Enzyme functionalized microgels enable precise regulation of dissolved oxygen and anaerobe culture

Anaerobes are a major constituent of the gut microbiome and profoundly influence the overall health of humans. However, the lack of a simple, cost-effective, and scalable system that mimics the anaerobic conditions of the human gut is hindering research on the gut microbiome and the development of therapeutics. Here, we address this gap by using glucose oxidase and catalase containing gelatin microparticles (GOx-CAT-GMPs) to precisely regulate dissolved oxygen concentration [O2] via GOx-mediated consumption of oxygen. Fluorescence images generated using conjugated polymer afterglow nanoparticles showed that [O2] can be tuned from 257.9 ​± ​6.2 to 0.0 ​± ​4.0 ​μM using GOx-CAT-GMPs. Moreover, when the obligate anaerobe Bacteroides thetaiotaomicron was inoculated in media containing GOx-CAT-GMPs, bacterial growth under ambient oxygen was comparable to control conditions in an anaerobic chamber (5.4 ​× ​105 and 8.8 ​× ​105 colony forming units mL-1, respectively). Finally, incorporating GOx-CAT-GMPs into a bioreactor that permitted continuous radial diffusion of oxygen and glucose generated a gut-mimetic [O2] gradient of 132.4 ​± ​2.6 ​μM in the outer ring of the reactor to 7.9 ​± ​1.7 ​μM at the core. Collectively, these results indicate that GOx-CAT-GMPs are highly effective oxygen-regulating materials. These materials can potentially be leveraged to advance gut microbiome research and fecal microbiota transplantation, particularly in low-resource settings.

Allosteric properties of cyanobacterial cytochrome c oxidase: inhibition of the coupled enzyme by ATP and stimulation by ADP

Thorough analysis of the cta operon of Synechocystis sp. PCC6803 (grown in high-concentration salt medium to enhance the expression of respiratory proteins) showed that, apart from ctaCDE and Fb genes potentially encoding subunits I, II, III, and a small pseudo-bacteria-like subunit-IV of unknown function, a large mitochondria-like cta-Fm gene and a pronounced terminator structure are additional components of the operon. The deduced cta Fm gene product shows approximately 50% and 20% sequence identity to the Saccharomyces cerevisiae and beef heart mitochondrial COIV proteins, respectively. It also shows amino acid regions (near the N terminus, on the cytosolic side) with conspicuous sequence similarities to adenylate-binding proteins such as ATP synthase beta subunit Walker A and B consensus regions or to adenylate kinase. We suggest that, similar to the situation with beef heart mitochondria, it is the mitochondria-like subunit-IV of the cyanobacterial aa3-type cytochrome-c oxidase that confers allosteric properties to the cyanobacterial enzyme, the H+/e- ratios of cytochrome c oxidation being significantly lowered by ATP (intravesicular or intraliposomal) but enhanced by ADP. Therefore, the antagonistic action of ATP and ADP was in a way that the redox reaction proper, was always significantly less affected than the coupled proton translocation. Evolutionary and ecological implications of the unusual allosteric regulation of a prokaryotic cytochrome-c oxidase is discussed.

Promiscuity of heme groups in the cyanobacterial cytochrome-C oxidase

The cyanobacteria Nostoc sp. strain Mac, Anabaena 7937, Synechocystis 6803, and Anacystis nidulans (Synechococcus 6301) were grown and incubated in the light under three different oxygen regimes: Phase-A cells were harvested from photoautotrophically growing cultures at a cell density of 2.8-3.2 microliter packed cell mass/ml and an oxygen concentration of approx. 350 microM (corresponding to > 150% air saturation). Phase-B cells were harvested 24 hrs after 20 microM 3-(3,4-dichlorophyl)-1,1-dimethylurea had been added to the culture and gassing switched to 1% oxygen (< 10 microM). Phase-C cells originated from phase-B cells after 12 hrs of gassing the illuminated, yet non-growing cultures with air (21% oxygen or 200-220 microM in the medium). Cytoplasmic membranes were isolated and purified from each of the three cell types. Non-covalently bound hemes were extracted and identified by reversed-phase high performance liquid chromatography. Besides ubiquitous heme B only heme A was detected in phase-A membranes while phase-B and phase-C membranes contained both hemes A and O proportions of which depended on the oxygen status of the cells. CO/difference spectra, photo-action spectra of CO-inhibited oxygen uptake, and polarographic determination of oxygen-affinities clearly showed that both hemes A and O were part of a functional form of cytochrome-c oxidase which, however, exhibited a single subunit-I apoprotein as verified by immunoblotting. Also electron transport characteristics did not give evidence for a quinol or any other alternate oxidase functioning in cyanobacteria.

Transient accumulation of heme O (cytochrome o) in the cytoplasmic membrane of semi-anaerobic Anacystis nidulans. Evidence for oxygenase-catalyzed heme O/A transformation

Incubation of obligately photoautotrophic and aerobic cyanobacterium Anacystis nidulans (Synechococcus sp. PCC 6301) in the light in the presence of the photo-system II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea and equilibrated with approximately 1% (v/v) O2 in N2 (10 microM O2 in solution) led to a decrease of the heme A content of isolated cytoplasmic membranes and to the appearance of heme O. The latter was not seen in membranes from fully aerated cells (> 210 microM dissolved O2). Non-covalently bound hemes extracted from the membranes were identified by reversed phase high performance liquid chromatography. Heme A and O contents of the membranes changed in a reversible fashion solely depending on the ambient oxygen regime. Both hemes A and O combine with the same apoprotein as suggested by immunoblotting. CO/reduced-minus-reduced optical difference spectra, photoaction spectra of CO-inhibited O2 uptake by the membranes, and pyridine hemochrome spectra pointed to either heme belonging to a functional form of the terminal oxidase. The NADH:O2 oxidoreductase reaction catalyzed by membranes from both high O2 and low O2 cells was strictly dependent on the addition of catalytic amounts of cytochrome c, fully inhibited by 1.2 microM KCN, and insensitive to 5 microM 2-n-heptyl-4-hydroxyquinoline-N-oxide. O2 uptake by the membranes was effectively catalyzed by N,N,N',N'-tetramethyl-p-phenylenediamine but not 2-methylnaphthoquinol or plastoquinol-1 as artificial substrates. Therefore we conclude that the cyanobacterial respiratory oxidase, irrespective of the type of heme in its O2-reducing center, is a cytochrome c rather than a quinol oxidase.

Deletion of cytochrome c oxidase genes from the cyanobacterium Synechocystis sp. PCC6803: Evidence for alternative respiratory pathways

An oligonucleotide directed against a highly conserved region of aa3-type cytochrome c oxidases was used to clone the cox genes from the cyanobacterium Synechocystis sp. PCC6803. Several overlapping clones were obtained that contained the coxB, coxA, and coxC genes, transcribed in the same direction in that order, coding for subunits II, I, and III, respectively. The deduced protein sequences of the three subunits showed high sequence similarity with the corresponding subunits of all known aa3-type cytochrome c oxidases. A 1.94-kb HindII fragment containing most of coxA and about half of coxC was deleted and replaced by a cassette coding for kanamycin resistance. Mutant cells that were homozygous for the deleted cox locus were obtained. They were viable under photoautotrophic and photoheterotrophic conditions, but contained no cytochrome c oxidase activity. Nevertheless, these mutant cells showed almost normal respiration, defined as cyanide-inhibitable O2 uptake by whole cells in the dark. It is concluded, therefore, that aa3-type cytochrome c oxidase is not the only terminal respiratory oxidase in Synechocystis sp. PCC6803.

The gene encoding cytochrome-c oxidase subunit I from Synechocystis PCC6803

The gene (coxI or CoxA) encoding subunit I (COI) of cytochrome-c oxidase (cytochrome aa3) of Synechocystis PCC6803, Synechococcus PCC7942 (Anacystis nidulans R2) and Nostoc PCC8002 (Nostoc Mac), was identified by heterologous hybridization of chromosomal digests with a 17-bp oligodeoxyribonucleotide (probe C) derived from the coxI of Paracoccus denitrificans. A single genomic fragment was found to bind to probe C in all chromosomal digests. Due to its favorable signal-to-noise ratio, the genome of Synechocystis was chosen for the isolation and sequencing of this gene. A genomic DNA library in pUC18 was screened with probe C. The two probe C-positive plasmids, pDAUV1 and pDAUV2, contained a 1-kb overlapping region, with the conserved 17-bp sequence encoding the CuB-binding region of the COI polypeptide. These plasmids were subcloned into competent Escherichia coli DH5 alpha cells, and the nucleotide sequences were determined. The deduced amino acid (aa) sequences of Synechocystis COI and homologous proteins from a variety of prokaryotic and eukaryotic organisms showed an overall similarity of between 38.6 and 45.8%. Hydropathy plots revealed 12 potential transmembrane helices. All of the six histidines needed for the binding of heme a and the heme a3/CuB bimetallic center are present in the expected positions of the Synechocystis COI protein (533 aa, M(r) 59,390). A monospecific antibody raised against P. denitrificans COI gave an unequivocal immunological cross-reaction on Western blots of membrane preparations from Synechocystis, Anacystis and Nostoc, showing that the product of gene coxI is indeed synthesized and incorporated into cyanobacterial membranes.

Characterization of a cta/CDE operon-like genomic region encoding subunits I-III of the cytochrome c oxidase of the cyanobacterium Synechocystis PCC 6803

Strong heterologous hybridization of a synthetic oligonucleotide probe of 17 bp originally used to clone subunit I of the Paracoccus denitrificans cytochrome c oxidase (M. Raitio, T. Jalli and M. Saraste (1987) EMBO J. 6, 2825-2833) to a single band was observed on Southern blots of Anacystis nidulans R2 (Synechococcus PCC 7942), Synechocystis PCC 6803, and Nostoc Mac PCC 8002 chromosomal DNA digests. Six pooled gene banks prepared from Synechocystis PCC 6803 contained regions that hybridized to the oligonucleotide (probe C) which is specifically directed toward the putative Cu-binding site VWAHHMY of subunit I. Two of these gene banks were transformed into Escherichia coli and screened for colonies hybridizing to probe C. Several clones were recovered, and one type of plasmid was identified from each gene bank. The two (overlapping) plasmids were called pDAUV1 and pDAUV2. A restriction map of the plasmids showed that the overlapping region contained an 80 bp PvuI-KpnI fragment binding to probe C. The two clones together permitted sequencing of the entire gene for cytochrome c oxidase subunit I from Synechocystis PCC 6803. Further systematic sequencing of approximately 1000 bp upstream and downstream each of the ctaD (subunit I) gene revealed the presence of two genes encoding subunits II (ctaC gene) and III (ctaE gene) due to conspicuous similarities to homologous genes from other cytochrome c oxidase-containing organisms. Yet, no indications of genes encoding additional subunits of the oxidase were found within the region sequenced.

Identification and characterization of the ctaC (coxB) gene as part of an operon encoding subunits I, II, and III of the cytochrome c oxidase (cytochrome aa3) in the cyanobacterium Synechocystis PCC 6803

The gene (coxII = coxB = ctaC) encoding subunit II of Synechocystis PCC 6803 cytochrome c oxidase has been isolated by screening a genomic DNA library in pUC18 with a 17-bp oligonucleotide probe (probe C) derived from coxI of Paracoccus denitrificans after Southern blots with a 19-kb oligonucleotide (probe A) derived from coxII of P. denitrificans had given equivocal results. A 2.2 kb PstI-KpnI restriction fragment was subcloned into pUC 18 and the resulting plasmid pDAUV26, which contained the probe C-binding site near the downstream end was found also to contain the whole coxII gene upstream of this site. The novel plasmid pDAUV 26 was used to transform competent E. coli cells, propagated therein, and the sequence determined. The 2.2 kb insert contained the entire coding region for the coxII gene together with a GAG start codon, a TAA stop codon, and a putative Shine-Dalgarno sequence. The deduced COII polypeptide is composed of 319 aa (calculated molecular mass of 32,800) plus a N-terminal leader sequence of 20 aa. The hydropathy plot suggests two lipophilic transmembrane domains near the N-terminus connected with an extremely hydrophilic aa stretch on the cytosolic side, while an unusually long (> 50 aa) aa stretch on the periplasmic (= intrathylakoidal) side leads to a typical cyanobacterial threonine in place of the first conserved glutamate of the cytochrome c-binding region in all other COII proteins. Together with a considerably shortened and interrupted aromatic aa stretch in this region, these differences are discussed in terms of the peculiar affinity of cyanobacterial cytochrome oxidases for acidic c-type cytochromes. Other invariant features such as the strictly conserved CuA-binding aa, however, are found in correct positions.