Isolation and characterization of a putative transcription factor involved in the regulation of the Rhodobacter sphaeroides pucBA operon

Multidimensional optimization for accelerating light-powered biocatalysis in Rhodopseudomonas palustris

BACKGROUND

Whole-cell biocatalysis has been exploited to convert a variety of substrates into high-value bulk or chiral fine chemicals. However, the traditional whole-cell biocatalysis typically utilizes the heterotrophic microbes as the biocatalyst, which requires carbohydrates to power the cofactor (ATP, NAD (P)H) regeneration.

RESULTS

In this study, we sought to harness purple non-sulfur photosynthetic bacterium (PNSB) as the biocatalyst to achieve light-driven cofactor regeneration for cascade biocatalysis. We substantially improved the performance of Rhodopseudomonas palustris-based biocatalysis using a highly active and conditional expression system, blocking the side-reactions, controlling the feeding strategy, and attenuating the light shading effect. Under light-anaerobic conditions, we found that 50 mM ferulic acid could be completely converted to vanillyl alcohol using the recombinant strain with 100% efficiency, and > 99.9% conversion of 50 mM p-coumaric acid to p-hydroxybenzyl alcohol was similarly achieved. Moreover, we examined the isoprenol utilization pathway for pinene synthesis and 92% conversion of 30 mM isoprenol to pinene was obtained.

CONCLUSIONS

Taken together, these results suggested that R. palustris could be a promising host for light-powered biotransformation, which offers an efficient approach for synthesizing value-added chemicals in a green and sustainable manner.

Ecology and Biogenesis of Functional Amyloids in Pseudomonas

Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.

Cytolysin gene expression in Enterococcus faecalis is regulated in response to aerobiosis conditions

Here we investigate the expression of cylL(L)and cylL(S), the genes that encode the structural subunits of the cytolysin/haemolysin of Enterococcus faecalis, in response to aerobiosis conditions. Haemolysis assays of E. faecalis strains cultured under aerobic and anaerobic conditions revealed three different haemolytic phenotypes, one of which exhibited greater haemolysis under anaerobic conditions than under aerobic conditions, and was shown to be associated with the presence of the cyl genes. Reporter gene studies revealed that cylL(L) L(S) promoter activity was significantly greater (up to 8.6-fold) under anaerobic compared to aerobic conditions throughout batch growth, demonstrating that these genes are regulated in response to the degree of aerobiosis. Band shift assays confirmed the binding of a protein factor to the region between 202 and 37 bp upstream of the cylL(L)start codon, and a higher level of binding was observed with anaerobically derived cell-free extracts than with extracts of aerobically grown cells. This is the first report of an oxygen-regulated virulence factor in E. faecalis (that is distinct from the quorum-sensing regulatory system reported previously), and may be of in vivo relevance for the bacterium in biofilms and other environments characterised by oxygen gradients.

Molecular characterisation of the pifC gene encoding translation initiation factor 3, which is required for normal photosynthetic complex formation in Rhodobacter sphaeroides NCIB 8253

In order to determine whether translation initiation events play a selective role in regulating the expression of photosynthetic complexes in the photosynthetic bacterium Rhodobacter sphaeroides, we have undertaken an initial study to investigate the potential role of translation initiation factor IF3, which also behaves as a pleiotropic regulatory factor in some bacteria. Following the isolation and purification of a 24-kDa IF3-like protein (PifC) from R. sphaeroides, we used nested PCR to clone and characterise the encoding gene, pifC (photosynthesis-affecting initiation factor). The 545-bp pifC encodes a protein exhibiting 60% identity (78.6% similarity) with the Escherichia coli IF3 (InfC) protein and, in common with all other IF3 genes identified to date, pifC possesses a rare initiation codon (AUA). Furthermore, in common with IF3, PifC was shown here to perform a discriminatory function towards CUG start codons, confirming its role and function as an IF3 in R. sphaeroides. Insertion of a kanamycin resistance cassette into the 5' end of pifC resulted in a viable phenotype which exhibits growth rates similar to wild type but which possesses reduced bacteriochlorophyll and photosynthetic complexes in semi-aerobic cultures. It is shown here that the mutant is still able to produce a PifC protein but that it possesses reduced IF3 activity. This may account for the viable nature of the mutant strain, and may indicate that the effect of the mutation on photosynthesis can be more severe than shown in the present study. The mechanisms by which PifC may exert its selective regulatory effect on photosynthesis expression are discussed.

appA, a novel gene encoding a trans-acting factor involved in the regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1

A new gene, the product of which is involved in the regulation of photosynthesis gene expression in the anoxygenic photosynthetic bacterium Rhodobacter sphaeroides 2.4.1, has been identified. The isolation of this gene, designated appA (activation of photopigment and puc expression), was based on its ability, when provided in extra copies, to partially suppress mutations in the two-component PrrB-PrrA regulatory system. The presence of extra copies of the appA gene in either prrB, prrA, or wild-type strains resulted in an activation of puc::lacZ expression under aerobic conditions. Constructed AppA null mutants did not grow photosynthetically and were impaired in the synthesis of both bacteriochlorophyll and carotenoids, as well as the structural proteins of the photosynthetic spectral complexes. When grown anaerobically in the dark, these mutants accumulated bacteriochlorophyll precursors. The expression of lacZ fusions to several photosynthesis genes and operons, including puc, puf, and bchF, was decreased in the AppA mutant strains in comparison with the wild type. To examine the role of AppA involvement in bacteriochlorophyll biosynthesis, we inactivated an early gene, bchE, of the bacteriochlorophyll pathway in both wild-type and AppA- mutant backgrounds. The double mutant, AppA- BchE-, was found to be severely impaired in photosynthesis gene expression, similar to the AppA- BchE+ mutant and in contrast to the AppA+ BchE- mutant. This result indicated that AppA is more likely involved in the regulation of expression of the bch genes than in the biosynthetic pathway per se. The appA gene was sequenced and appears to encode a protein of 450 amino acids with no obvious homology to known proteins.

Early steps in carotenoid biosynthesis: sequences and transcriptional analysis of the crtI and crtB genes of Rhodobacter sphaeroides and overexpression and reactivation of crtI in Escherichia coli and R. sphaeroides

In the purple photosynthetic bacterium Rhodobacter sphaeroides, the desaturation of phytoene has already been implicated in the assembly of the light-harvesting 2 complex (H.P. Lang and C.N. Hunter, Biochem. J. 298:197-205, 1994). The phytoene synthase and desaturase enzymes mediate the first steps specific for carotenoid biosynthesis up to and including the synthesis of the colored carotenoid neurosporene. In this report, we present the DNA and deduced amino acid sequences of the genes encoding these proteins, namely, crtB and crtI, from R. sphaeroides and present evidence for the existence of a crtIB operon. Both genes have been shown to possess putative puc and puf operon-like promoter sequences, and oxygen regulation and the point of initiation of the crtI transcript have been demonstrated. The complete crtI gene has been overexpressed in Escherichia coli and R. sphaeroides and shown to catalyze three desaturations of phytoene to give neurosporene. This activity was shown to be ATP dependent, and the cofactor requirement was investigated by using a spectroscopic assay for in vitro carotenogenic activity. Although the crtI and crtB genes have been sequenced from a number of different organisms, the transcriptional organization and regulation of these genes have not been analyzed in detail. In this report, we have located the transcription initiation point and have shown that R. sphaeroides possesses an oxygen-regulated CrtI-type phytoene desaturase gene that forms a transcriptional operon with crtB.

Introduction of new carotenoids into the bacterial photosynthetic apparatus by combining the carotenoid biosynthetic pathways of Erwinia herbicola and Rhodobacter sphaeroides

Carotenoids have two major functions in bacterial photosynthesis, photoprotection and accessory light harvesting. The genes encoding many carotenoid biosynthetic pathways have now been mapped and cloned in several different species, and the availability of cloned genes which encode the biosynthesis of carotenoids not found in the photosynthetic genus Rhodobacter opens up the possibility of introducing a wider range of foreign carotenoids into the bacterial photosynthetic apparatus than would normally be available by producing mutants of the native biosynthetic pathway. For example, the crt genes from Erwinia herbicola, a gram-negative nonphotosynthetic bacterium which produces carotenoids in the sequence of phytoene, lycopene, beta-carotene, beta-cryptoxanthin, zeaxanthin, and zeaxanthin glucosides, are clustered within a 12.8-kb region and have been mapped and partially sequenced. In this paper, part of the E. herbicola crt cluster has been excised and expressed in various crt strains of Rhodobacter sphaeroides. This has produced light-harvesting complexes with a novel carotenoid composition, in which the foreign carotenoids such as beta-carotene function successfully in light harvesting. The outcome of the combination of the crt genes in R. sphaeroides with those from E. herbicola has, in some cases, resulted in an interesting rerouting of the expected biosynthetic sequence, which has also provided insights into how the various enzymes of the carotenoid biosynthetic pathway might interact. Clearly this approach has considerable potential for studies on the control and organization of carotenoid biosynthesis, as well as providing novel pigment-protein complexes for functional studies.

Cloning and nucleotide sequence of regA, a putative response regulator gene of Rhodobacter sphaeroides

A 0.9 kb DNA fragment carrying the Rhodobacter capsulatus regA gene, which encodes an oxygen-dependent, positively-acting response regulator of photosynthetic gene expression, was used as a probe in Southern hybridisation experiments to determine whether a similar gene occurs in R. sphaeroides. A strongly hybridising DNA fragment isolated from a R. sphaeroides plasmid gene bank was isolated, sequenced and found to contain an open reading frame which exhibits 75% identity with the R. capsulatus regA gene. The deduced amino acid sequence of 184 residues shows 81% identity and 89% similarity with the R. capsulatus RegA protein, and significant similarities with other response regulators of the two component sensor-regulator type. Introduction of the R. sphaeroides gene into a R. capsulatus regA mutant, which exhibits abnormally low levels of membrane-bound photosynthetic complexes, resulted in a 22-33-fold increase in these complexes to approximately 62-65% of wild-type levels. This is the first study to identify a putative response regulator in R. sphaeroides and to complement a regulatory mutation in R. capsulatus with a gene from another species. Further studies of associated genes may identify the different mechanisms by which the regulation of photosynthesis complex formation occurs in response to environmental stimuli in R. sphaeroides and R. capsulatus.

A putative transcription factor binding to the upstream region of the puf operon in Rhodobacter sphaeroides

Gel shift assays of the upstream region of the puf operon in Rhodobacter sphaeroides were performed using cell-free extracts from cells grown under various culture conditions. The results suggested that a protein binding to the upstream region functioned as a repressor-like substance of the expression of the operon by oxygen tension or light. The density of the shifted band of cell-free extracts from cells irradiated with blue light under semi-aerobic conditions was higher than that with red light. Phosphatase treatment of the cell-free extracts strongly increased the DNA-binding affinity of the protein.

Control of photosystem genes in Rhodobacter capsulatus

Two environmental factors, oxygen and high light intensity, are known to repress synthesis of the Rhodobacter capsulatus photosystem. One level of regulation is the control of light harvesting and reaction centre gene expression at the point of transcription initiation. This has recently been shown to involve transcriptional activators which exhibit sequence similarity to members of the 'two-component' class of prokaryotic regulators. An additional level of regulation involves the formation of 'superoperons' that transcriptionally link pigment biosynthesis operons with operons that code for the light harvesting and reaction centre structural genes. A final level of regulation involves the selective degradation of reaction centre mRNA transcripts which influence the stoichiometric synthesis of the light harvesting and reaction centre complexes.