Expression of a cloned beta-glucanase gene from Bacillus amyloliquefaciens in an Escherichia coli relA strain after plasmid amplification

Synaptic and circuit development of the primary sensory cortex

Animals, including humans, optimize their primary sensory cortex through the use of input signals, which allow them to adapt to the external environment and survive. The time window at the beginning of life in which external input signals are connected sensitively and strongly to neural circuit optimization is called the critical period. The critical period has attracted the attention of many neuroscientists due to the rapid activity-/experience-dependent circuit development that occurs, which is clearly differentiated from other developmental time periods and brain areas. This process involves various types of GABAergic inhibitory neurons, the extracellular matrix, neuromodulators, transcription factors, and neurodevelopmental factors. In this review, I discuss recent progress regarding the biological nature of the critical period that contribute to a better understanding of brain development.

Characterization and upregulation of bifunctional phosphoglucomutase/phosphomannomutase enzyme in an exobiopolymer overproducing strain of Acinetobacter haemolyticus

Several members of the Acinetobacter spp. produce exobiopolymer (EBP) of considerable biotechnological interest. In a previous study, we reported phosphate removal capacity of EBP produced by Acinetobacter haemolyticus. Insertional mutagenesis was attempted to develop EBP-overproducing strains of A. haemolyticus and mutant MG606 was isolated. In order to understand the underlying mechanism of overproduction, the EBP overproducing mutant MG606 was analyzed and compared with the wild type counterpart for its key EBP synthetic enzymes. The EBP produced by MG606 mutant was 650 mg/L compared to 220 mg/L in its wild type counterpart. Significantly high (p<0.05) levels of phosphoglucomutase/phosphomannomutase (PGM/PMM) in MG606 mutant was noted, whereas activities of other enzymes responsible for EBP synthesis showed no significant change (p>0.05). The up-regulation of PGM/PMM expression in mutant was further confirmed by real time reverse transcriptase (RT)-PCR of PGM/PMM transcripts. The optimal conditions for PGM/PMM activity were found to be 35 °C and pH 7.5; PGM/PMM activity was inhibited by ions such as lithium, zinc, nickel. Further, incubation of cells with a PGM inhibitor (lithium) resulted in a concentration-dependent decrease in EBP production further confirming the role of PGM/PMM overexpression in enhanced EBP production by the mutant. Overall the results of our study indicate a key role of PGM/PMM in enhanced EBP production, as evident from enhanced enzyme activity, increased PGM/PMM transcripts and reduction in EBP synthesis by a PGM inhibitor. We envisage a potential exploitation of the insights so obtained to effectively engineer strains of Acinetobacter for overproducing phosphate binding EBP.

Why is transcription coupled to translation in bacteria?

Active mechanisms exist to prevent transcription that is uncoupled from translation in the protein-coding genes of bacteria, as exemplified by the phenomenon of nonsense polarity. Bacterial transcription-translation coupling may be viewed as one among several co-transcriptional processes, including those for mRNA processing and export in the eukaryotes, that operate in the various life forms to render the nascent transcript unavailable for formation of otherwise deleterious R-loops in the genome.

Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering

1,3-1,4-beta-Glucanases (or lichenases, EC 3.2.1.73) hydrolyse linear beta-glucans containing beta-1,3 and beta-1,4 linkages such as cereal beta-glucans and lichenan, with a strict cleavage specificity for beta-1,4 glycosidic bonds on 3-O-substituted glucosyl residues. The bacterial enzymes are retaining glycosyl hydrolases of family 16 with a jellyroll beta-sandwich fold and a substrate binding cleft composed of six subsites. The present paper reviews the structure-function aspects of the enzymatic action including mechanistic enzymology, protein engineering and X-ray crystallographic studies.

Replication of plasmids during bacterial response to amino acid starvation

Amino acid starvation of bacterial cells leads to expression of the stringent (in wild-type strains) or relaxed (in relA mutants) response (also called the stringent or relaxed control, respectively). The stringent control is a pleiotropic response which changes drastically almost the entire cell physiology. Although starvation is a rule rather than an exception in natural environments of bacteria, and DNA replication is a fundamental cell process, until recently our knowledge about regulation of DNA replication in amino acid-starved cells has been unexpectedly poor. Within recent years the stringent control of DNA replication has been investigated mainly on plasmid models. Several plasmid replicons have been studied, including oriC plasmids, ColE1-like replicons, pSC101, F, R1, RK2, and R6K, and plasmids derived from bacteriophages lambda and P1. However, molecular models of replication regulation in amino acid-starved cells have been proposed to date only for lambda plasmids and ColE1-like replicons. Although further extensive studies are necessary in the understanding of molecular mechanisms of the stringent and relaxed control of replication of other plasmids, the results obtained to date (summarized and discussed in this review) show that studies on DNA replication in amino acid-starved cells may provide new insights into the regulatory mechanisms and lead to more general conclusions.

Replication of plasmids derived from P1, F, R1, R6K and RK2 replicons in amino acid-starved Escherichia coli stringent and relaxed strains

Replication of mini-plasmids derived from bacteriophage P1 and naturally existing plasmids F, R1, R6K and RK2 in otherwise isogenic relA+ and relA- Escherichia coli strains during amino acid starvation and limitation was investigated. Since it was previously demonstrated that inhibition of DNA synthesis or amplification of plasmid DNA may depend on the nature of deprived amino acid, we starved bacteria for five different amino acids. We found differential replication of all these plasmids but RK2 (which did not replicate at all in amino acid-starved bacteria) during the stringent and relaxed response. While in almost all cases plasmid DNA replication was inhibited during the stringent response irrespective of the nature of deprived amino acid, wild-type or copy-up mini-P1, mini-F and mini-R1 plasmids replicated in relA- bacteria depending on the kind of starvation. R6K-derived plasmids harbouring ori beta and gamma (but not those containing ori alpha, beta and gamma or only ori gamma) were able to replicate in relA- bacteria starved for all tested amino acids. Possible explanations for the mechanisms of regulation of replication of plasmids derived from P1, F, R1, R6K and RK2 during amino acid starvation are discussed. Our results also indicate that, like in the case of some other replicons, appropriate amino acid starvation or limitation may be used as a method for efficient amplification of plasmids derived from P1, F, R1 and R6K.

Differential amplification efficiency of pMB1 and p15A (ColE1-type) replicons in Escherichia coli stringent and relaxed strains starved for particular amino acids

It was demonstrated previously that ColE1-type plasmids, the most commonly used vectors in molecular cloning, can be amplified in amino acid-starved relA mutants of Escherichia coli. Subsequent studies demonstrated that replication of at least some plasmids during amino acid starvation depends not only on the host relA allele but also on temperature and on the nature of deprived amino acid. Therefore, we investigated efficiency of amplification of two types of ColE1 plasmids (pMB1- and p15A-derived replicons) in E. coli relA+ and relA- hosts starved for different amino acids at 30 degrees C, 37 degrees C and 43 degrees C. We found differential amplification efficiency of plasmids pBR328 (pMB1-derived replicon) and pACYC184 (p15A-derived replicon) in the relA mutant during starvation for particular amino acids. Although amplification of pBR328 was negligible in the relA+ host, significant increase in pACYC184 content was observed in this strain starved for some (but not all) amino acids. The amplification efficiency of pBR328 and pACYC184 was found to be dependent on temperature. These results indicate that for maximal amplification of particular plasmid appropriate amino acid starvation and optimal temperature should be chosen. Our findings are in agreement with recently proposed model of the regulation of ColE1-type plasmid replication in amino acid-starved E. coli cells.

Amplification of lambda plasmids in Escherichia coli relA mutants

It was previously demonstrated that, contrary to wild-type stringent (rel+) strains of Escherichia coli, in amino acid-starved relaxed (relA) mutants the replication of lambda plasmid proceeds for several hours. The replication leads to amplification of lambda plasmid DNA. Here, the conditions for this amplification have been optimized. The amplification efficiency depends on the temperature as well as on the nature of amino acid starvation, but it is only little or totally not dependent on the pH value of the medium in a range from 6.0 to 8.0. It seems that the most efficient amplification can be achieved by overnight cultivation of E. coli relA arg strain harbouring lambda plasmid at 36-39 degrees C in minimal medium containing Casamino acids. Under these conditions, the copy number of lambda plasmid increases from about 40 to about 300 per cell giving greater than 7-fold amplification.

Effect of increased ppGpp concentration on DNA replication of different replicons in Escherichia coli

The plasmids harbouring the relA gene under an inducible promoter allowed us to increase the guanosine 5'-diphosphate-3'-diphosphate (ppGpp) concentration in Escherichia coli cells without any starvation and thus, to directly investigate the effect of ppGpp on DNA replication. We studied all types of replicons which were investigated previously in amino acid-starved bacteria and found that ColE1, oriC, lambda plasmid and pSC101 but not RK2 replicons are sensitive to high ppGpp level. To our knowledge, this paper presents the first direct evidence that replication of most, but not all, replicons is dependent on ppGpp concentration and thus, is under stringent control.

Cloning and DNA sequencing of bgaA, a gene encoding an endo-beta-1,3-1,4-glucanase, from an alkalophilic Bacillus strain (N137)

The gene bgaA encoding an alkaline endo-beta-1,3-1,4-glucanase (lichenase) from an alkalophilic Bacillus sp. strain N137, isolated in our laboratory, was cloned and expressed from its own promoter in Escherichia coli. The nucleotide sequence of a 1,416-bp DNA fragment containing bgaA was determined and revealed an open reading frame of 828 nucleotides. The deduced protein sequence consists of 276 amino acids and has a 31-amino-acid putative signal peptide which is functional in E. coli, in which the BgaA protein is located mainly in the periplasmic space. The lichenase activity of BgaA is stable between pH 6 and 12, it shows optimal activity at a temperature between 60 and 70 degrees C, and it retains 65% of its activity after incubation at 70 degrees C for 1 h. This protein is similar to some other lichenases from Bacillus species such as B. amyloliquefaciens, B. brevis, B. licheniformis, B. macerans, B. polymyxa, and B. subtilis. However, it has a lysine-rich region at the carboxy terminus which is not found in any other published lichenase sequence and might be implicated in the unusual biochemical properties of this enzyme. The location of the mRNA 5' end was determined by primer extension and corresponds to nucleotide 235. A typical Bacillus sigma A promoter precedes the transcription start site.

Cloning and characterization of heat-inducible promoters of Bacillus subtilis

Heat-inducible DNA fragments of Bacillus subtilis were cloned with two different promoter probe vectors. The increased synthesis of the reporter enzymes seemed to be due to a transient increase in the transcription of the encoding genes. The structure of the heat-sensitive promoters resembles the consensus sequence of promoters recognized by the vegetative form of RNA polymerase of B. subtilis. Our results support data in literature that the heat shock response of B. subtilis is regulated by a different mechanism than in Escherichia coli, where alternative sigma factors direct the transcription of heat shock genes.

Molecular cloning, expression and nucleotide sequence of the endo-beta-1,3-1,4-D-glucanase gene from Bacillus licheniformis. Predictive structural analyses of the encoded polypeptide

A Bacillus licheniformis gene coding for an endo-beta-1,3-1,4-D-glucanase have been cloned in Escherichia coli and sequenced. The open reading frame contains a sequence of 731 bp, encoding a polypeptide of 243 amino acid residues, with a molecular mass of 27404 Da (24418 Da without the putative signal peptide), which corresponds to the enzyme we had previously isolated and characterized. The signal peptide is functional in E. coli. More than 60% of the endo-beta-1,3-1,4-D-glucanase activity is extracellular or periplasmic. The polypeptide is highly similar to other reported Bacillus beta-glucanases. Several structural predictive analyses (secondary structure, hydropathic plots, similarity with other related enzymes, etc.) have been performed. From these analyses we assign a tentative three-functional-domain structure for the enzyme (signal peptide, substrate binding and catalytic domains) and a putative lysozyme-like active site.

RelA mutation and pBR322 plasmid amplification in amino acid-starved cells of Escherichia coli

Plasmid pBR322 is amplified following amino-acid limitation in Escherichia coli relA hosts. In relA+ hosts there was no significant amplification or a much smaller one. Plasmid amplification is due to the relA mutation; when the relA+ allele is transferred into the relA mutant CP79 this strain no longer amplifies plasmid DNA during amino acid starvation. It is concluded that ppGpp is a negative effector of plasmid replication. Amplification is temperature dependent, being maximal at 32 degrees C and negligible at 37 degrees C.