Molecular cloning and characterization of the Streptomyces hygroscopicus alpha-amylase gene

A highly divergent α-amylase from Streptomyces spp.: An evolutionary perspective

The present study deals with the genetic changes observed in the protein sequence of an α-amylase from Streptomyces spp. and its structural homologs from Pseudoalteromonas haloplanktis, invertebrates and mammals. The structural homologs are renowned for their important features such as chloride binding triad and a serine-protease like catalytic triad (a triad which is reported to be strictly conserved in all chloride-dependent α-amylases). These conserved regions are essential for allosteric activation of enzyme and conformational stability, respectively. An evaluation of these distinctive features in Streptomyces α-amylases revealed the role of mutations in conserved regions and evolution of chloride-independent α-amylases in Streptomyces spp. Besides, the study also discovers a highly divergent α-amylase from Streptomyces spp. which varies greatly even within the homologs of the same genus. Another very important feature is the number of disulfide bridges in which the structural homologs own eight Cys residues to form four disulfide bridges whereas Streptomyces α-amylases possess only seven Cys to form three disulfide bridges. The study also highlights the unique evolution of carbohydrate binding module 20 domain (CBM20 also known as raw starch binding domain or E domain) in Streptomyces α-amylases which is completely absent in α-amylases of other structural homologs.

Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger

In the genome sequence of Aspergillus niger CBS 513.88, three genes were identified with high similarity to fungal alpha-amylases. The protein sequences derived from these genes were different in two ways from all described fungal alpha-amylases: they were predicted to be glycosylphosphatidylinositol anchored, and some highly conserved amino acids of enzymes in the alpha-amylase family were absent. We expressed two of these enzymes in a suitable A. niger strain and characterized the purified proteins. Both enzymes showed transglycosylation activity on donor substrates with alpha-(1,4)-glycosidic bonds and at least five anhydroglucose units. The enzymes, designated AgtA and AgtB, produced new alpha-(1,4)-glycosidic bonds and therefore belong to the group of the 4-alpha-glucanotransferases (EC 2.4.1.25). Their reaction products reached a degree of polymerization of at least 30. Maltose and larger maltooligosaccharides were the most efficient acceptor substrates, although AgtA also used small nigerooligosaccharides containing alpha-(1,3)-glycosidic bonds as acceptor substrate. An agtA knockout of A. niger showed an increased susceptibility towards the cell wall-disrupting compound calcofluor white, indicating a cell wall integrity defect in this strain. Homologues of AgtA and AgtB are present in other fungal species with alpha-glucans in their cell walls, but not in yeast species lacking cell wall alpha-glucan. Possible roles for these enzymes in the synthesis and/or maintenance of the fungal cell wall are discussed.

Utilization of soluble starch by a recombinant Corynebacterium glutamicum strain: Growth and lysine production

Corynebacterium glutamicum, well known for the industrial production of amino acids, grows aerobically on a variety of mono- and disaccharides and on alcohols and organic acids as single or combined sources of carbon and energy. Members of the genera Corynebacterium and Brevibacterium were here tested for their ability to use the homopolysaccharide starch as a substrate for growth. None of the 24 type strains tested showed growth on or degradation of this substrate, indicating that none of the strains synthesized and secreted starch-degrading enzymes. Introducing the Streptomyces griseus amy gene on an expression vector into the lysine-producer C. glutamicum DM1730, we constructed a C. glutamicum strain synthesizing and secreting alpha-amylase into the culture broth. Although some high-molecular-weight degradation products remained in the culture broth, this recombinant strain effectively used soluble starch as carbon and energy substrate for growth and also for lysine production. Thus, employment of our construct allows avoidance of the cost-intensive enzymatic hydrolysis of the starch, which commercially is used as a substrate in industrial amino acid fermentations.

Development of recombinant Streptomyces for biotechnological and environmental uses

Recombinant DNA techniques for manipulation of genes in Streptomyces are well developed, and currently there is a high level of activity among researchers interested in applying molecular cloning and protoplast fusion techniques to strain development within this commercially important group of bacteria. A number of efficient plasmid and phage vector systems are being used for the molecular cloning of genes, primarily those encoding antibiotic biosynthesis enzymes, but also for a variety of other bioactive proteins and enzymes of known or potential commercial value. In addition, cloning aimed at constructing specialized bioconversion strains for use in the production of chemicals from organic carbon substrates is underway in numerous laboratories. This review discusses the current status of research involving recombinant DNA technologies applied to biotechnological applications using Streptomyces. The topic of potential environmental uses of recombinant Streptomyces is also reviewed, as is the status of current research aimed at assessing the fate and effects of recombinant Streptomyces in the environment. Also summarized is recent research that has confirmed that genetic exchange occurs readily among Streptomyces in the soil environment and which has shown the potential for exchange between recombinant Streptomyces and native soil bacteria.

Physiology of antibiotic production in actinomycetes and some underlying control mechanisms

Some of the accumulated information on the physiology and nutritional control of antibiotic production in actinomycetes can now be related to recent discoveries in the field of actinomycete molecular biology. This review focuses on aspects of genetic and metabolic control of antibiotic biosynthesis. It surveys some well established principles in the relationship between primary and secondary metabolism, and summarizes briefly the areas where progress is being made in elucidating the molecular organization of regulatory systems underlying this relationship.

Characterization of the hom-thrC-thrB cluster in aminoethoxyvinylglycine-producing Streptomyces sp. NRRL 5331

Three genes from the aminoethoxyvinylglycine (AVG)-producing Streptomyces sp. NRRL 5331 involved in threonine biosynthesis, hom, thrB and thrC, encoding homoserine dehydrogenase (HDH), homoserine kinase (HK) and threonine synthase (TS), respectively, have been cloned and sequenced. The hom and thrC genes appear to be organized in a bicistronic operon as deduced by disruption experiments. The thrB gene, however, is transcribed as a monocistronic transcript. The encoded proteins are quite similar to the HDH, HK and TS proteins from other bacterial species. The overall organization of these three genes, in the order hom-thrC-thrB, differs from that in other bacteria and is similar to that reported in the Streptomyces coelicolor genome sequence. This is the first time in which the gene cluster for the three last steps of threonine biosynthesis has been characterized from a streptomycete. Disruption of thrC indicated that threonine is not a direct precursor for AVG biosynthesis in Streptomyces sp. NRRL 5331 and suggested that the branching point of the aspartic acid-derived biosynthetic route of this metabolite should lie earlier on the threonine biosynthetic route.

Primary metabolism and its control in streptomycetes: a most unusual group of bacteria

Streptomycetes are Gram-positive bacteria with a unique capacity for the production of a multitude of varied and complex secondary metabolites. They also have a complex life cycle including differentiation into at least three distinct cell types. Whilst much attention has been paid to the pathways and regulation of secondary metabolism, less has been paid to the pathways and the regulation of primary metabolism, which supplies the precursors. With the imminent completion of the total genome sequence of Streptomyces coelicolor A3(2), we need to understand the pathways of primary metabolism if we are to understand the role of newly discovered genes. This review is written as a contribution to supplying these wants. Streptomycetes inhabit soil, which, because of the high numbers of microbial competitors, is an oligotrophic environment. Soil nutrient levels reflect the fact that plant-derived material is the main nutrient input; i.e. it is carbon-rich and nitrogen- and phosphate-poor. Control of streptomycete primary metabolism reflects the nutrient availability. The variety and multiplicity of carbohydrate catabolic pathways reflects the variety and multiplicity of carbohydrates in the soil. This multiplicity of pathways has led to investment by streptomycetes in pathway-specific and global regulatory networks such as glucose repression. The mechanism of glucose repression is clearly different from that in other bacteria. Streptomycetes feed by secreting complexes of extracellular enzymes that break down plant cell walls to release nutrients. The induction of these enzyme complexes is often coordinated by inducers that bear no structural relation to the substrate or product of any particular enzyme in the complex; e.g. a product of xylan breakdown may induce cellulase production. Control of amino acid catabolism reflects the relative absence of nitrogen catabolites in soil. The cognate amino acid induces about half of the catabolic pathways and half are constitutive. There are reduced instances of global carbon and nitrogen catabolite control of amino acid catabolism, which again presumably reflects the relative rarity of the catabolites. There are few examples of feedback repression of amino acid biosynthesis. Again this is taken as a reflection of the oligotrophic nature of the streptomycete ecological niche. As amino acids are not present in the environment, streptomycetes have rarely invested in feedback repression. Exceptions to this generalization are the arginine and branched-chain amino acid pathways and some parts of the aromatic amino acid pathways which have regulatory systems similar to Escherichia coli and Bacillus subtilis and other copiotrophic bacteria.

Cloning and heterologous expression of the gene for BLIP-II, a beta-lactamase-inhibitory protein from Streptomyces exfoliatus SMF19

A beta-lactamase-inhibitory protein (BLIP-II) was purified from the culture filtrate of Streptomyces exfoliatus SMF 19 and its N-terminal amino acid sequence was determined. A clone containing the gene encoding BLIP-II (bliB) was selected from a cosmid library by colony hybridization using an oligonucleotide probe based on the N-terminal amino acid sequence of BLIP-II. The bliB gene was isolated and sequenced. Analysis of the nucleotide sequence revealed that the gene consists of 1116 bp and encodes a mature protein of 332 amino acids preceded by a 40 amino acid signal sequence. bliB, expressed under the control of the T7 promoter in Escherichia coli, was accumulated in an inactive form in inclusion bodies, but beta-lactamase-inhibitory activity was recovered after refolding. In addition, bliB was heterologously expressed in Streptomyces lividans TK24 using the melC1 promoter. The BLIP-II protein produced in recombinant strains of S. lividans was secreted into the culture supernatant in a biologically active form.

Cloning and characterization of a new alpha-amylase gene from Streptomyces lividans TK24

Streptomyces lividans TK24 possesses a very weak amylolytic activity, nevertheless Southern blot analysis carried out at high stringency revealed that this strain does contain a gene strongly related to the well expressed alpha-amylase gene (amlSL) of Streptomyces limosus. To clone this related gene, three genomic banks of S. lividans TK24 were constructed into the multicopy plasmid vector pIJ699 and transformed into the same strain. Two different genes were isolated. One (amlA) has been previously described, whereas the other (amlB) has never been described. Sub-cloning experiments localized amlB to a 3 kb BamHI-NotI fragment that was sequenced. Frame analysis on sequence data revealed the presence of a 1719 bp long open reading frame encoding a 573 amino acid protein of 61214 kDa. Northern blot analysis identified a unique 1.8 kb monocistronic transcript. Primer extension allowed the localization of the transcription start point 108 bp upstream of the translational start codon and demonstrated that the gene was transcribed from a unique typical eubacterial-like promoter. AmlB shares 74.7% amino acid identity with the alpha-amylase of S. limosus and only 27.2% with the amylolytic enzyme encoded by amlA.

Roles of the signal peptide and mature domains in the secretion and maturation of the neutral metalloprotease from Streptomyces cacaoi

The neutral metalloprotease (Npr) of Streptomyces cacaoi is synthesized as a prepro-Npr precursor form consisting of a secretory signal peptide, a propeptide and the mature metalloprotease. The maturation of Npr occurs extracellularly via an autoproteolytic processing of the secreted pro-Npr. The integrity of the propeptide is essential for the formation of mature active Npr but not for its secretion [Chang, Chang and Lee (1994) J. Biol. Chem. 269, 3548-3554]. In this study we investigated whether the secretion and maturation of Npr require the integrity of its signal peptide region and mature protease domain. Five signal peptide mutants were generated, including the substitution mutations at the positively charged region (mutant IR6LE), the central hydrophobic region (mutants GI19EL and G19N), the boundary of the hydrophobic core-cleavage region (mutant P30L) and at the residues adjacent to the signal peptidase cleavage site (mutant YA33SM). All these lesions delayed the export of Npr to the growth medium and also resulted in a 2-10-fold decrease in Npr export. The most severe effect was noted in mutants GI19EL and P30L. When these signal peptide mutations were fused separately with the propeptide lacking the Npr mature domain, the secretory defect on the propeptide was also observed, and this impairment was again more severely expressed in mutants GI19EL and P30L. Thus the Npr signal peptide seems to have more constraints on the hydrophobic core region and at the proline residue within the boundary of the hydrophobic core-cleavage site. Deletion mutations within the C-terminal mature protease domain that left its active site intact still blocked the proteolytic processing of mutant precursor forms of pro-Npr, although their secretions were unaffected. These results, together with our previous findings, strongly suggest that the signal peptide of Npr plays a pivotal role in the secretion of both Npr and the propeptide, but not in the maturation of Npr. On the contrary, the integrity of mature domain and propeptide is not critical for secretion of the Npr derivative but is essential for the formation of a functional Npr. Therefore the secretion and maturation of Npr are dependent on the integrity of the signal peptide, propeptide and mature protease domains, and the roles of these domains in this regard are functionally distinct.

Production and secretion of proteins by streptomycetes

Streptomycetes produce a large number of extracellular enzymes as part of their saprophytic mode of life. Their ability to synthesize enzymes as products of their primary metabolism could lead to the production of many proteins of industrial importance. The development of high-yielding expression systems for both homologous and heterologous gene products is of considerable interest. In this article, we review the current knowledge on the various factors that affect the production and secretion of proteins by streptomycetes and try to evaluate the suitability of these bacteria for the large-scale production of proteins of industrial importance.

The gene amyE(TV1) codes for a nonglucogenic alpha-amylase from Thermoactinomyces vulgaris 94-2A in Bacillus subtilis

We isolated the gene amyE(TV1) from Thermoactinomyces vulgaris 94-2A encoding a nonglucogenic alpha-amylase (AmyTV1). A chromosomal DNA fragment of 2,247 bp contained an open reading frame of 483 codons, which was expressed in Escherichia coli and Bacillus subtilis. The deduced amino acid sequence of the AmyTV1 protein was confirmed by sequencing of several peptides derived from the enzyme isolated from a T. vulgaris 94-2A culture. The amino acid sequence was aligned with several known alpha-amylase sequences. We found 83% homology with the 48-kDa alpha-amylase part of the Bacillus polymyxa beta-alpha-amylase polyprotein and 50% homology with Taka amylase A of Aspergillus oryzae but only 45% homology with another T. vulgaris amylase (neopullulanase, TVA II) recently cloned from strain R-47. The putative promoter region was characterized with primer extension and deletion experiments and by expression studies with B. subtilis. Multiple promoter sites (P3, P2, and P1) were found; P1 alone drives about 1/10 of the AmyTV1 expression directed by the native tandem configuration P3P2P1. The expression levels in B. subtilis could be enhanced by fusion of the amyE(TV1) coding region to the promoter of the Bacillus amyloliquefaciens alpha-amylase gene.

Cloning, expression, and nucleotide sequence of the alpha-amylase gene from the haloalkaliphilic archaeon Natronococcus sp. strain Ah-36

The alpha-amylase gene of a Natronococcus sp. (1,512 bp) contained a signal peptide of 43 amino acids. Haloferax volcanii expressed the gene and cleaved the signal peptide accurately. The signal peptide shared an extremely high amino acid sequence identity with that of a protease from the halophilic archaeon 172P1.

Cloning and sequence analysis of a Streptomyces cholesterol esterase gene

Streptomyces lavendulae H646-SY2 produces cholesterol esterase (CHE; EC 3.1.1.13) extracellularly. A genomic library of the strain, prepared in plasmid pUC119, was screened with probes based on the amino acid sequence of the protein. A plasmid, designated as pKX101 and identified by hybridization with the probes, contained a 2.7-kb insert from Streptomyces DNA. We determined the 17-N-terminal amino acid sequence of mature CHE and the nucleotide sequence of the 0.9-kb segment containing the CHE gene (che). We found that the N-terminal of the mature CHE was Ala39 and an open reading frame consisting of 681 bp starts at ATG and ends at TGA, suggesting that a precursor and a mature CHE consist of 227 and 189 amino acids, with a calculated relative molecular mass of 24,362 and 20,650, respectively. The leader peptide extends over 38 amino acids and has the characteristics of a signal sequence, including basic amino acids near the N-terminus and a hydrophobic core near the signal cleavage site.

Effect of growth rate and cultivation environments on cloned gene stability and the cloned gene product formation in Streptomyces lividans

The growth rate and environmental effects on the stability of recombinant plasmid, pDML6 containing beta-lactamase gene, and the cloned gene product formation in Streptomyces lividans were studied. A maximum production rate of the cloned gene product was obtained at a specific growth rate 0.106 h-1 in glucose-limited chemostat cultivations without genetic selection pressure. Optimum environmental conditions for the recombinant plasmid stability and maximum formation rates of the cloned gene product were determined using continuous cultivations at the optimum specific growth rate. The fractions of plasmid harboring mycelium in prolonged cultivation up to 50 generations were varied from 77 to 95%. The recombinant plasmid was stably maintained in the host cells grown in different temperatures (24 to 36 degrees C) and pH (6.0 to 8.5). The formation of the cloned gene product was optimum at pH 7.0 and 27 degrees C, at which the maximum enzyme production rate was 0.82 kU g-1 h-1. Continuous cultivations varying the dissolved oxygen tension (10 to 80% air saturation) showed that the plasmids were maintained stably and the specific enzyme production rates were increased with increasing dissolved oxygen levels.

Sequence of the Streptomyces thermoviolaceus CUB74 alpha-amylase-encoding gene and its transcription analysis in Streptomyces lividans

The alpha-amylase (Amy)-encoding gene (amy) of Streptomyces thermoviolaceus CUB74, previously cloned in Escherichia coli and S. lividans and localised on a 1.7-kb BamHI-SphI genomic DNA fragment, has been sequenced. A single open reading frame of 1380 bp, which could encode an Amy protein of 460 amino acids (aa), was identified. The deduced aa sequence of the thermophilic Amy is similar (up to 69.5%) to the mesophilic Amy of S. griseus, S. limosus, S. venezuelae and S. hygroscopicus. A 40% sequence similarity was found between the extracellular forms of the S. thermoviolaceus and the pig pancreatic Amy. In addition, the activity of the S. thermoviolaceus Amy is strongly inhibited by tendamistat, a potent inhibitor of mammalian Amy. The nucleotide sequence at the 5' end of amy was able to initiate transcription in S. lividans and contains a promoter whose sequence is identical to the promoters of the S. limosus, S. venezuelae and S. griseus amy.

Cloning and characterization of an alpha-amylase gene from Streptomyces lividans

The alpha-amylase gene (amy) of Streptomyces lividans TK24 was cloned in an amylase deficient mutant strain S. lividans M2. The cloned gene contained an open reading frame (ORF) of 2757 nucleotides (919 amino acids) coding for a protein of 100 kDa. Sequencing of the amino terminus of the extracellular alpha-amylase protein revealed the presence of a signal peptide of 33 amino acid residues. The transcriptional initiation site was mapped by the primer extension method with T4 DNA polymerase and was found to be transcribed from an unique promoter. The alpha-amylase protein produced by S. lividans was larger than those derived from other origins. It also contained the four common conserved regions characteristic of other alpha-amylase proteins.

Cloning, expression, and characterization of the Micromonospora viridifaciens neuraminidase gene in Streptomyces lividans

We have cloned the Micromonospora viridifaciens neuraminidase (EC 3.2.1.18) gene (nedA) in Streptomyces lividans. This was accomplished by using the vector pIJ702 and BglII-BclI libraries of M. viridifaciens chromosomal inserts created in S. lividans. The libraries were screened for the expression of neuraminidase by monitoring the cleavage of the fluorogenic neuraminidase substrate 2'-(4-methylumbelliferyl)-alpha-D-N-acetyl-neuraminic acid. Positive clones (BG6, BG7, BC4, and BC8) contained the identical 2-kb BclI-BglII fragment and expressed neuraminidase efficiently and constitutively using its own promoter in the heterologous host. From the nucleotide sequence analysis, an open reading frame of 1,941 bp which encodes a polypeptide with an M(r) of 68,840 was detected. The deduced amino acid sequence has five Asp boxes, -Ser-X-Asp-X-Gly-X-Thr-Trp, showing great similarity to other bacterial and viral neuraminidases. We have also identified the catalytic domain by using truncated proteins produced in S. lividans.

Extracellular α-amylase from Streptomyces rimosus

A purification procedure for an extracellular alpha-amylase from Streptomyces rimosus, oxytetracycline-producing strain, is described. The enzyme obtained was shown to be an acidic (pI 4.75) monomer with a relative molecular mass (M(r)) of 43,000, containing three cysteines involved in the catalytic activity of the enzyme. Its amino-terminal part has 57-67% homology with amylases from other Streptomyces species. S. rimosus alpha-amylase is sensitive to higher temperatures, and partially stabilized by Ca2+ ions. It hydrolyses starch (optimum at pH 5.0-6.0) in an endohydrolase manner giving rise to maltotriose, maltotetraose and higher oligosaccharides. Starch granules, except those from rice, were not significantly affected by the isolated alpha-amylase.

Heterologous expression and secretion of a Streptomyces scabies esterase in Streptomyces lividans and Escherichia coli

The esterase gene from Streptomyces scabies FL1 was cloned and expressed in Streptomyces lividans on plasmids pIJ486 and pIJ702. In S. lividans, the esterase gene was expressed during later stages of growth and was regulated by zinc, as is seen with S. scabies. The 36-kDa secreted form of the esterase was purified from S. lividans. N-terminal amino acid sequencing indicated that the processing site utilized in S. lividans for the removal of the signal sequence was the same as that recognized for processing in S. scabies. Western blots (immunoblots) revealed the presence of a 40-kDa precursor form of the esterase in cytoplasmic extracts. A 23-amino-acid deletion was introduced into the putative signal sequence for the esterase. When this deleted form of the esterase was expressed in S. lividans, a cytoplasmic 38-kDa precursor protein was produced but no secreted esterase was detected, suggesting the importance of the deleted sequence for efficient processing and secretion. The esterase gene was also cloned into the pUC119 plasmid in Escherichia coli. By using the lac promoter sequence, the esterase gene was expressed, and the majority of the esterase was localized to the periplasmic space.

Compilation and analysis of DNA sequences associated with apparent streptomycete promoters

The DNA sequences associated with 139 apparent streptomycete transcriptional start sites are compiled and compared. Of these, 29 promoters appeared to belong to a group which are similar to those recognized by eubacterial RNA polymerases containing sigma 70-like subunits. The other 110 putative promoter regions contain a wide diversity of sequences; several of these promoters have obvious sequence similarities in the -10 and/or -35 regions. The apparent Shine-Dalgarno regions of 44 streptomycete genes are also examined and compared. These were found to have a wide range of degree of complementarity to the 3' end of streptomycete 16S rRNA. Eleven streptomycete genes are described and compared in which transcription and translation are proposed to be initiated from the same or nearby nucleotide. An updated consensus sequence for the E sigma 70-like promoters is proposed and a potential group of promoter sequences containing guanine-rich -35 regions also is identified.

Characterization of the alpha-amylase-encoding gene from Thermomonospora curvata

The nucleotide sequence of a 3007-bp DNA fragment from Thermomonospora curvata CCM3352 containing the coding and regulatory region of the alpha-amylase-encoding gene (tam) was determined. Primer extension mapping was used to determine the 5' end of the transcript, and it was demonstrated that the gene is transcribed from a unique promoter which is also functional in Streptomyces lividans TK24. Transcription of tam in T. curvata was induced by maltose, even in the presence of glucose. In S. lividans, tam was expressed constitutively. The deduced amino acid sequence reveals a considerable similarity with alpha-amylases from streptomycetes.

Streptomyces: a host for heterologous gene expression

Streptomyces species offer many potential advantages as hosts for the expression and secretion of eukaryotic gene products. In this review we discuss the expression and localization signals that have been used to direct heterologous gene expression and the applications of these signals. Finally, we discuss future strategies aimed at increasing the capacity of this host for the high level production of biologically active eukaryotic gene products.

Review of the Streptomyces lividans/vector pIJ702 system for gene cloning

Interest in the biology of the Streptomyces and application of these soil bacteria to production of commercial antibiotics and enzymes has stimulated the development of efficient cloning techniques and a variety of streptomycete plasmid and phage vectors. Streptomyces lividans is routinely employed as a host for gene cloning, largely because this species recognizes a large number of promoters and appears to lack a restriction system. Vector pIJ702 was constructed from a variant of a larger autonomous plasmid and is often used as a cloning vehicle in conjunction with S. lividans. The host range of vector pIJ702 extends beyond Streptomyces spp., and its high copy number has been exploited for the overproduction of cloned gene products. This combination of host and vector has been used successfully to investigate antibiotic biosynthesis, gene structure and expression, and to map various Streptomyces mutants.

Effects of replacement of promoters and modification of the leader peptide region of the amy gene of Streptomyces griseus on synthesis and secretion of alpha-amylase by Streptomyces lividans

Five different mutations were introduced into the leader peptide region of the alpha-amylase gene of Streptomyces griseus IMRU 3570. A mutation which increased the positive charge of the N-terminal region of the leader peptide enhanced the secretion of alpha-amylase by two- to threefold. Replacement of the native promoter of the amylase gene by the promoter of the Tn5 neo gene or by the promoter of the saf gene resulted in a 16-fold increase in alpha-amylase secretion. The enhanced secretion of alpha-amylase obtained by using the most efficient promoters was due to a correlated increase in the amount of transcript formed. The translation and secretion processes in S. lividans are not a bottleneck for enzyme secretion even at very high transcription rates, since stimulation of transcription of the alpha-amylase gene results in a proportionate increase in secretion of the enzyme.

Characterization of the Butyrivibrio fibrisolvens glgB gene, which encodes a glycogen-branching enzyme with starch-clearing activity

A Butyrivibrio fibrisolvens H17c glgB gene, was isolated by direct selection for colonies that produced clearing on starch azure plates. The gene was expressed in Escherichia coli from its own promoter. The glgB gene consisted of an open reading frame of 1,920 bp encoding a protein of 639 amino acids (calculated Mr, 73,875) with 46 to 50% sequence homology with other branching enzymes. A limited region of 12 amino acids showed sequence similarity to amylases and glucanotransferases. The B. fibrisolvens branching enzyme was not able to hydrolyze starch but stimulated phosphorylase alpha-mediated incorporation of glucose into alpha-1,4-glucan polymer 13.4-fold. The branching enzyme was purified to homogeneity by a simple two-step procedure; N-terminal sequence and amino acid composition determinations confirmed the deduced translational start and amino acid sequence of the open reading frame. The enzymatic properties of the purified enzyme were investigated. The enzyme transferred chains of 5 to 10 (optimum, 7) glucose units, using amylose and amylopetin as substrates, to produce a highly branched polymer.

Cloning, nucleotide sequence, and enzymatic characterization of an alpha-amylase from the ruminal bacterium Butyrivibrio fibrisolvens H17c

A Butyrivibrio fibrisolvens amylase gene was cloned and expressed by using its own promoter on the recombinant plasmid pBAMY100 in Escherichia coli. The amylase gene consisted of an open reading frame of 2,931 bp encoding a protein of 976 amino acids with a calculated Mr of 106,964. In E. coli(pBAMY100), more than 86% of the active amylase was located in the periplasm, and TnphoA fusion experiments showed that the enzyme had a functional signal peptide. The B. fibrisolvens amylase is a calcium metalloenzyme, and three conserved putative calcium-binding residues were identified. The amylase showed high sequence homology with other alpha-amylases in the three highly conserved regions which constitute the active centers. These and other conserved regions were located in the N-terminal half, and no similarity with any other amylase was detected in the remainder of the protein. Deletion of approximately 40% of the C-terminal portion of the amylase did not result in loss of amylolytic activity. The B. fibrisolvens amylase was identified as an endo-alpha-amylase by hydrolysis of the Phadebas amylase substrate, hydrolysis of gamma-cyclodextrin to maltotriose, maltose, and glucose and the characteristic shape of the blue value and reducing sugar curves. Maltotriose was the major initial hydrolysis product from starch, although extended incubation resulted in its hydrolysis to maltose and glucose.

Characterization, expression in Streptomyces lividans, and processing of the amylase of Streptomyces griseus IMRU 3570: two different amylases are derived from the same gene by an intracellular processing mechanism

Extracellular amylase in Streptomyces lividans was undetectable in starch-supplemented medium. However, S. lividans produced fivefold-higher levels of amylase than Streptomyces griseus IMRU 3570 when transformed with the S. griseus amy gene. Two major proteins of 57 and 50 kDa with amylase activity accumulated in the culture broths of the donor S. griseus and S. lividans transformed with the amy gene. Both proteins were also present in protoplast lysates in the same relative proportion; they gave a positive reaction with antibodies against the 57-kDa amylase. They did not differ in substrate specificity or enzyme kinetics. The two amylases were purified to homogeneity by a two-step procedure. Both proteins showed the same amino-terminal sequence of amino acids, suggesting that both proteins are derived from the same gene. The deduced signal peptide has 28 amino acids with two positively charged arginines near the amino-terminal end. When an internal NcoI fragment was removed from the amy gene, the resulting S. lividans transformants did not synthesize any of the two amylase proteins and showed no reaction in immunoblotting. Formation of the 50-kDa protein was observed when pure 57-kDa amylase was treated with supernatants of protoplast lysates but not when it was treated with membrane preparations, indicating that the native 57-kDa amylase could be processed intracellularly.

Isolation of a new gene (SW A2) encoding an alpha-amylase from Schwanniomyces occidentalis and its expression in Saccharomyces cerevisiae

A new gene (SW A2) encoding a secretory alpha-amylase activity from Schwanniomyces occidentalis has been cloned from this yeast and then expressed in Saccharomyces cerevisiae. Both Sw, occidentalis and a transformant of S. cerevisiae incorporating SW A2 contain a transcript of 2.1 kb which hybridizes to DNa carrying the SW A2 gene. This indicates that the transcript is a product of the SW A2 gene. Transcription of the SW A2 gene seems to be regulated in both Sw. occidentalis and S. cerevisiae. Furthermore, the secretion of alpha-amylase activity is drastically repressed by glucose in both Sw. occidentalis and a transformant of S. cerevisiae containing SW A2.

Cloning, characterization and expression of an alpha-amylase gene from Streptomyces griseus IMRU3570

A gene, amy, encoding an alpha-amylase, was cloned on a 4.8 kb Sau3A fragment from the DNA of Streptomyces griseus IMRU3570. The gene was localized to a 2.27 kb fragment by subcloning and deletion mapping experiments. The gene contained an open reading frame (ORF) of 1698 nucleotides that encoded a protein of 566 amino acids with a deduced Mr of 59713 Da. Dot-blot analysis revealed that the copy number of the transcript in S. lividans transformed with the amy gene was 2.8-fold higher than in the donor S. griseus strain in good agreement with the proportionally higher secretion of amylase in S. lividans. A transcription initiation site was found approximately 64 bp upstream from the ATG translation start codon. The promoter of the amy gene was subcloned on a 290 bp HindIII--EcoRI fragment. Expression of a neomycin resistance gene from the amy promoter was negatively regulated by glucose. A 219 nucleotide fragment extending from the single BstEII site to the end of the amy gene was dispensable since active alpha-amylase was secreted after deletion of this region and coupling of a TGA translation stop codon.

Localization and characterization of a temporally regulated promoter from the Streptomyces aureofaciens 2201 plasmid pSA 2201

An RNA polymerase-binding 167 bp HinfI fragment from a low-copy Streptomyces plasmid pSA 2201 has been shown to have promoter activity in vivo using a promoter-probe vector. This promoter (A1) is probably involved in expression of the genes responsible for the production of an antibiotic compound, found to be located on this plasmid. A 2600 nucleotides (nt) long transcript starting from this promoter has been identified by Northern hybridization analysis. The transcription start point has been determined using high-resolution S1 mapping and confirmed by in vitro transcription analysis with purified S. aureofaciens 2201 RNA polymerase. The A1 promoter shows no homology in the -10 and -35 consensus sequence of the typical bacterial promoters, and expression from this promoter is temporally dependent on the phase of growth having the maximum transcription activity in the stationary phase.

Regulation of a thermostable alpha-amylase of Streptomyces thermoviolaceus CUB74: maltotriose is the smallest inducer

We have examined induction and repression by various sugars and carbon sources of the synthesis of a thermostable alpha-amylase in its natural host, S thermoviolaceus CUB74. The smallest molecule capable of inducing synthesis of the enzyme was maltotriose whereas maltose had no effect which might suggest a different control system from that found in other streptomycete amylases. Addition of mannitol to the growth medium impeded the alpha-amylase induction whereas glucose had no effect. After cloning of its gene into a new streptomycete host, S lividans TK24, the S thermoviolaceus alpha-amylase could not be induced by any of the sugars tested.

Cloning, sequencing, and regulation of expression of an extracellular esterase gene from the plant pathogen Streptomyces scabies

The gene that encodes the extracellular esterase produced by Streptomyces scabies has been cloned and sequenced. The gene was identified by hybridization to a synthetic oligonucleotide that corresponds to the amino-terminal amino acid sequence determined for the secreted form of the esterase. Nucleotide sequence analysis predicted a 345-amino-acid open reading frame, a putative ribosome-binding site, and 39 amino acids at the amino terminus of the sequence that is not found in the secreted protein. This 39-amino-acid sequence has many of the characteristics common to known signal peptides. End mapping the esterase transcript revealed a single 5' end of the mRNA located 51 nucleotides upstream from the start point for translation. Northern (RNA) hybridization analysis of the esterase message by using the cloned esterase gene as a probe indicated that the esterase mRNA is about 1,440 nucleotides in length and was detected only when the cells were grown in the presence of zinc. These results suggest that the level of esterase mRNA detected in the cells is regulated by zinc.

Isolation and characterization of a beta-lactamase-inhibitory protein from Streptomyces clavuligerus and cloning and analysis of the corresponding gene

Culture filtrates of Streptomyces clavuligerus contain a proteinaceous beta-lactamase inhibitor (BLIP) in addition to a variety of beta-lactam compounds. BLIP was first detected by its ability to inhibit Bactopenase, a penicillinase derived from Bacillus cereus, but it has also been shown to inhibit the plasmid pUC- and chromosomally mediated beta-lactamases of Escherichia coli. BLIP showed no inhibitory effect against Enterobacter cloacae beta-lactamase, and it also showed no activity against an alternative source of B. cereus penicillinase. BLIP was purified to homogeneity, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave a size estimate for BLIP of 16,900 to 18,000. The interaction between purified BLIP and the E. coli(pUC) beta-lactamase was investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and determined to be noncovalent, with an estimated 1:1 molar stoichiometry. The BLIP gene was isolated on a 13.5-kilobase fragment of S. clavuligerus chromosomal DNA which did not overlap a 40-kilobase region of DNA known to contain genes for beta-lactam antibiotic biosynthesis. The gene encoded a mature protein with a deduced amino acid sequence of 165 residues (calculated molecular weight of 17,523) and also encoded a 36-amino-acid signal sequence. No significant sequence similarity to BLIP was found by pairwise comparisons using various protein and nucleotide sequence data banks or by hybridization experiments, and no BLIP activity was detected in the culture supernatants of other Streptomyces spp.

An operon containing the genes for cholesterol oxidase and a cytochrome P-450-like protein from a Streptomyces sp

The nucleotide sequence of the promoter region of the gene for cholesterol oxidase (choA) from Streptomyces sp. strain SA-COO was determined. We found an open reading frame (choP) that is located between a potential promoter sequence and the structural gene for the ChoA protein. Deletion analysis showed that the promoter region for choP is essential for expression of the choA gene. Mappings of S1 nuclease and primer extension of transcripts generated in vivo suggested that the synthesis of mRNA starts at a site 41 bases upstream from the ATG initiation codon of the choP gene. By Northern (RNA) blot analysis of the transcripts, we found a 2.9-kilobase transcript that is identical in size to the total sequence of the choP and choA genes. These results suggest that the two genes, choP and choA, are transcribed polycistronically under the control of the promoter that is upstream from the structural gene for choP. The choP gene encodes a protein of 381 amino acids with a calculated Mr of 41,668. The nucleotide sequence of the choP gene has a high degree of similarity to the sequence of the genes for cytochrome P-450s from humans and Pseudomonas species. A region of homology with the cytochrome P-450s from various organisms was identified in the choP protein and may represent a region associated with a binding site for heme iron. Analysis of the CO difference spectrum of an extract of Streptomyces lividans cells that carry a plasmid which includes the choP gene revealed a unique peak, characteristic of cytochrome P-450, which is identical to that obtained with the parent strain.

Cloning and characterization of a gene of Streptomyces griseus that increases production of extracellular enzymes in several species of Streptomyces

A 7.2 kb Bg/II restriction fragment, which increases the production of several extracellular enzymes, including alkaline phosphatase, amylase, protease, lipase and beta-galactosidase, was cloned in Streptomyces lividans from the DNA of S. griseus ATCC 10137. This gene (named saf) showed a positive gene dosage effect on production of extracellular enzymes. When the saf gene was introduced into cells in high copy numbers it delayed the formation of pigments and spores in S. lividans and also retarded actinorhodin production in Streptomyces coelicolor. The saf gene hybridized with specific bands in the DNA of several Streptomyces strains tested. A 1 kb fragment containing the saf gene was sequenced and contains an open reading frame (ORF) of 306 nucleotides which encodes a polypeptide of Mr 10,500. This ORF is contained within a fragment of 432 bp which retained activity in Streptomyces. A fragment with promoter activity is present upstream of the saf reading frame. The predicted Saf polypeptide has a strong positive charge, and does not show a typical amino acid composition for a membrane protein, and contains a DNA-binding domain similar to those found in several regulatory proteins.

Tandem promoters, tsrp1 and tsrp2, direct transcription of the thiostrepton resistance gene (tsr) of Streptomyces azureus: transcriptional initiation from tsrp2 occurs after deletion of the -35 region

Nuclease S1 protection experiments indicated that the thiostrepton resistance gene (tsr) of Streptomyces azureus is transcribed from tandem promoters, tsrp1 and tsrp2, that initiate transcription 45 and 173 nucleotides, respectively, upstream of the presumptive translational start codon. The -10 regions of both promoters show similarity to the consensus sequence for the major class of prokaryotic promoters, but the -35 regions do not, although they show some similarity to each other. Replacement of sequences upstream of position -22 relative to the tsrp2 start site with two different DNA segments affected the levels of the tsrp2 transcript but did not alter the tsrp2 initiation site. In vitro transcription assays using RNA polymerase from Streptomyces coelicolor A3(2) also confirmed the location of tsrp2 and identified additional start sites near tsrp2 that were barely detectable with in vivo synthesised RNA. Transcripts corresponding to initiation in vitro at trsp1 could not be detected, suggesting that additional factors are required for utilisation of this promoter.

Transcription from the P1 promoters of Micromonospora echinospora in the absence of native upstream DNA sequences

We demonstrated previously that the 0.4-kilobase DNA fragment from Micromonospora echinospora contains multiple tandem promoters, P1a, P1b, P1c, and P2, which are also functional when cloned into Streptomyces lividans. We now show by in vitro transcription with Streptomyces RNA polymerase that each of these promoters is an authentic initiation site, rather than a processing site for transcripts which initiate further upstream. The DNA sequence requirements for the closely spaced promoters P1a, P1b, and P1c, which are coordinately induced during stationary phase in M. echinospora, were examined by deletional analysis in S. lividans. The P1a and P1b promoters were functional despite deletion of native sequences 5 and 17 base pairs upstream of each initiation site, respectively. Thus, P1a and P1b had greatly reduced upstream DNA sequence requirements compared with typical procaryotic promoters. In contrast, transcription from promoter P1c was significantly decreased when native sequences 34 base pairs upstream were replaced.

Cloning and Expression of a Schwanniomyces occidentalis α-Amylase Gene in Saccharomyces cerevisiae

An α-amylase gene ( AMY ) was cloned from Schwanniomyces occidentalis CCRC 21164 into Saccharomyces cerevisiae AH22 by inserting Sau 3AI-generated DNA fragments into the Bam HI site of YEp16. The 5-kilobase insert was shown to direct the synthesis of α-amylase. After subclones containing various lengths of restricted fragments were screened, a 3.4-kilobase fragment of the donor strain DNA was found to be sufficient for α-amylase synthesis. The concentration of α-amylase in culture broth produced by the S. cerevisiae transformants was about 1.5 times higher than that of the gene donor strain. The secreted α-amylase was shown to be indistinguishable from that of Schwanniomyces occidentalis on the basis of molecular weight and enzyme properties.