Tetrapyrrole biosynthesis in Rhodobacter capsulatus is transcriptionally regulated by the heme-binding regulatory protein, HbrL

Bioproduction of porphyrins, phycobilins, and their proteins using microbial cell factories: engineering, metabolic regulations, challenges, and perspectives

Porphyrins, phycobilins, and their proteins have abundant π-electrons and strongly absorb visible light, some of which bind a metal ion in the center. Because of the structural and optical properties, they not only play critical roles as an essential component in natural systems but also have attracted much attention as a high value specialty chemical in various fields, including renewable energy, cosmetics, medicines, and foods. However, their commercial application seems to be still limited because the market price of porphyrins and phycobilins is generally expensive to apply them easily. Furthermore, their petroleum-based chemical synthesis is energy-intensive and emits a pollutant. Recently, to replace petroleum-based production, many studies on the bioproduction of metalloporphyrins, including Zn-porphyrin, Co-porphyrin, and heme, porphyrin derivatives including chlorophyll, biliverdin, and phycobilins, and their proteins including hemoproteins, phycobiliproteins, and phytochromes from renewable carbon sources using microbial cell factories have been reported. This review outlines recent advances in the bioproduction of porphyrins, phycobilins, and their proteins using microbial cell factories developed by various microbial biotechnology techniques, provides well-organized information on metabolic regulations of the porphyrin metabolism, and then critically discusses challenges and future perspectives. Through these, it is expected to be able to achieve possible solutions and insights and to develop an outstanding platform to be applied to the industry in future research.

Porphyrin Excretion Resulting From Mutation of a Gene Encoding a Class I Fructose 1,6-Bisphosphate Aldolase in Rhodobacter capsulatus

This paper describes a mutant (called SB1707) of the Rhodobacter capsulatus wild type strain SB1003 in which a transposon-disrupted rcc01707 gene resulted in a ∼25-fold increase in the accumulation of coproporphyrin III in the medium of phototrophic (anaerobic) cultures grown in a yeast extract/peptone medium. There was little or no stimulation of pigment accumulation in aerobic cultures. Therefore, this effect of rcc01707 mutation appears to be specific for the anaerobic coproporphyrinogen III oxidase HemN as opposed to the aerobic enzyme HemF. The protein encoded by rcc01707 is homologous to Class I fructose 1,6-bisphosphate aldolases, which catalyze a glycolytic reaction that converts fructose 1, 6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, precursors of pyruvate. There were significant differences in coproporphyrin III accumulation using defined media with individual organic acids and sugars as the sole carbon source: pyruvate, succinate and glutamate stimulated accumulation the most, whereas glucose suppressed coproporphyrin III accumulation to 10% of that of succinate. However, although quantitatively lesser, similar effects of carbon source on the amount of accumulated pigment in the culture medium were seen in a wild type control. Therefore, this mutation appears to exaggerate effects also seen in the wild type strain. It is possible that mutation of rcc01707 causes a metabolic bottleneck or imbalance that was not rectified during growth on the several carbon sources tested. However, we speculate that, analogous to other fructose 1,6-bisphosphate aldolases, the rcc01707 gene product has a “moonlighting” activity that in this case is needed for the maximal expression of the hemN gene. Indeed, it was found that the rcc01707 gene is needed for maximal expression of a hemN promoter-lacZ reporter. With the decrease in hemN expression due to the absence of the rcc01707 gene product, coproporphyrinogen III accumulates and is released from the cell, yielding the spontaneous oxidation product coproporphyrin III.

Biochemical characterization of protoporphyrinogen dehydrogenase and protoporphyrin ferrochelatase of Vibrio vulnificus and the critical complex formation between these enzymes

BACKGROUND

Protoporphyrin IX (PPn), an intermediate in the heme biosynthesis reaction, generates singlet oxygen upon exposure to UV light. It has been proposed that PPn is channeled directly to ferrochelatase within a protoporphyrinogen dehydrogenase (PgdH1)-protoporphyrin ferrochelatase (PpfC) complex as a way to avoid this damaging side reaction. However, the PgdH1-PpfC complex has not been characterized, and the question of how heme affects the activities of PgdH1 has not been addressed.

METHODS

Protein interactions were explored through pull-down assays and western blotting, and the importance of this complex in vivo was examined using inter-species combinations of the two proteins. The purified PgdH1-PpfC complex was characterized kinetically and used for heme binding studies.

RESULTS

In Vibrio vulnificus, PgdH1 and PpfC formed an 8:8 heterohexadecameric complex that was important for maintaining PPn at low levels. PpfC catalyzed PPn efficiently whether or not it was part of the complex. Notably, heme was a noncompetitive inhibitor of V. vulnificus PgdH1, but a competitive inhibitor of the human protoporphyrinogen oxidase PgoX.

CONCLUSION

The PdgH1-PpfC complex is important for protective channeling of PPn and for efficient catalysis of free PPn. The production of PPn by PgdH1 is regulated by feedback inhibition by heme.

GENERAL SIGNIFICANCE

Both proteobacteria and eukaryotes have evolved mechanisms to prevent the harmful accumulation of the heme biosynthesis intermediate PPn. The data presented here suggest two previously unknown mechanisms: the channeling of PPn through the PgdH1-PpfC complex, and the direct inhibition of PgdH1 activity (PgoX activity as well) by heme.

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.

Quantification of labile heme in live malaria parasites using a genetically encoded biosensor

Malaria parasites degrade substantial quantities of hemoglobin to release heme within a specialized digestive vacuole. Most of this heme is sequestered in an inert crystal. However, the concentration of bioavailable, labile heme in the parasite’s cytosol was unknown. We developed a biosensor to provide the first quantitative insights into labile heme concentrations in malaria parasites. We find that ∼1.6 µM labile cytosolic heme is maintained, including during a period coincident with intense hemoglobin degradation. The heme-binding antimalarial drug, chloroquine, which interferes with heme crystallization, specifically induces an increase in labile heme. The ability to quantify labile heme in malaria parasites opens opportunities for better understanding heme homeostasis, signaling, and metabolism, and its association with antimalarial potency.

Heme is ubiquitous, yet relatively little is known about the maintenance of labile pools of this cofactor, which likely ensures its timely bioavailability for proper cellular function. Quantitative analysis of labile heme is of fundamental importance to understanding how nature preserves access to the diverse chemistry heme enables, while minimizing cellular damage caused by its redox activity. Here, we have developed and characterized a protein-based sensor that undergoes fluorescence quenching upon heme binding. By genetically encoding this sensor in the human malarial parasite, Plasmodium falciparum, we have quantified cytosolic labile heme levels in intact, blood-stage parasites. Our findings indicate that a labile heme pool (∼1.6 µM) is stably maintained throughout parasite development within red blood cells, even during a period coincident with extensive hemoglobin degradation by the parasite. We also find that the heme-binding antimalarial drug chloroquine specifically increases labile cytosolic heme, indicative of dysregulation of this homeostatic pool that may be a relevant component of the antimalarial activity of this compound class. We propose that use of this technology under various environmental perturbations in P. falciparum can yield quantitative insights into fundamental heme biology.

A new biological function of heme as a signaling molecule

This mini-review presents a recent development of a new function of heme as a signaling molecule especially in the regulation of gene expression. Heme is biosynthesized as a prosthetic group for heme proteins, which play crucial roles for respiration, photosynthesis, and many other metabolic reactions. In some bacteria, exogenous heme molecules are used as a heme or an iron sources to be uptaken into cytoplasm. As free heme molecules are cytotoxic, the intracellular concentrations of biosynthesized or uptaken heme should be strictly controlled. In this mini-review, we summarize the biochemical and biophysical properties of the transcriptional regulators and heme-sensor proteins responsible for these regulatory systems to maintain heme homeostasis.

Role of HemF and HemN in the heme biosynthesis of Vibrio vulnificus under S-adenosylmethionine-limiting conditions

Vibrio vulnificus contains two coproporphyrinogen III oxidases (CPOs): O2-dependent HemF and O2-independent HemN. The growth of the hemF mutant HF1 was similar to wild-type cells at pH 7.5 under 2% O2 conditions where HemN was active and had a half-life of 64 min. However, HF1 did not grow when the medium pH decreased to pH 5.0, where oxidative stress affects endogenous S-adenosylmethionine (SAM) levels. The growth of HF1 was restored not only by elevating the expression of MnSOD but also through the exogenous addition of SAM. For HF1 to grow under these SAM-limiting conditions, a mutation arose in hemN, encoding HemNY74F . Refolding of the denatured enzymes in vitro revealed that the apparent binding affinity of HemNY74F for the cofactor SAM1, which coordinates the 4Fe-4S cluster, was approximately sixfold higher than that of HemN. The Km of HemNY74F for the co-substrate SAM2, which provides radicals for CPO reactions, was threefold lower than that of HemN. Thus, affinities for both SAM1 and SAM2 were higher with the Y74F mutation. Taken together, when SAM is limiting, HemN is apparently nonfunctional, and heme synthesis is continued by HemF.

The LysR-type transcription factor HbrL is a global regulator of iron homeostasis and porphyrin synthesis in Rhodobacter capsulatus

The purple bacterium Rhodobacter capsulatus is unique among Rhodobacteriacae as it contains a putative iron response regulator (Irr) but does not possess a copy of the ferric uptake regulator (Fur). Interestingly, an in-frame deletion mutant of Irr shows no major role in iron homeostasis. Instead, we showed that the previously identified activator of haem gene expression HbrL is a crucial regulator of iron homeostasis. We demonstrated that an HbrL deletion strain is unable to grow in iron-limited medium in aerobic, semi-aerobic and photosynthetic conditions and that suppressor strains can be isolated with mutations in iron uptake genes. Gene expression studies revealed that HbrL is a transcriptional activator of multiple ferrous and ferric iron uptake systems in addition to a haem uptake system. Finally, HbrL activates the expression of numerous haem biosynthesis genes. Thus, HbrL has a central role in controlling the amount of iron transport in conjunction with the synthesis of its cognate tetrapyrrole haem.

Controlling the delicate balance of tetrapyrrole biosynthesis

Tetrapyrroles are a family of compounds that contain four pyrrole rings. They are involved in many fundamental biological processes such as photoreception, electron transport, gas transport and also as cofactors for enzymatic reactions. As regulators of protein activity, tetrapyrroles mediate cellular response to light, oxygen and nutrient levels in the surrounding environment. Biosynthesis of haem tetrapyrroles shares, conserved pathways and enzymes among all three domains of life. This is contrasted by chlorophyll biosynthesis that is only present in eubacteria and chloroplasts, or cobalamin biosynthesis that is only present in eubacteria and archaea. This implicates haem as the most ancient, and chlorophyll as the most recent, of the common tetrapyrroles that are currently synthesized by existing organisms. Haem and chlorophyll are both toxic when synthesized in excess over apo-proteins that bind these tetrapyrroles. Accordingly, the synthesis of these tetrapyrroles has to be tightly regulated and coordinated with apo-protein production. The mechanism of regulating haem and chlorophyll synthesis has been studied intensively in Rhodobacter species and will be discussed.

The tetrapyrrole biosynthetic pathway and its regulation in Rhodobacter capsulatus

The purple anoxygenic photosynthetic bacterium Rhodobacter capsulatus is capable of growing in aerobic or anaerobic conditions, in the dark or using light, etc. Achieving versatile metabolic adaptations from respiration to photosynthesis requires the use of tetrapyrroles such as heme and bacteriochlorophyll, in order to carry oxygen, to transfer electrons, and to harvest light energy. A third tetrapyrrole, cobalamin (vitamin B(12)), is synthesized and used as a cofactor for many enzymes. Heme, bacteriochlorophyll, and vitamin B(12) constitute three major end products of the tetrapyrrole biosynthetic pathway in purple bacteria. Their respective synthesis involves a plethora of enzymes, several that have been characterized and several that are uncharacterized, as described in this review. To respond to changes in metabolic requirements, the pathway undergoes complex regulation to direct the flow of tetrapyrrole intermediates into a specific branch(s) at the expense of other branches of the pathway. Transcriptional regulation of the tetrapyrrole synthesizing enzymes by redox conditions and pathway intermediates is reviewed. In addition, we discuss the involvement of several transcription factors (RegA, CrtJ, FnrL, AerR, HbrL, Irr) as well as the role of riboswitches. Finally, the interdependence of the tetrapyrrole branches on each other synthesis is discussed.

A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides

The AppA protein of Rhodobacter sphaeroides is unique in its ability to sense and transmit redox signals as well as light signals. By functioning as antagonist to the PpsR transcriptional repressor, it regulates the expression of photosynthesis genes in response to these environmental stimuli. Here we show binding of the cofactor haem to a domain in the C-terminal part of AppA and redox activity of bound haem. This is supported by the findings that: (i) the C-terminal domain of AppA (AppADeltaN) binds to haemin agarose, (ii) AppADeltaN isolated from Escherichia coli shows absorbance at 411 nm and absorbances at 424 nm and 556 nm after reduction with dithionite and (iii) AppADeltaN can be reconstituted with haem in vitro. Expression of AppA variants in R. sphaeroides reveals that the haem binding domain is important for normal expression levels of photosynthesis genes and for normal light regulation in the presence of oxygen. The haem cofactor affects the interaction of the C-terminal part of AppA to PpsR but also its interaction to the N-terminal light sensing AppA-BLUF domain. Based on this we present a model for the transmission of light and redox signals by AppA.

The ChrA-ChrS and HrrA-HrrS signal transduction systems are required for activation of the hmuO promoter and repression of the hemA promoter in Corynebacterium diphtheriae

Transcription of the Corynebacterium diphtheriae hmuO gene, which encodes a heme oxygenase involved in heme iron utilization, is activated in a heme- or hemoglobin-dependent manner in part by the two-component system ChrA-ChrS. Mutation of either the chrA or the chrS gene resulted in a marked reduction of hemoglobin-dependent activation at the hmuO promoter in C. diphtheriae; however, it was observed that significant levels of hemoglobin-dependent expression were maintained in the mutants, suggesting that an additional activator is involved in regulation. A BLAST search of the C. diphtheriae genome sequence revealed a second two-component system, encoded by DIP2268 and DIP2267, that shares similarity with ChrS and ChrA, respectively; we have designated these genes hrrS (DIP2268) and hrrA (DIP2267). Analysis of hmuO promoter expression demonstrated that hemoglobin-dependent activity was fully abolished in strains from which both the chrA-chrS and the hrrA-hrrS two-component systems were deleted. Similarly, deletion of the sensor kinase genes chrS and hrrS or the genes encoding both of the response regulators chrA and hrrA also eliminated hemoglobin-dependent activation at the hmuO promoter. We also show that the regulators ChrA-ChrS and HrrA-HrrS are involved in the hemoglobin-dependent repression of the promoter upstream of hemA, which encodes a heme biosynthesis enzyme. Evidence for cross talk between the ChrA-ChrS and HrrA-HrrS systems is presented. In conclusion, these findings demonstrate that the ChrA-ChrS and HrrA-HrrS regulatory systems are critical for full hemoglobin-dependent activation at the hmuO promoter and also suggest that these two-component systems are involved in the complex mechanism of the regulation of heme homeostasis in C. diphtheriae.

The AppA and PpsR proteins from Rhodobacter sphaeroides can establish a redox-dependent signal chain but fail to transmit blue-light signals in other bacteria

The AppA protein of Rhodobacter sphaeroides has the unique ability to sense and transmit redox and light signals. In response to decreasing oxygen tension, AppA antagonizes the transcriptional regulator PpsR, which represses the expression of photosynthesis genes, including the puc operon. This mechanism, which is based on direct protein-protein interaction, is prevented by blue-light absorption of the BLUF domain located in the N-terminal part of AppA. In order to test whether AppA and PpsR are sufficient to transmit redox and light signals, we expressed these proteins in three different bacterial species and monitored oxygen- and blue-light-dependent puc expression either directly or by using a luciferase-based reporter construct. The AppA/PpsR system could mediate redox-dependent gene expression in the alphaproteobacteria Rhodobacter capsulatus and Paracoccus denitrificans but not in the gammaproteobacterium Escherichia coli. Analysis of a prrA mutant strain of R. sphaeroides strongly suggests that light-dependent gene expression requires a balanced interplay of the AppA/PpsR system with the PrrA response regulator. Therefore, the AppA/PpsR system was unable to establish light signaling in other bacteria. Based on our data, we present a model for the interdependence of AppA/PpsR signaling and the PrrA transcriptional activator.