Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline)

This study describes for the first time the comprehensive characterization of tetrapyrrole cofactor biosynthetic pathways developed for bacterial community (BC) inhabiting shale rock. Based on the genomic and proteomic metadata, we have detailed the biosynthesis of siroheme, heme, cobalamin, and the major precursor uroporphyrinogen III by a deep BC living on a rock containing sedimentary tetrapyrrole compounds. The obtained results showed the presence of incomplete heme and cobalamin biosynthesis pathways in the studied BC. At the same time, the production of proteins containing these cofactors, such as cytochromes, catalases and sulfite reductase, was observed. The results obtained are crucial for understanding the ecology of bacteria inhabiting shale rock, as well as their metabolism and potential impact on the biogeochemistry of these rocks. Based on the findings, we hypothesize that the bacteria may use primary or modified sedimentary porphyrins and their degradation products as precursors for synthesizing tetrapyrrole cofactors. Experimental testing of this hypothesis is of course necessary, but its evidence would point to an important and unique phenomenon of the tetrapyrrole ring cycle on Earth involving bacteria.     

Biosynthesis of phycobilins. Formation of the chromophore of phytochrome, phycocyanin and phycoerythrin

Phycobiliproteins play important roles in photomorphogenesis and photosynthesis. The light-absorbing chromophores of the phycobiliproteins are linear tetrapyrroles (bilins) very similar in structure to the mammalian bile pigments. 5-Aminolaevulinate (5-ALA) is the first committed intermediate in phycobilin synthesis. The biosynthesis of 5-ALA, destined for phycobilins, occurs via the five-carbon pathway, now well established for tetrapyrrole synthesis in plants and distinct from the mammalian pathway. The phycobilins are formed by reduction of biliverdin which results from the synthesis and degradation of haem. This haem is an essential intermediate in the biosynthesis of phycobilins. Phycocyanobilin, the blue-green pigment found in certain algae and cyanobacteria, is formed from biliverdin via phytochromobilin, the chromophore of phytochrome. This leads to the likelihood that phytochromobilin is formed as an end product, or intermediate, in the synthesis of all phycobilins.     

Biliverdin reduction by cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) proceeds via linear tetrapyrrole radical intermediates

Cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the four electron reduction of biliverdin IXalpha (BV) to phycocyanobilin, a key step in the biosynthesis of the linear tetrapyrrole (bilin) prosthetic groups of cyanobacterial phytochromes and the light-harvesting phycobiliproteins. Using an anaerobic assay protocol, optically detected bilin-protein intermediates, produced during the PcyA catalytic cycle, were shown to correlate well with the appearance and decay of an isotropic g approximately 2 EPR signal measured at low temperature. Absorption spectral simulations of biliverdin XIIIalpha reduction support a mechanism involving direct electron transfers from ferredoxin to protonated bilin:PcyA complexes.     

PHOTODESTRUCTION OF TUMOR CELLS BY INDUCTION OF ENDOGENOUS ACCUMULATION OF PROTOPORPHYRIN IX: ENHANCEMENT BY 1, 10-PHENANTHROLINE

Rapidly proliferating transformed mammalian cells can be photodestroyed in vitro upon inducing the accumulation of endogenous protoporphyrin IX (Proto). Proto biosynthesis and accumulation were triggered by manipulation of the porphyrin-heme biosynthetic pathway. Proto accumulation in cultured cells was induced by treatment with 1.0 mM delta-aminolevulinic acid (ALA), a naturally occurring 5-carbon amino acid, for 3.5 h. In darkness, significant Proto accumulation became evident within 3.5 h of incubation. In the light, the accumulated tetrapyrroles triggered destruction of treated cells within the first 30 min of illumination, probably via the rapid oxidation of cellular constituents by singlet oxygen. Protoporphyrin IX accumulation and specific cell lysis increased significantly by inclusion of 0.75 mM 1,10-phenanthroline (Oph), a tetrapyrrole biosynthesis modulator. Slower growing untransformed cells did not accumulate significant amounts of Proto following ALA and Oph treatment unless stimulated to proliferate with the mitogenic lectin Concanavalin A.     

Molecular Engineering of Free‐Base Porphyrins as Ligands—The N−H⋅⋅⋅X Binding Motif in Tetrapyrroles

The core N?H units of planar porphyrins are often inaccessible to forming hydrogen‐bonding complexes with acceptor molecules. This is due to the fact that the amine moieties are “shielded” by the macrocyclic system, impeding the formation of intermolecular H‐bonds. However, methods exist to modulate the tetrapyrrole conformations and to reshape the vector of N?H orientation outwards, thus increasing their availability and reactivity. Strategies include the use of porpho(di)methenes and phlorins (calixphyrins), as well as saddle‐distorted porphyrins. The former form cavities due to interruption of the aromatic system. The latter are highly basic systems and capable of binding anions and neutral molecules via N?H???X‐type H‐bonds. This Review discusses the role of porphyrin(oid) ligands in various coordination‐type complexes, means to access the core for hydrogen bonding, the concept of conformational control, and emerging applications, such as organocatalysis and sensors.     

基于微生物体系合成无机纳米材料的研究进展

无机纳米材料在能源、生物医学等领域应用非常广泛,过去几十年间关于无机纳米材料合成方法的研究一直受到广泛关注。自然界中普遍存在的生物矿化过程赋予了生物体合成含有特殊结构和功能的无机纳米材料的能力。微生物体系合成的无机纳米材料具有环境友好、成本低廉、生物相容性好等优点,正成为纳米材料科学的一个重要研究领域。我们主要聚焦于微生物体系合成无机纳米材料的机理、影响因素、材料分类及其应用,总结了近年来关于微生物体系合成无机纳米材料的研究历程,并对该领域面临的挑战及未来的发展方向进行了展望。     

Nature of the near‐IR band in the electronic absorption spectra of neutral bis(tetrapyrrole) rare earth(III) complexes: Time‐dependent density functional theory calculations

The nature of the near‐IR band in the electronic absorption spectra of bis(tetrapyrrole) rare earth(III) complexes Y(Pc)₂ (1), La(Pc)₂ (2), Y(Pc)(Por) (3), Y(Pc)[Pc(α‐OCH₃)₄] (4), Y(Pc)[Pc(α‐OCH₃)₈] (5), and Y(Pc)[Pc(β‐OCH₃)₈] (6) was studied on the basis of time‐dependent density functional theory (TD‐DFT) calculations. The electronic dipole moment along the z‐axis in the electronic transition of the near‐IR band in all the studied neutral bis(tetrapyrrole) yttrium(III) and lanthanum(III) double‐deckers is well explained on the basis of the composition analysis of the orbitals involved. The electronic transition in the near‐IR band causes the reversion of the orbital orientation of one tetrapyrrole ring in both homoleptic and heteroleptic bis(tetrapyrrole) rare earth complexes and induces electron transfer from the tetrapyrrole ring with lower orbital energy to the other ring in the heteroleptic bis(tetrapyrrole) rare earth(III) complexes. The near‐IR band can work as an ideal characteristic absorption band to reflect the π–π interaction between the two tetrapyrrole rings in bis(tetrapyrrole) rare earth(III) double‐decker complexes because of its peculiar electronic transition nature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Chloroplast biogenesis 87: Evidence of resonance excitation energy transfer between tetrapyrrole intermediates of the chlorophyll biosynthetic pathway and chlorophyll a

The thorough understanding of photosynthetic membrane assembly requires a deeper knowledge of the coordination of chlorophyll (Chl) and thylakoid apoprotein biosynthesis. As a working model for future investigations, we have proposed three Chl-thylakoid apoprotein biosynthesis models, namely, a single-branched Chl biosynthetic pathway (SBP) single-location model, an SBP multilocation model and a multibranched Chl biosynthetic pathway (MBP) sublocation model. Rejection or validation of these models can be probed by determination of resonance excitation energy transfer between various tetrapyrrole intermediates of the Chl biosynthetic pathway and various thylakoid Chl-protein complexes. In this study we describe the detection of resonance energy transfer between protoporphyrin IX (Proto), Mg-Proto and its monomethyl ester (Mp(e)) and divinyl and monovinyl protochlorophyllide a (Pchlide a) and several Chl-protein complexes. Induction of various amounts of tetrapyrrole accumulation in green photoperiodically grown cucumber cotyledons and barley leaves was achieved by dark incubation of excised tissues with delta-aminolevulinic acid (ALA) and various concentrations of 2,2'-dipyridyl for various periods of time. Controls were incubated in distilled water. After plastid isolation, treated and control plastids were diluted in buffered glycerol to the same Chl concentration. Excitation spectra were then recorded at 77 K at emission maxima of about 686, 694 and 738 nm. Resonance excitation energy transfer from Proto, Mp(e) and Pchlide a to Chl-protein complexes emitting at 686, 694 and 738 nm was observed by calculation of treated minus control difference excitation spectra. The occurrence of resonance excitation energy transfer between anabolic tetrapyrroles and Chl-protein complexes appeared as well-defined excitation bands with excitation maxima corresponding to those of Proto, Mp(e) and Pchlide a. Furthermore, it appeared that resonance excitation energy transfer from multiple short-wavelength, medium-wavelength and long-wavelength Proto, Mp(e) and Chlide a sites to various Chl-protein complexes took place. Because resonance excitation transfer from donors to acceptors cannot take place at distances larger than 100 A, it is proposed that the observed resonance excitation energy transfers are not compatible with the SBP single-location Chl biosynthesis thylakoid membrane biogenesis model. The latter assumes that a single-branched Chl biosynthetic pathway located in the center of a 450 x 130 A photosynthetic unit generates all of the Chl needed for the assembly of all Chl-protein complexes.     

Heteroleptic Tetrapyrrole‐Fused Dimeric and Trimeric Skeletons with Unusual Non‐Frustrated Fluorescence

Phthalocyanine (Pc) and porphyrin (Por) chromophores have been fused through the benzo[α]pyrazine moiety, resulting in unprecedented heteroleptic tetrapyrrole‐fused dimers and trimers. The heteroleptic tetrapyrrole nature has been clearly revealed based on single‐crystal X‐ray diffraction analysis of the zinc dimer. Electrochemical analysis, theoretical calculations, and time‐resolved spectroscopic results disclose that the two/three‐tetrapyrrole‐fused skeletons behave as one totally π‐conjugated system as a result of the strong conjugative interaction between/among the tetrapyrrole chromophores. In particular, the effectively extended π‐electron system through the fused‐bridge induced strong electronic communication between the Pc and Por moieties and large transition dipole moments in the Pc–Por‐fused systems, providing high fluorescence quantum yields (>0.13) and relatively long excited state lifetimes (>1.3 ns) in comparison with their homo‐tetrapyrrole‐fused analogues.     

Synthesis of sapphyrins, heterosapphyrins, and carbasapphyrins by a "4 + 1" approach

Sapphyrins are an important group of expanded porphyrins that show valuable anion binding characteristics. In this study, a "4 + 1" route to sapphyrin systems has been developed. Reaction of dialdehydes with a known tetrapyrrole intermediate 11b incorporating a bipyrrolic subunit afforded a wide range of sapphyrin-type products. The best conditions for these reactions involved carrying out the condensation of the dialdehydes with the tetrapyrrole in TFA-dichloromethane, followed by oxidation with dilute aqueous solutions of ferric chloride. A pyrrole dialdehyde reacted under these conditions to give sapphyrin in 50% yield, while furan and thiophene dialdehydes afforded the corresponding oxa- and thiasapphyrins in 66-90% yield. Pyrrole dialdehydes with fused phenanthrene or acenaphthylene rings also reacted with 11b to give the related phenanthro- and acenaphthosapphyrins in excellent yields. As was the case for acenaphthoporphyrins, the acenaphthosapphyrin gave longer wavelength absorptions than the corresponding phenanthrene fused structure, although the differences were not as marked as those seen in the porphyrin series. Reaction of 11b with 1,3-diformylindene gave a benzocarbasapphyrin in 38% yield, while a triformyl cyclopentadiene reacted with the tetrapyrrole to give a carbasapphyrin aldehyde in 7-12% yield. The free base carbasapphyrins were unstable but the monoprotonated hydrochloride salts could easily be isolated and characterized. Carbasapphyrins retain a strong diatropic ring current due to the presence of 22pi electron delocalization pathways. In the presence of trifluoroacetic acid, C-protonated dications are generated. Condensation of 1,3-azulenedicarbaldehyde with 11b gave an azulisapphyrin dihydrochloride salt in 35% yield, and this also showed a strong diatropic ring current. Addition of base gave the unstable free base form, while pyrrolidine formed an unstable adduct that showed an intense Soret band at 480 nm. These results demonstrate that many of the themes observed for modified porphyrins and carbaporphyrins also apply to the sapphyrin series, although in some cases reduced stability hampers these investigations.     

Ring-opening with one dioxygen molecule in the coupled oxidation of iron tetraarylporphyrins

A dioxygen molecule was activated on the iron complex of tetraarylporphyrins and both oxygen atoms of the O₂ molecule were added to cleave the macrocycle to yield a linear tetrapyrrole intermediate, from which two linear tetrapyrrole products, biladienone and bilindione, are formed, as revealed by isotope labeling experiments with oxygen-18.     

Absorption and fluorescence spectra of open-chain tetrapyrrole pigments–bilirubins,biliverdins, phycobilins,and synthetic analogues

Open-chain tetrapyrroles are ubiquitous and abundant in living organisms (algae, animals, bacteria, and plants), including examples such as bilirubin, biliverdin, phycocyanobilin, phycoerythrobilin, and urobilin. The open-chain tetrapyrroles, collectively termed bilins, arise from biosynthesis or degradation of tetrapyrrole macrocycles. Bilins are now known to play a wide variety of biological roles encompassing light-harvesting (in phycobiliproteins), photomorphogenesis, signaling, and redox chemistry. The absorption spectra of bilins spans the ultraviolet (UV), visible, to near-infrared (NIR) regions depending on the degree of conjugation, thereby providing a wide range of colors from red/orange to blue/green. The fluorescence intensity of bilins is often quite low and hence fewer spectra are available, but can be increased substantially by structural rigidification, as evidenced by the wide use of biliproteins as fluorescent labels. The present article describes a database of absorption and fluorescence spectra of bilins from natural and synthetic origins for 220 compounds (270 absorption and 13 fluorescence spectral traces). Spectral traces of bilins published over the past ∼50 years have been digitized and assembled along with information concerning solvent, photochemical properties (molar absorption coefficient and fluorescence quantum yield), and literature references. The spectral traces (xy-coordinate data files) can be viewed, downloaded, and accessed at www.photochemcad.com. The accessibility of spectral traces in digital format should facilitate identification and quantitative calculations of interest in diverse scientific areas.     

Conformational control of cofactors in nature--functional tetrapyrrole conformations in the photosynthetic reaction centers of purple bacteria

Chemically identical tetrapyrrole cofactors such as hemes and chlorophylls participate in functionally diverse biological roles. An analysis of the available protein structural data for the bacteriochlorophylls in the photosynthetic reaction center gives statistically reliable evidence of the hypothesis that the protein induced cofactor conformation is a modulator of the bio-molecular function of each reaction center. The results serve as a general model to illustrate conformational control of tetrapyrrole cofactors in other proteins.     

An unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase

Porphobilinogen synthase (PBGS), which catalyzes the first common step in tetrapyrrole biosynthesis, contains a unique phylogenetic variation in the use of metal ions. Using sequence, structure, and enzymological information, this work codifies the phylogenetic segregation of metal utilization in PBGS from archaea, bacteria, and eucarya. All PBGS contain an active site metal binding sequence, determined herein to be either DXCXCX(Y/F)X(3)G(H/Q)CG or DXALDX(Y/F)X(3)G(H/Q)DG. The former dictates a requirement for zinc. Most PBGS that do not require zinc require magnesium and/or potassium instead. Most PBGS are also found to contain the binding determinants for an allosteric magnesium that resides outside the active site. The phylogenetic distribution of PBGS metal ion utilization suggests that the primordial PBGS required zinc and supports a hypothesis that the loss of the zinc site was concurrent with the advent of oxygenic photosynthesis.     

Origin of Ketones in Sediments of Qinghai Lake

This paper analysed the ketone fractions in sediments and living organisms of Qinghai Lake using GC-MS and discussed their origin,n-Alkan-2-ones detected in the sediments ranged from C_(12) to C_(33) with a maximum at n-C_(25) or n-C_(29) and showed a strong odd predominance, n-Alkan-2-ones in the living organisms analysed ranged from C_(15) to C_(31) with a maximum at n-C_(27).The authors believed that ketones in modern sediments may directly derive from biosynthesis.     

Identification of a cluster of genes that directs desferrioxamine biosynthesis in Streptomyces coelicolor M145

Desferrioxamines are a structurally related family of tris-hydroxamate siderophores that form strong hexadentate complexes with ferric iron. Desferrioxamine B has been used clinically for the treatment of iron overload in man. We have unambiguously identified desferrioxamine E as the major desferrioxamine siderophore produced by Streptomyces coelicolor M145 and have identified a cluster of four genes (desA-D) that directs desferrioxamine biosynthesis in this model actinomycete. On the basis of comparative sequence analysis of the proteins encoded by these genes, we propose a plausible pathway for desferrioxamine biosynthesis. The desferrioxamine biosynthetic pathway belongs to a new and rapidly emerging family of pathways for siderophore biosynthesis, widely distributed across diverse species of bacteria, which is biochemically distinct from the better known nonribosomal peptide synthetase (NRPS) pathway used in many organisms for siderophore biosynthesis.     

Origin of Aldehydes in Sediments of Qinghai Lake

This paper has analysed the aldehyde fractions in sediments and living organisms of Qinghai Lake using GC-MS and discussed their origin, n-Aldehydes detected in the sediments ranged from C_(16) to C_(32) with a maximum at C_(22) C_(24) or C_(26) and showed a strong even over odd predominance. n-Aldehydes in the living organisms analysed ranged from C_(16) to C_(32) with a maximum at C_(26) or C_(28). The authors believed that aldehydes in modern sediments may directly derive from biosynthesis.     

Novel small-molecule inhibitors of arylamine N-acetyltransferases: drug discovery by high-throughput screening

Arylamine N-acetyltransferases (NATs) are a family of enzymes found in eukaryotes and prokaryotes. While the precise endogenous function of NAT remains unknown for most organisms, recent evidence has shown that the expression of human NAT1 is up-regulated in estrogen receptor positive breast cancer. Additionally, NAT in mycobacteria is required for mycobacterial cell wall biosynthesis and survival of the organisms within macrophage. It is therefore important to develop small molecule inhibitors of NATs as molecular tools to study the function of NATs in various organisms. Such inhibitors may also prove useful in future drug design, for example in the development of anti tubercular agents. We describe a high-throughput screen of a proprietary library of 5016 drug-like compounds against three prokaryotic NAT enzymes and two eukaryotic NAT enzymes.     

An in vitro screen of bacterial lipopolysaccharide biosynthetic enzymes identifies an inhibitor of ADP-heptose biosynthesis

The lipopolysaccharide (LPS)-rich outer membrane of gram-negative bacteria provides a protective barrier that insulates these organisms from the action of numerous antibiotics. Breach of the LPS layer can therefore provide access to the cell interior to otherwise impermeant toxic molecules and can expose vulnerable binding sites for immune system components such as complement. Inhibition of LPS biosynthesis, leading to a truncated LPS molecule, is an alternative strategy for antibacterial drug development in which this vital cellular structure is weakened. A significant challenge for in vitro screens of small molecules for inhibition of LPS biosynthesis is the difficulty in accessing the complex carbohydrate substrates. We have optimized an assay of the enzymes required for LPS heptose biosynthesis that simultaneously surveys five enzyme activities by using commercially available substrates and report its use in a small-molecule screen that identifies an inhibitor of heptose synthesis.     

The biosynthesis of cyclitols

Information has recently been obtained, mainly with the aid of radioactive compounds, about the biosynthesis of various cyclitols. It was found that the most widely occurring cyclitol, meso-inositol, is biosynthesized by a pathway probably common to all organisms, in which the cyclohexane ring is formed by ring closure between the two terminal carbon atoms of D -glucose. Cell-free extracts or enzyme systems that catalyse the conversion of D -glucose into meso-inositol can be prepared from various biological materials. The biosynthesis of the other hexahydroxycyclohexanes (inositols) involves meso-inositol as an intermediate. A few steps in the conversion of meso-inositol into other inositols have been studied.