Angela Duilio

Recombinant Protein Production in Antarctic Gram-Negative Bacteria

This review reports some results from our laboratory on the setting up of a psychrophilic expression system for the homologous/heterologous protein production in cold-adapted bacteria by using natural plasmids as cloning vectors. By screening some Antarctic bacteria for the presence of extrachromosomal elements, we identified three new plasmids, pMtBL from Pseudoalteromonas haloplanktis TAC125, and pTAUp and pTADw, from Psychrobacter sp. TA144. The latter autoreplicating elements were isolated, cloned, and fully sequenced and their molecular characterisation was carried out; however, we focused our attention on the small multicopy plasmid, pMtBL, from the Gram-negative P. haloplanktis TAC125 strain. This episome turned out to be an interesting extrachromosomal element, since it displays unique molecular features as its transcriptional inactivity. Being cryptic, the inheritance of pMtBL totally relied on the efficiency of its replication function. This function was bound to a region of about 850 bp, identified by an in vivo assay based on the possibility to efficiently mobilize plasmidic DNA from a mesophilic donor (Escherichia coli) to psychrophilic recipient by intergeneric conjugation. This information was instrumental in the construction of a shuttle vector, able to replicate either in E. coli or in several cold-adapted hosts (clone Q). Since the conversion of a cloning system into an expression vector requires the insertion of transcription and translation regulative sequences, the corresponding signals from the aspartate aminotransferase gene isolated from P. haloplanktis TAC125 were inserted, generating the pFF vector. To investigate the possibility of obtaining recombinant proteins in this cold-adapted host, we used the psychrophilic alpha-amylase from the Antarctic bacterium P. haloplanktis TAB23 (previously known as Alteromonas haloplanktis A23) as a model enzyme to be produced. Our results demonstrate that the cold-adapted enzyme was not only produced but also efficiently secreted by the recombinant PhTAC125 cells. The described expression system represents the first example of heterologous protein production based on a true cold-adapted replicon.

Promoters from a cold-adapted bacterium: definition of a consensus motif and molecular characterization of UP regulative elements

Although low-temperature tolerant micro-organisms were discovered long ago, limited information is still available on the transcription machinery in cold-adapted bacteria. This knowledge represents a necessary background for the investigation of the adaptation of gene-expression mechanisms at low temperatures. The recent development of a shuttle genetic system for the transformation of the cold-adapted Gram-negative bacterium Pseudoalteromonas haloplanktis strain TAC125 has made possible the isolation of the psychrophilic promoters described in this paper. TAC125 genomic DNA fragments were cloned in the shuttle vector and the promoter-containing recombinant clones were selected for their ability to express a promoter-less lacZ gene. The nucleotide sequence of several selected inserts and the transcription start points of the transcribed m-RNAs were determined. A promoter consensus sequence for Pseudoalteromonas haloplanktis TAC125 was proposed on the basis of a sequence comparison between the various active promoters. Furthermore, the identification and the functional characterization of two UP elements from this cold-adapted bacterium are also reported.

Expression of the Neuron-Specific FE65 Gene Marks the Development of Embryo Ganglionic Derivatives

The major transcript of the FE65 gene is a neuron-specific mRNA that encodes a nuclear protein whose aminoterminal domain strongly activates the transcription of a reporter gene when fused to a heterologous DNA-binding domain. FE65 gene expression is regulated during neuronal differentiation of the NTERA-2 cell line, and it is temporally and spatially restricted during mouse embryo development. It is first detected around day 10 of gestation in the basal plate of the neural tube, and then, at the subsequent stages of development and in the newborn animals, it is found solely in neural structures. Its expression is most abundant in the neural crest derivatives (e.g. spinal and encephalic ganglia), ganglionic structures of sense organs (ganglionic layer of the retina and olfactory epithelium), as well as the ganglionic structures of the autonomic nervous system. Thus FE65 gene expression can be considered a marker of the development of embryo ganglionic derivatives.

Secretion of alpha-amylase from Pseudoalteromonas haloplanktis TAB23: two different pathways in different hosts.

Secretion of cold-adapted alpha-amylase from Pseudoalteromonas haloplanktis TAB23 was studied in three Antarctic bacteria. We demonstrated that the enzyme is specifically secreted in the psychrophilic hosts even in the absence of a protein domain that has been previously reported to be necessary for alpha-amylase secretion in Escherichia coli. The occurrence of two different secretion pathways in different hosts is proposed.

PRUNE is crucial for normal brain development and mutated in microcephaly with neurodevelopmental impairment

Zollo et al. report that mutations in PRUNE1, a phosphoesterase superfamily molecule, underlie primary microcephaly and profound global developmental delay in four unrelated families from Oman, India, Iran and Italy. The study highlights a potential role for prune during microtubule polymerization, suggesting that prune syndrome may be a tubulinopathy.

Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125

The capability of microorganisms to utilize different carbohydrates as energy source reflects the availability of these substrates in their habitat. Investigation of the proteins involved in carbohydrate usage, in parallel with analysis of their expression, is then likely to provide information on the interaction between microorganisms and their ecosystem. We analysed the growth behaviour of the marine Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in the presence and in the absence of different carbon source. A marked increase in the optical density was detected when l-malate was added to the growth medium. Bacterial proteins differently expressed in the presence of l-malate were identified by proteomic profiling experiments. On the basis of their relative increase, six proteins were selected for further analyses. Among these, the expression of a putative outer membrane porin was demonstrated to be heavily induced by l-malate. The presence of a functionally active two-component regulatory system very likely controlled by l-malate was found in the upstream region of the porin gene. A non functional genomic porin mutant was then constructed showing a direct involvement of the protein in the uptake of l-malate. To the best of our knowledge, the occurrence of such a regulatory system has never been reported in Pseudoalteromonads so far and might constitute a key step in the development of an effective inducible cold expression system.

Preferential DNA damage prevention by the E. coli AidB gene: A new mechanism for the protection of specific genes.

aidB is one of the four genes of E. coli that is induced by alkylating agents and regulated by Ada protein. Three genes (ada, alkA, and alkB) encode DNA repair proteins that remove or repair alkylated bases. However, the role of AidB remains unclear despite extensive efforts to determine its function in cells exposed to alkylating agents. The E. coli AidB protein was identified as a component of the protein complex that assembles at strong promoters. We demonstrate that AidB protein preferentially binds to UP elements, AT rich transcription enhancer sequences found upstream of many highly expressed genes, several DNA repair genes, and housekeeping genes. AidB allows efficient transcription from promoters containing an UP element upon exposure to a DNA methylating agent and protects downstream genes from DNA damage. The DNA binding domain is required to target AidB to specific genes preferentially protecting them from alkylation damage. However, deletion of AidBs DNA binding domain does not prevent its antimutagenic activity, instead this deletion appears to allow AidB to function as a cytoplasmic alkylation resistance protein. Our studies identify the role of AidB in alkylating agent exposed cells and suggest a new cellular strategy in which a subset of the genome is preferentially protected from damage by alkylating agents.

Regulated Recombinant Protein Production in the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125

This review reports results from our laboratory on the development of an effective inducible expression system for the homologous/heterologous protein production in cold-adapted bacteria. Recently, we isolated and characterized a regulative genomic region from Pseudoalteromonas haloplanktis TAC125; in particular, a two-component regulatory system was identified. It is involved in the transcriptional regulation of the gene coding for an outer membrane porin (PSHAb0363) that is strongly induced by the presence of L: -malate in the growth medium.We used the regulative region comprising the two-component system located upstream the PSHAb0363 gene to construct an inducible expression vector - named pUCRP - under the control of L: -malate. Performances of the inducible system were tested using the psychrophilic β-galactosidase from P. haloplanktis TAE79 as model enzyme to be produced. Our results demonstrate that the recombinant cold-adapted enzyme is produced in P. haloplanktis TAC125 in good yields and in a completely soluble and catalytically competent form. Moreover, an evaluation of optimal induction conditions for protein production was also carried out in two consecutive steps: (1) definition of the optimal cellular growth phase in which the gene expression has to be induced; (2) definition of the optimal inducer concentration that has to be added in the growth medium.

The Ribosomal Protein L2 Interacts with the RNA Polymerase α Subunit and Acts as a Transcription Modulator in Escherichia coli

Identification of interacting proteins in stable complexes is essential to understand the mechanisms that regulate cellular processes at the molecular level. Transcription initiation in prokaryotes requires coordinated protein-protein and protein-DNA interactions that often involve one or more transcription factors in addition to RNA polymerase (RNAP) subunits. The RNAP alpha subunit (RNAPalpha) is a key regulatory element in gene transcription and functions through direct interaction with other proteins to control all stages of this process. A clear description of the RNAPalpha protein partners should greatly increase our understanding of transcription modulation. A functional proteomics approach was employed to investigate protein components that specifically interact with RNAPalpha. A tagged form of Escherichia coli RNAPalpha was used as bait to determine the molecular partners of this subunit in a whole-cell extract. Among other interacting proteins, 50S ribosomal protein L2 (RPL2) was clearly identified by mass spectrometry. The direct interaction between RNAPalpha and RPL2 was confirmed both in vivo and in vitro by performing coimmunoprecipitation and bacterial two-hybrid experiments. The functional role of this interaction was also investigated in the presence of a ribosomal promoter by using a beta-galactosidase gene reporter assay. The results clearly demonstrated that RPL2 was able to increase beta-galactosidase expression only in the presence of a specific ribosomal promoter, whereas it was inactive when it was assayed with an unrelated promoter. Interestingly, other ribosomal proteins (L1, L3, L20, and L27) did not have any effect on rRNA expression. The findings reported here strongly suggest that in addition to its role in ribosome assembly the highly conserved RPL2 protein plays a specific and direct role in regulation of transcription.

The thiol-disulfide oxidoreductase system in the cold-adapted bacterium Pseudoalteromonas haloplanktis TAC 125: discovery of a novel disulfide oxidoreductase enzyme.

In prokaryotes, protein disulfide bond oxidation, reduction and isomerization are catalyzed by members of the thioredoxin superfamily, characterized by the conserved C–X–X–C motif in their active site. Thioredoxins and glutaredoxins contribute to the reducing power in the cytoplasm, while the Dsb system catalyzes disulfide bonds formation in the periplasmic space.This paper addresses the question of disulfide bonds formation in a cold-adapted micro-organism, Pseudoalteromonashaloplanktis TAC 125 (PhTAC125) by characterizing the DsbA system. We found distinctive features respect mesophilic counterparts that highlighted for the first time the occurrence of two adjacent chromosomal DsbA genes organised in a functional operon. The sophisticated transcriptional regulation mechanism that controls the expression of these two genes was also defined. The two DsbA proteins, named PhDsbA and PhDsbA2, respectively, were expressed in Escherichia coli and characterized.Results reported in this paper provide some insights into disulfide bonds formation in a micro organism isolated in the Antarctic sea water.