomponent protein complex) was labelled with 32P by phosphorylation with a protein kinase present in a partially purified 'hemin-controlled repressor' preparation. The interaction of the labelled factor with the 40 S ribosomal subunit during the course of initiation was followed. It binds to the 40 S subunit in the absence of other initiation factors and inhibits the Mg2+-dependent reassociation of the 40 S with the 60 S ribosomal subunit. It stimulates the binding of the ternary complex (eIF-2, GTP, Met-tRNAf) to the 40 S subunit, and earlier work (Trachsel, H., Schreier, M.H., Erni, B. and Staehelin, T. (1977) J. Mol. Biol. 116, 745-767) also showed it to be essential for the subsequent binding of mRNA. The factor is released from the 40 S initiation complex during the 60 S subunit joining reaction.     

Novel subunit in C4b-binding protein required for protein S binding

C4b-binding protein (C4BP) is a multimeric protein with regulatory functions in the complement system. It also interacts with vitamin K-dependent protein S, which is involved in the regulation of the coagulation system. It has been demonstrated that C4BP consists of seven disulfide-linked, identical 70-kDa subunits, which are arranged to give the molecule a spider-like structure. We now have evidence for the presence of a new subunit in C4BP. On sodium dodecyl sulfate-poly-acrylamide gel electrophoresis it appears as a weakly stainable band with a molecular weight of approximately 45,000. The subunit was isolated by gel filtration in 6 M guanidine hydrochloride of reduced and carboxymethylated C4BP. Its amino-terminal sequence is distinct from previously known protein sequences. The stoichiometry of 45- to 70-kDa subunits was estimated to be 1:9, indicating the presence of one 45-kDa subunit per C4BP molecule. The new subunit was demonstrated to be a disulfide-linked component of the central core of C4BP. It was sensitive to proteolysis by chymotrypsin, and when cleaved the protein S binding ability of C4BP was lost. With protein S bound to C4BP, the 45-kDa subunit was protected from degradation by chymotrypsin, and the protein S binding site remained intact. These data suggest that the new subunit is directly involved in protein S binding.     

Sucrose density gradient centrifugation of human myometrial and myomal progestin receptors

Progestin receptors present in cytosols of myomal and myometrial origin were analyzed on sucrose density gradients of low ionic strength using a vertical tube rotor. Short term incubations (90 min) contained mainly 8S receptors. Most myometrial but few myomal preparations contained an additional 4S component, the presence of which was hormone dependent. None could be detected if the serum concentration of estradiol was high. Myometrial receptors incubated over night exhibited only a 4S peak, whereas many myomal ones still sedimented as 8S peaks. The 8 to 4S shift represented a transformation of the receptors and not a sequential interaction of the hormone with first an 8S and then a 4S entity. The transforming activity contained in the myometrial cytosol could also attack the myomal receptor as shown by mixing experiments. Only the 8S peak was observed, whenever the cytosol was first fractionated and then incubated with the hormone. Thus the transformation occurred only in presence of [3H]promegestone. It could be suppressed with protease inhibitors. It is concluded that these tissues contain a receptor processing protease which (1) is much less prominent in myomal than myometrial cytosol, which (2) attacks only the occupied receptors, and (3) the activity of which is hormone dependent.     

Crystal structure study on human S100A13 at 2.0 A resolution

The S100 protein family is the largest group of calcium-binding protein families, which consists of at least 25 members. S100A13, which is widely expressed in a variety of tissues, is a unique member of the S100 protein family. Previous reports showed that S100A13 might be involved in the stress-induced release of some signal peptide-less proteins (such as FGF-1 and IL-1alpha) and also associated with inflammatory functions. It was also reported that S100A13 is a new angiogenesis marker. Here we report the crystal structure of the Ca(2+)-bound form of S100A13 at 2.0 A resolution. S100A13 is a homodimer with four EF-hand motifs in an asymmetric unit, displaying a folding pattern similar to other S100 members. However, S100A13 has the unique structural feature with all alpha-helices being amphiphilic, which was not found in other members of S100s. We propose that this characteristic structure of S100A13 might be related to its ability to mediate the release of FGF-1 and IL-1alpha.     

Adhesion dependence of coagulase-negative staphylococci to biomaterials and PIA polysaccharide synthesis on icaADBC operon presence

Both Staphylococcus epidermidis and Staphylococcus haemolyticus are important causes of infections associated with catheters and other medical devices. This infections result in significant morbidity, mortality and economic cost. It has recently been shown that not only S. epidermidis but also S. haemolyticus can produce slime and carries the ica operon responsible for and slime production. In the operon, coexpression of icaA and icaD is required for full slime synthesis. This study is focused on detecting icaA and icaD genes in S. haemolyticus and comparison of these two species. It turned out that strain representatives within the same species behave very differently and a single tested strain from each species is unlikely to be representative of the species as a whole. Contrary to S. epidermidis, S. haemolyticus strain appeared to carry no icaA-like and icaD-like genes, but was able to form biofilm in vitro.     

4.5S ribonucleic acid, a novel ribosome component in the chloroplasts of flowering plants.

A species of low-molecular-weight ribosomal RNA, referred to as '4.5S rRNA', was found in addition to 5S rRNA in the large subunit of chloroplast ribosomes of a wide range of flowering plants. It was shown by sequence analysis that several variants of this RNA may occur in a plant. Furthermore, although in most flowering plants the predominant variant contains about 100 nucleotides, in the broad bean it has less than 80. It seems, therefore, to be much more diverse in size and sequence than the other ribosomal RNA species. Like 5S rRNA , it does not contain modified nucleotides and it is also unusual in having an unphosphorylated 5'-end. It is apparently neither a homologue of cytosol 5.8S rRNA nor a fragment of 23S rRNA.     

Interaction of isoforms of subfragment-1 of myosin, containing fluorescently labelled alkaline light chains, with muscle fiber actin

Using polarization microfluorimetry, the interaction of myosin subfragment 1 (S1) isoforms containing alkali light chains A1 and A2 respectively (S1(A1) and S1(A2] with F-actin of single glycerinated rabbit skeletal muscle fibers was studied. The alkali light chains of S1 were substituted by reassociation for A1 or A2 chains modified by a fluorescent label (1.5-IAEDANS) at the single SH-group located in the C-terminus. It was found that in S1(A1) bound to muscle fiber F-actin the mobility of the fluorescent label is lower than in S1(A2). At the same time the S1(A1) and S1(A2) interaction with F-actin induces similar changes in polarized fluorescence of rhodamine linked to falloidine which, in turn, is specifically bound to F-actin. It is concluded that the both S1 isoforms bind to F-actin and produce similar effects on the conformational state of actin filaments in muscle fibers. Local differences between S1(A1) and S1(A2) seem to be due to the interaction of the N-terminus of A1 within S1(A1) with the C-terminal region of actin.     

Isolation and physical study of the 13S fragment of 16S RNA and its complex with ribosomal protein S4

A fragment of E. coli 16S RNA has been obtained by its hydrolysis with pancreatic RNAase A coupled to Sepharose 4B. This fragment has a molecular weight of 170 000 and a sedimentation coefficient of 13S. It does not aggregate in solution and binds with the ribosomal protein S4. The 13S fragment and it complex with the protein S4 have been studied by different physical methods in the first place, by neutron scattering. It has been shown that this fragment is compact in solution. The radii of gyration of the fragment (50 +/- 3 A) and of the protein S4 within the complex (17 +/- 3 A) coincide, within limits of experimental error, with the radii of gyration for the free RNA fragment (47 +/- 2 A) and the free ribosomal protein S4 in solution (18 +/- 2 A). Hence, the conclusion is made that the compactness of the 13S fragment of the 16S RNA and the ribosomal protein S4 does not change at the complex formation. The compact 13S fragment of the 16S RNA is shown to be contrast matched in the H2O/D2O mixture containing 70% D2O which corresponds to its partial specific volume v equal to 0.537 cm3/g.     

Studies on the low molecular weight RNA associated with 28S ribosomal RNA from Crotalus durissus terrificus liver.

A low molecular weight RNA was released from the purified rattlesnake 28 S RNA by brief heat treatment as well as by treatment with 80% dimethylsulfoxide or formamide. The sedimentation coeficient of this low molecular weight RNA was found to be 5.5 S, corresponding to a nucleotide number of 140 and a molecular weight of 46 000. It was also observed that 5.5S RNA is present in equimolar ratio to 5 S rRNA. Heat treatment of the purified 60 S ribosomal subunit also released the 5.5 S RNA. The possibility that this low molecular weight RNA is located on the surface of the large ribosomal subunit is discussed.     

An elongated model of the Xenopus laevis transcription factor IIIA-5S ribosomal RNA complex derived from neutron scattering and hydrodynamic measurements.

The precise molecular composition of the Xenopus laevis TFIIIA-5S ribosomal RNA complex (7S particle) has been established from small angle neutron and dynamic light scattering. The molecular weight of the particle was found to be 95,700 +/- 10,000 and 86,700 +/- 9000 daltons from these two methods respectively. The observed match point of 54.4% D2O obtained from contrast variation experiments indicates a 1:1 molar ratio. It is concluded that only a single molecule of TFIIIA, a zinc-finger protein, and of 5S RNA are present in this complex. At high neutron scattering contrast radius of gyration of 42.3 +/- 2 A was found for the 7S particle. In addition a diffusion coefficient of 4.4 x 10(-11) [m2 s-1] and a sedimentation coefficient of 6.2S were determined. The hydrodynamic radius obtained for the 7S particle is 48 +/- 5 A. A simple elongated cylindrical model with dimensions of 140 A length and 59 A diameter is compatible with the neutron results. A globular model can be excluded by the shallow nature of the neutron scattering curves. It is proposed that the observed difference of 15 A in length between the 7S particle and isolated 5S RNA most likely indicates that part(s) of the protein protrudes from the end(s) of the RNA molecule. There is no biochemical evidence for any gross alteration in 5S RNA conformation upon binding to TFIIIA.     

Ionic strength-dependent isoforms of sea urchin egg dynein

Unfertilized sea urchin eggs provide a reservoir of molecules which later are involved in microtubule-mediated movements during embryonic development. Among these molecules is egg dynein, which has been isolated in two forms, 20 S and 12 S. Evidence obtained previously from our laboratory indicates that 20 S dynein is a latent activity precursor of ciliary dynein. In contrast, others have suggested that 12 S egg dynein functions in the mitotic apparatus. It is therefore important to determine the relationship between these egg dyneins. Here we demonstrate that the sedimentation velocity of the egg dynein is dependent on the ionic strength of the extraction conditions. The 20 S dynein is obtained with low ionic strength extraction, and the 12 S form is obtained in high salt (0.6 M KCl). The 20 S dynein, after collection from a sucrose gradient, can be converted quantitatively to the 12 S form by exposure to salt, and this conversion can be followed over time. Further, the 20 S dynein can be converted entirely to 12 S dynein and then partially reconstituted to a faster sedimenting species. During these conversions, the dynein high Mr heavy chains are always coincident with the MgATPase activity, and antibodies show that the dynein heavy chains of the 20 S, 12 S, and converted species are indistinguishable immunologically. These data suggest that 12 S dynein is an ionic strength-dependent isoform of 20 S dynein that results from a partial dissociation of the 20 S polypeptide complex, similar to the relationship between 12 and 21 S sperm flagellar dynein. If the 20 and 12 S enzymes are isoforms of the same dynein, then there is compelling evidence for only a single dynein in the unfertilized egg, and that dynein is probably a ciliary precursor.