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Characterization of a Thermomonospora fusca exocellulase.

The exocellulase E3 gene was cloned on a 7.1 kb NotI fragment from Thermomonospora fusca genomic DNA into Escherichia coli and expressed in Streptomyces lividans. The E3 gene was sequenced and encoded a 596 residue peptide. The molecular masses of the native and cloned E3s were determined by mass spectrometry, and the value for E. coli E3, 59,797 Da, agreed well with that predicted from the DNA sequence, 59,646 Da. The value of 61,200 Da for T. fusca E3 is consistent with E3 being a glycoprotein. E3 is thermostable, retaining full activity after 16 h at 55 degrees C. It also has a broad pH optimum around 7-8, retaining 90% of its maximal activity between pH 6 and 10. The cloned E3s were identical to the native enzyme in their activity, cellulose binding, and thermostability. Papain digestion produced a 45.7 kDa catalytic domain with 77% of the native activity on amorphous cellulose and 33% on crystalline cellulose. E3 belongs to cellulase family B and retains the residues that have been identified to be crucial for catalytic activity in Trichoderma reesei cellobiohydrolase II and T. fusca E2. The E3 gene contains a 14 bp inverted repeat regulatory sequence 212 bp before the translational start codon instead of the 30-70 bp found for the other T. fusca cellulase genes. An additional copy of this sequence with one base changed is 314 bp before the translational start codon. The transcriptional start site of the E3 gene was shown to be between these two inverted repeats.

Actinomycetales↗

The reverse transcriptase gene of cauliflower mosaic virus is translated separately from the capsid gene.

Cauliflower mosaic virus (CaMV) possesses start codons at the beginning of its reverse transcriptase (RT) gene (ORF V) suggesting that, unlike in retroviruses and retrotransposons, it is translated independently from the capsid gene (ORF IV). To test this hypothesis a mutational analysis of the CaMV ORF IV/V overlapping region was performed. Mutants in which both ORFs are separated by stop codons in all three reading frames are viable and stable, while mutations affecting the first two AUG codons of ORF V are either lethal or unstable, giving rise to true and second site reversions. Mutants in which the AUG codons were replaced by ACG or AAG reverted only slowly and ACG could direct the synthesis of small amounts of reporter enzyme in transfected plant protoplasts, showing that this codon can act in plant cells as a weak start codon. CaMV has apparently developed a strategy for translation of the RT gene different from that in retroviruses and retrotransposons, but similar to that of hepadnaviruses, another group of pararetroviruses. The separate translation of the RT gene as a common feature of pararetroviruses might reflect the difference in their life cycle in comparison with retroviruses.

Base Sequence↗

Bacteriophage T4 gene 21 encodes two proteins essential for phage maturation.

The T4 prohead protease (T4 PPase) is the key enzyme in the morphopoietic pathway of the T4 phage head. It is responsible for the proteolytic processing of all head proteins allowing protein rearrangement and head expansion. To study its biochemistry and gene regulation, T4 gene 21 was cloned into an expression vector under the control of the inducible tac promoter. Two proteins of apparent molecular weights of 21.5 and 27.5 kDa were detected after induction. These proteins are synthesized using two different start codons in the same reading frame. Destruction of either start codon resulted in the loss of the respective protein. Complementation experiments with bacteriophage T4 21(-)-infected cells showed that both proteins are functional in vivo and essential for T4 phage assembly.

Base Sequence↗

Cloning and characterization of the 5alpha-reductase type 2 promoter in the rat epididymis.

Steroid 5alpha-reductase converts testosterone to the more potent androgen, dihydrotestosterone. The molecular mechanisms responsible for maintaining high concentrations of the 5alpha-reductase type 2 mRNA in the caput epididymidis and for regulating its region-specific expression are unknown. To gain insight into its transcriptional regulation, the cloning and characterization of the 5' upstream region of 5alpha-reductase type 2 were undertaken. Sequential deletion analysis was done to map the 2243-base pair (bp) cloned 5' upstream region, and the constructs were transfected into epididymal PC1 cells and prostatic PC3 cells. In both cell lines, regulatory elements and the minimal promoter were mapped to the 485-bp region upstream of the start codon. Primer extension and 5' RACE identified one transcriptional start site at 33-bp upstream of the start codon. Using electrophoretic mobility shift assay, a specific band was observed in the -68- to -32-bp region in the presence of nuclear extracts. Supershift and mutational studies confirmed the binding of SP1 and, to a lesser extent, SP3 to the two potential SP1 binding sites and the preference of these proteins to one binding site over the other. SP1 and SP3 were both predominantly immunolocalized to the principal cells of the epididymis and follow distinct distribution patterns in this tissue. These results provide a framework crucial in the further investigation of the transcriptional regulation of 5alpha-reductase type 2 in the rat epididymis.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗

Purification and characterization of an endoglucanase from Streptomyces lividans 66 and DNA sequence of the gene.

The endoglucanase isolated from culture filtrates of Streptomyces lividans IAF74 was shown to have an Mr of 46,000 and a pI of 3.3. The specific enzyme activity of 539 IU/mg, determined by the reducing assay method on carboxymethyl cellulose, is among the highest reported in the literature. The cellulase showed typical endo-type activity when reacting on oligocellodextrins. Optimal enzyme activity was obtained at 50 degrees C and pH 5.5. The kinetic constants for this endoglucanase, determined with carboxymethyl cellulose as the substrate, were a Vmax of 24.9 IU/mg of enzyme and a Km of 4.2 mg/ml. Activity was found against neither methylumbelliferyl- nor p-nitrophenyl-cellobiopyranoside nor with xylan. The DNA sequence contains one possible reading frame validated by the N terminus of the mature purified protein. However, neither ATG nor GTG starting codons were identified near the ribosome-binding site. A putative TTG codon was found as a good candidate for the start codon. Comparison of the primary amino acid sequence of the endoglucanase of S. lividans revealed that the N terminus contains a bacterial cellulose-binding domain. The catalytic domain at the C terminus showed similarity to endoglucanases from a Bacillus sp. Thus, the endoglucanase CelA belongs to family A of cellulases as described before (N. R. Gilkes, B. Henrissat, D. G. Kilburn, R. C. Miller, Jr., and R. A. J. Warren, Microbiol. Rev. 55:303-315, 1991.

Amino Acid Sequence↗

Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase Mycobacterium tuberculosis.

The sigA and sigB genes of Mycobacterium tuberculosis encode two sigma 70-like sigma factors of RNA polymerase. While transcription of the sigA gene is growth rate independent, sigB transcription is increased during entry into stationary phase. The sigA gene transcription is unresponsive to environmental stress but that of sigB is very responsive, more so in stationary-phase growth than in log-phase cultures. These data suggest that SigA is a primary sigma factor which, like sigma70, controls the transcription of the housekeeping type of promoters. In contrast, SigB, although showing some overlap in function with SigA, is more like the alternative sigma factor, sigmaS, which controls the transcription of the gearbox type of promoters. Primer extension analysis identified the RNA start sites for both genes as 129 nucleotides upstream to the GTG start codon of sigA and 27 nucleotides from the ATG start codon of sigB. The -10 promoter of sigA but not that of sigB was similar to the sigma70 promoter. The half-life of the sigA transcript was very long, and this is likely to play an important part in its regulation. In contrast, the half-life of the sigB transcript was short, about 2 min. These results demonstrate that the sigB gene may control the regulons of stationary phase and general stress resistance, while sigA may be involved in the housekeeping regulons.

Bacterial Proteins↗

Radioresistance induced by the high molecular forms of the basic fibroblast growth factor is associated with an increased G2 delay and a hyperphosphorylation of p34CDC2 in HeLa cells.

The basic fibroblast growth factor-(bFGF) mediated signal transduction pathway has been implicated in cellular resistance to ionizing radiation. bFGF is synthesized from the same mRNA in four isoforms resulting from alternative initiations of translation at three CUG start codons (24, 21.5, and 21 kDa) and one AUG start codon (18 kDa). We analyzed the implication of high- and low-molecular forms of bFGF in radioresistance acquisition. For this, we transfected HeLa cells with retroviral vector containing either the CUG-initiated 24-kDa molecular form (HeLa 3A cells), the AUG-initiated 18-kDa molecular bFGF form (HeLa 5A cells), or the vector alone (HeLa PINA cells). A significantly increased radioresistance was obtained only in HeLa 3A cells (Dq = 810 +/- 24 cGy) compared with wild-type cells (Dq = 253 +/- 49 cGy) or HeLa PINA cells (Dq = 256 +/- 29 cGy; P < 0.001). This radioprotective effect was independent of an inhibition of radiation-induced apoptosis but related to an increased G2 duration after irradiation and to an hyperphosphorylation of p34cdc2 kinase. Knowledge of the high-molecular bFGF form-induced radioresistance pathway could offer novel targets for decreasing the radioresistance phenotype of tumors expressing high amounts of bFGF, such as glioblastoma.

Apoptosis↗

Structure and chromosomal localization of the human and mouse muscle fructose-1,6-bisphosphatase genes.

Mammalian skeletal muscle contains fructose-1,6-bisphosphatase (Fru-1,6-P(2)ase), a key enzyme of glyconeogenesis. We have shown previously that muscle Fru-1,6-P(2)ase is encoded by a gene different from that coding for the liver isoenzyme. Starting with genomic YAC libraries and based on the cDNA sequences of human and mouse muscle Fru-1,6-P(2)ases together with the known gene structures of two mammalian liver fructose-1,6-bisphosphatases, we have PCR-amplified and sequenced all functional parts of the human and mouse muscle fructose-1,6-bisphosphatase genes and determined their chromosomal localization. The human gene (FBP2), localized at chromosome 1p36.1-2, spans about 30 kb, while the mouse gene (Fbp2) at chromosome 13B3-C1 is more compact (about 21 kb). Intron lengths are only poorly conserved between the two genes, while intron number and positions are identical in all hitherto analyzed mammalian fructose-1,6-bisphosphatase isoenzyme genes. Transcriptional start sites were found to be located 97 and 95bp before the start codon in the human gene and 35 bp before the start codon in the mouse homolog. A comparison of the 5'-flanking sequences of the two genes revealed a 56% homology up to human bp -607 before the first transcriptional start point, while upstream of this region we found no similarity. The data presented in this paper provide a basis for further studies of the mechanism of expression regulation and the elucidation of the physiological role of the enzyme.

Animals↗

In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations.

The translation start site, immediately downstream from the start codon, is a dominant factor for gene expression in Escherichia coli. At present, no method exists to improve the expression level of cloned genes, since it remains difficult to find the best codon combination within the region. We determined the expression parameters that correspond to all sense codons within the first four codons using GFPuv which encodes a derivative of green fluorescent protein. Using a genetic algorithm (GA)-based computer program, these parameters were incorporated in a simple, static model for the prediction of translation efficiency, and optimized to the expression level for 137 randomly isolated GFPuv genes. The calculated initial translation index (ITI), also proven for the DsRed2 gene that encodes a red fluorescent protein, should provide a solution to overcome the gene expression problem in cloned genes whose expression is often inherently blocked at the translation process. The proposed method facilitates heterologous protein production in E. coli, the most commonly used host in biological and industrial fields.

Cloning, Molecular↗

S gene expression and the timing of lysis by bacteriophage lambda.

The S gene of bacteriophage lambda encodes the holin required for release of the R endolysin at the onset of phage-induced host lysis. S is the promoter-proximal gene on the single lambda late transcript and spans 107 codons. S has a novel translational initiation region with dual start codons, resulting in the production of two protein products, S105 and S107. Although differing only by the Met-1-Lys-2... N-terminal extension present on S107, the two proteins are thought to have opposing functions, with the shorter polypeptide acting as the lysis effector and the longer one acting as an inhibitor. The expression of wild-type and mutant alleles of the holin gene has been assessed quantitatively with respect to the scheduling of lysis. S mRNA accumulates during the late gene expression period to a final level of about 170 molecules per cell and is maintained at that level for at least the last 15 min before lysis. Total S protein synthesis, partitioned at about 2:1 in favor of the S105 protein compared with the other product, S107, accumulates to a final level of approximately 4,600 molecules per cell. The kinetics of accumulation of S is consistent with a constant translational rate of less than one S protein per mRNA per minute. Mutant alleles with alterations in the translational initiation region were studied to determine how the translational initiation region of S achieves the proper partition of initiation events at the two S start codons and how the synthesis of S105 and S107 relates to lysis timing. The results are discussed in terms of a model for the pathway by which the 30S ribosome-fMet-tRNA complex binds to the translational initiation region of S. In addition, analysis of the relationship between lysis timing and the levels of the two S gene products suggests that S107 inhibits S105, the lethal lysis effector, by a stoichiometric titration.

Amino Acid Sequence↗

The promoter region of the carbamoyl-phosphate synthetase III gene of Squalus acanthias.

Carbamoyl-phosphate synthetase III (CPSase III) of Squalus acanthias (spiny dogfish) is a nuclear-encoded mitochondrial enzyme that catalyzes glutamine-dependent formation of carbamoyl phosphate for urea synthesis. In this paper we report the results of cloning a 10-kb segment of genomic DNA which includes the region flanking the 5' end of the spiny dogfish CPSase III gene. A total of 1,295 base pairs of sequence straddling the start codon was obtained. Primer extension experiments revealed that the transcription start site is the G located 114 residues upstream of the translation start codon ATG. The first exon has 240 base pairs, including the 5' untranslated region, the coding sequence for the signal peptide (38 amino acids), and the four N-terminal amino acids of the mature enzyme. The boundary of the first exon and the first intron of the CPSase III gene is concordant with that of rat and frog (Rana catesbeiana) CPSase I, which have been suggested to have evolved from CPSase III. The putative TATA box sequence, TACAAA, is located at position -31 with an uncommonly found C at the third position. Two C/EBP binding site sequences, ATTCTGCAAG (-405 to -397) and GTGCAGTAAG (-168 to -160), were identified in the promoter region, which suggests that spiny dogfish CPSase III might be subjected to transactivation of transcription by C/EBP-related proteins, as has been reported for rat CPSase I. The preparation and binding of a recombinant RcC/EBP-1 protein (the R. catesbeiana homolog of the mammalian C/EBP alpha) to the two spiny dogfish C/EBP binding sequences are described. Two putative heat-shock binding elements were also identified in the promoter region.

Amino Acid Sequence↗

Molecular cloning and characterization of rainbow trout (Oncorhynchus mykiss) C5a anaphylatoxin receptor.

In the course of suppression subtractive hybridization between the cDNA of phytohemagglutinin-stimulated and non-stimulated head kidney cells in rainbow trout (Oncorhynchus mykiss), a cDNA clone was obtained that showed most similarity to mammalian receptor for the anaphylatoxin of the fifth complement component (C5aR). The rainbow trout C5aR cDNA contains a 1,679-bp nucleotide sequence that encodes a 350-amino-acid putative protein with 29.0-31.5% identity to mammalian C5aR. Rainbow trout C5aR has seven putative transmembrane domains that are common to mammalian C5aR. A cysteine residue in the second cytoplasmic domain in mammalian C5aR, required for formation of disulfide-linked dimers, is seen in trout C5aR but not in other similar rhodopsin-like receptors. An arginine residue in the fifth transmembrane domain, which is critical for activation of the C5aR by C5a, is also conserved in rainbow trout C5aR. The rainbow trout C5aR gene has a 1.9-kb intron in the position 12 bp upstream of the start codon, which is similar to that seen right after the start codon in human C5aR gene. These results indicate that the clone is a rainbow trout homologue of mammalian C5aR. Southern blot hybridization suggested that C5aR is a single-copy gene. Northern blotting and RT-PCR analyses detected higher amounts of the transcript in head kidney and posterior kidney, but much lower levels in peripheral blood leukocytes and spleen, faint expression in brain and gills, heart, intestine and very faint expression in liver and muscle.

Amino Acid Sequence↗

The nucleotide sequence of the fusion protein gene of the peste des petits ruminants virus: the long untranslated region in the 5'-end of the F-protein gene of morbilliviruses seems to be specific to each virus.

cDNA corresponding to the fusion protein (F) gene of the vaccine strain of peste des petits ruminants virus (PPRV) was cloned and sequenced. The gene was 2321 nucleotides long excluding the poly(A) tail. As with other morbilliviruses, it had a long G/C rich stretch of about 525 nucleotides. There was no start codon before position 489 in the nucleotide sequence. From the 489th nucleotide to the 549th nucleotide, there were 4 ATG codons, two of which were in frame. The fourth ATG codon was in the best context to act as a start codon for encoding a protein which will be composed of 546 amino acids with a predicted molecular weight 59,310 Da. The comparison of the nucleic acid sequences of different morbillivirus F-protein genes revealed that the 5'-end sequence of the mRNA is specific to each virus. This sequence contains a long stretch of nucleotides rich in G/C content. When protein sequences were compared, it appears that, during evolution, substitutions in amino acid occurred in the F-protein of morbilliviruses such that the structure required for the fusion activity remains unchanged. These substitutions appear to have only occurred in the leader and the membrane anchor sequences, probably as an adaptation of the protein to the host cell.

Amino Acid Sequence↗

Transcription in Mycoplasma pneumoniae.

Very little is understood of the structure of mycoplasma promoters, and this limits interpretation of genomic sequence data in these species. In this study the transcriptional start points of 22 genes of Mycoplasma pneumoniae were identified and the regions 5' to the start point compared. Although a strong consensus -10 region could be seen, there was only a weak consensus in the -35 region. A high proportion of transcripts had heterogeneous 5'-ends and characterisation of the sequence of the 5'-ends of two transcripts established that the heterogeneity was derived from initiation of transcription at reduced levels between 1 and 4 bases 5' to the major starting point. In addition to this apparently unique feature, a high proportion of transcripts lacked a 5' untranslated leader region that could contain a ribosomal binding site. Such leaderless transcripts are seen rarely in other bacterial species. Although the promoter regions for a number of members of lipoprotein multigene families were examined, no obvious explanation for regulation of expression was apparent. Using the data from this study an improved matrix for prediction of M.pneumoniae promoters was derived. Application of this matrix to the sequences immediately 3' and 5' to each predicted start codon in the genome suggested that most M. pneumoniae transcriptional start points were likely to occur between 5 and 30 bases 5' to the start codon.

Base Composition↗

Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid.

Replication of the IncL/M plasmid pMU604 is controlled by a small antisense RNA molecule (RNAI), which, by inhibiting the formation of an RNA pseudoknot, regulates translation of the replication initiator protein, RepA. Efficient translation of the repA mRNA was shown to require the translation and correct termination of the leader peptide, RepB, and the formation of the pseudoknot. Although the pseudoknot was essential for the expression of repA, its presence was shown to interfere with the translation of repB. The requirement for pseudoknot formation could in large part be obviated by improving the ribosome binding region of repA, either by replacing the GUG start codon by AUG or by increasing the spacing between the start codon and the Shine-Dalgarno sequence (SD). The spacing between the distal pseudoknot sequence and the repA SD was shown to be suboptimal for maximal expression of repA.

Bacterial Proteins↗

The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity.

An ATP-dependent glucokinase of the hyperthermophilic aerobic crenarchaeon Aeropyrum pernix was purified 230-fold to homogeneity. The enzyme is a monomeric protein with an apparent molecular mass of about 36 kDa. The apparent K(m) values for ATP and glucose (at 90 degrees C and pH 6.2) were 0.42 and 0.044 mM, respectively; the apparent V(max) was about 35 U/mg. The enzyme was specific for ATP as a phosphoryl donor, but showed a broad spectrum for phosphoryl acceptors: in addition to glucose, which showed the highest catalytic efficiency (k(cat)/K(m)), the enzyme also phosphorylates glucosamin, fructose, mannose, and 2-deoxyglucose. Divalent cations were required for maximal activity: Mg(2+), which was most effective, could partially be replaced with Co(2+), Mn(2+), and Ni(2+). The enzyme had a temperature optimum of at least 100 degrees C and showed significant thermostability up to 100 degrees C. The coding function of open reading frame (ORF) APE2091 (Y. Kawarabayasi, Y. Hino, H. Horikawa, S. Yamazaki, Y. Haikawa, K. Jin-no, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, H. Nakazawa, M. Takamiya, S. Masuda, T. Funahashi, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, and H. Kikuchi, DNA Res. 6:83-101, 145-152, 1999), previously annotated as gene glk, coding for ATP-glucokinase of A. pernix, was proved by functional expression in Escherichia coli. The purified recombinant ATP-dependent glucokinase showed a 5-kDa higher molecular mass on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but almost identical kinetic and thermostability properties in comparison to the native enzyme purified from A. pernix. N-terminal amino acid sequence of the native enzyme revealed that the translation start codon is a GTG 171 bp downstream of the annotated start codon of ORF APE2091. The amino acid sequence deduced from the truncated ORF APE2091 revealed sequence similarity to members of the ROK family, which comprise bacterial sugar kinases and transcriptional repressors. This is the first report of the characterization of an ATP-dependent glucokinase from the domain of Archaea, which differs from its bacterial counterparts by its monomeric structure and its broad specificity for hexoses.

Adenosine Triphosphate↗

Enterovirus 71 contains a type I IRES element that functions when eukaryotic initiation factor eIF4G is cleaved.

Human enterovirus 71 (EV71) is a member of the Enterovirus genus of the Picornaviridae family. Other members of this family utilize an unusual mechanism of translation initiation whereby ribosomes are recruited internally to the viral RNA by an internal ribosome site (IRES) located in their 5' noncoding regions (5' NCR). Using dicistronic reporter constructs, we demonstrate that the 5' NCRs of the 7423/MS/87 and BrCr strains of EV71 function as an IRES both in extracts and in cultured cells. Preincubation of translation extracts with purified coxsackievirus 2A protease cleaved elF4G, a component of the cap binding complex, resulting in a significant decrease in translation of capped mRNAs. In contrast, the translational efficiency of the EV71 IRES was enhanced under this condition, demonstrating that the EV71 IRES functions similar to other enterovirus IRES elements when components of the cap binding protein complex are cleaved. Finally, insertion of an upstream, out-of-frame start codon in the 5' NCR of the EV71 genome inhibited IRES activity, suggesting that EV71 can be classified as a type I IRES, in which ribosomes first bind upstream of the initiation codon and then scan the mRNA until an appropriate downstream AUG start codon is encountered and protein synthesis commences.

5' Untranslated Regions↗

Partial transcriptional mapping of the fowlpox virus genome and analysis of the EcoRI L fragment.

Several fowlpox virus (FPV) DNA fragments were selected by differential hybridization using cDNA of transcripts that were strongly transcribed early and/or later after infection of QT-35 cells. The EcoRI L fragment contained three strongly transcribed FPV genes: L1L, a late 1452 bp partial (amino end) ORF; L2R, an early/late 522 bp ORF; and L3R, a late 948 bp ORF. The protein products of L1L, L2R and L3R shared homology with the products of vaccinia virus (VV) genes H4L (RAP94), H5R (Ag35) and H6R (topoisomerase), respectively, suggesting a conservation of gene structure and order between VV and FPV. The 5' upstream non-coding sequences of L1L and L3R were A + T rich and the sequence 5' TAAATG 3' overlapped the predicted translation start codon. Primer extension analysis of the L2R transcript mapped the transcriptional start sites of early and late mRNAs 14 nt downstream of a VV early promoter-like critical region sequence, AAAATTGAA-AAAAAAA. A VV-like TAAAT late transcriptional element was present 20 nt upstream of the L2R ATG translational start codon. A plasmid with the putative early L2R promoter cloned upstream of the Newcastle disease virus haemagglutinin-neuraminidase (HN) cDNA as a reporter gene was at least 6-fold more effective in generating HN MRNa than plasmids containing the P7.5 or P11 VV promoters in transient expression assays in FPV-infected CEF cells treated with cytosine arabinoside. The L2R promoter was also able to express an amount of HN mRNA equal to that expressed by the VV promoters late in infection.

Amino Acid Sequence↗