Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B12 anaerobic pathway

3A novel carbazole-based AIE-active fluorescent sensor for fast and ultrasensitive detection of Cu2+ and Co2+ in normal saline system

A novel phenyl-carbazole-based fluorescent sensor (PCBP) has been synthesized and investigated to selectively detect Cu²⁺ or Co²⁺. The PCBP molecule exhibits the excellent fluorescent property with the aggregation-induced emission (AIE) effect. In given THF/normal saline (f_w = 95%) system, the PCBP sensor shows turn-off fluorescence performance at 462 nm with Cu²⁺ or Co²⁺. It reveals excellent characteristics of good selectivity, and ultra-high sensitivity, strong anti-interference ability, wide pH applicable range, as well as ultra-fast detection response. The limit of detection (LOD) of the sensor reaches 1.1 × 10^-9 mol·L^-1 and 1.1 × 10^-8 mol·L^-1 for Cu²⁺ and Co²⁺ in turn. The formation mechanism of AIE fluorescence of PCBP molecules is attributed to the synergistic effect of intramolecular & intermolecular charge transfer (I&ICT). Meanwhile, the PCBP sensor has good repeatability for the detection of Cu²⁺, and performs excellent stability and sensitivity for the detection of Cu²⁺ in real water sample. The PCBP-based fluorescent test strips present reliable capacity for the detection of Cu²⁺ and Co²⁺⁺ in aqueous solution.

A new diformyl phenol based chemosensor selectively detects Zn2+ and Co2+ in the nanomolar range in 100% aqueous medium and HCT live cells

A new diformyl phenol based chemosensor that can sense Zn2+ and Co2+ in the nanomolar range in 100% aqueous solution and in HCT cells was explored.

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

Discovery of a novel camphor-based fluorescent probe for Co2+ in fresh vegetables with high selectivity and sensitivity

Cobalt is an essential micronutrient for human beings. The excessive intake of cobalt may lead to heart-related diseases. In this work, a novel fluorescent probe 1,1'-(((6,11,11-trimethyl-6,7,8,9-tetrahydro-6,9-methanopyridazino[4,5-b]quinoxaline-1,4-diyl)bis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol) (PDS) was synthesized from camphor. The probe PDS could be utilized to selectively recognize Co²⁺ over other metal ions. There is a good linear relationship between fluorescence intensity of PDS and Co²⁺ concentration within 0-20 μM, and its detection limt was found to be 0.925 μM, which is far lower than the national standard for cobalt in drinking water in China. The possible coordination mechanism of PDS with Co²⁺ was determined by nuclear magnetic resonance (NMR), high resolution mass spectrometry (HRMS) and density functional theory (DFT). The probe PDS was also successfully applied in detection of Co²⁺ in tap water and fresh vegetables.

Selective and sensitive colorimetric determination of cobalt ions using Ag–Au bimetallic nanoparticles

Selective and sensitive colorimetric detection of Co²⁺based on the aggregation of Ag–Au BNPs is due to the formation of positively charged (en)₂CoS₂O₃⁺on the negative nanoparticle surface.

Highly selective and sensitive colorimetric chemosensor for detection of Co2+ in a near-perfect aqueous solution

An outstanding colorimetric chemosensor was developed to selectively detect Co²⁺ with the lowest detection limit through the color change from colorless to yellow.

Biosynthesis and Use of Cobalamin (B12)

This review summarizes research performed over the last 23 years on the genetics, enzyme structures and functions, and regulation of the expression of the genes encoding functions involved in adenosylcobalamin (AdoCbl, or coenzyme B12) biosynthesis. It also discusses the role of coenzyme B12 in the physiology of Salmonella enterica serovar Typhimurium LT2 and Escherichia coli. John Roth's seminal contributions to the field of coenzyme B12 biosynthesis research brought the power of classical and molecular genetic, biochemical, and structural approaches to bear on the extremely challenging problem of dissecting the steps of what has turned out to be one of the most complex biosynthetic pathways known. In E. coli and serovar Typhimurium, uro'gen III represents the first branch point in the pathway, where the routes for cobalamin and siroheme synthesis diverge from that for heme synthesis. The cobalamin biosynthetic pathway in P. denitrificans was the first to be elucidated, but it was soon realized that there are at least two routes for cobalamin biosynthesis, representing aerobic and anaerobic variations. The expression of the AdoCbl biosynthetic operon is complex and is modulated at different levels. At the transcriptional level, a sensor response regulator protein activates the transcription of the operon in response to 1,2-Pdl in the environment. Serovar Typhimurium and E. coli use ethanolamine as a source of carbon, nitrogen, and energy. In addition, and unlike E. coli, serovar Typhimurium can also grow on 1,2-Pdl as the sole source of carbon and energy.

Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp

The importance of Dehalobacter species in bioremediation as dedicated degraders of chlorinated organics has been well recognized. However, still little is known about Dehalobacter's full genomic repertoires, including the genes involved in dehalogenation. Here we report the first insights into the genome sequence of Dehalobacter sp. E1 that grows in strict co-culture with Sedimentibacter sp. B4. Based on the co-culture metagenome and the genome of strain B4 (4.2 Mbp) we estimate the genome sequence of strain E1 to be 2.6 Mbp. Ten putative reductive dehalogenase homologue (Rdh)-encoding gene clusters were identified. One cluster has a putative tetrachloroethene Rdh-encoding gene cluster, similar to the pceABCT operon previously identified in Dehalobacter restrictus. Metagenome analysis indicated that the inability of strain E1 to synthesize cobalamin, an essential cofactor of reductive dehalogenases, is complemented by Sedimentibacter. The metagenomic exploration described here maps the extensive dechlorinating potential of Dehalobacter, and paves way for elucidation of the interactions with its co-cultured Sedimentibacter.

An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis

The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.

A new fluorescent chemosensor detecting Co2+ and K+ in DMF buffered solution

A new fluorescent chemosensor 2-(2-thiophene)imidazo [4,5,f]-1,10-phenanthroline (L) was prepared and characterized. By adding univalent or divalent metal ions such as Na(+), K(+), Mg(2+), Ba(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+) and Hg(2+) ions into the solution of L in DMF under buffered conditions with the working pH ranging from 7.0 to 8.0, we found that L could be used to detect K(+) ratiometricly and it could also be applied to sense Co(2+) with the phenomenon of fluorescence quenching of L. While the response behavior of L was not discernibly affected by other examined metal ions.

Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes

Two new cobalt corrinoid intermediates, cobalt-precorrin 5A and cobalt-precorrin 5B, have been synthesized with the aid of overexpressed enzymes of the vitamin B(12) pathway of Salmonella entericaserovar typhimurium. These compounds were made in several regioselectively (13)C-labeled forms, and their structures have been established by multidimensional NMR spectroscopy. The addition of CbiF to the enzymes known to synthesize cobalt-precorrin 4 resulted in the formation of cobalt-precorrin 5A, and the inclusion of CbiG with CbiF produced cobalt-precorrin 5B, which has allowed us to define the role of these enzymes in the anaerobic biosynthetic pathway. CbiF is the C-11 methylase, and CbiG, an enzyme which shows homology with CobE of the aerobic pathway, is the gene product responsible for the opening of the ring A delta-lactone and extrusion of the "C(2)" unit. The discovery of these long-sought intermediates paves the way for defining the final stages of the anaerobic pathway. It is of considerable evolutionary interest that nature uses two distinct pathways to vitamin B(12), both conserved over several billion years and featuring completely different mechanisms for ring-contraction of the porphyrinoid to the corrinoid ring system. Thus the aerobic pathway utilizes molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the "C(2)" unit as acetic acid from a metal-free intermediate, whereas the anaerobic route features internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the "C(2)" unit as acetaldehyde, using cobalt complexes as substrates.

Elucidation of substrate specificity in the cobalamin (vitamin B12) biosynthetic methyltransferases. Structure and function of the C20 methyltransferase (CbiL) from Methanothermobacter thermautotrophicus

Ring contraction during cobalamin (vitamin B12) biosynthesis requires a seemingly futile methylation of the C20 position of the tetrapyrrole framework. Along the anaerobic route, this reaction is catalyzed by CbiL, which transfers a methyl group from S-adenosyl-L-methionine to cobalt factor II to generate cobalt factor III. CbiL belongs to the class III methyltransferases and displays similarity to other cobalamin biosynthetic methyltransferases that are responsible for the regiospecific methylation of a number of positions on the tetrapyrrole molecular canvas. In an attempt to understand how CbiL selectively methylates the C20 position, a detailed structure function analysis of the enzyme has been undertaken. In this paper, we demonstrate that the enzyme methylates the C20 position, that its preferred substrate is cobalt factor II, and that the metal ion does not undergo any oxidation change during the course of the reaction. The enzyme was crystallized, and its structure was determined by x-ray crystallography, revealing that the 26-kDa protein has a similar overall topology to other class III enzymes. This helped in the identification of some key amino acid residues (Asp(104), Lys(176), and Tyr(220)). Analysis of mutant variants of these groups has allowed us to suggest potential roles that these side chains may play in substrate binding and catalysis. EPR analysis of binary and ternary complexes indicate that the protein donates a fifth ligand to the cobalt ion via a gated mechanism to prevent transfer of the methyl group to water. The chemical logic underpinning the methylation is discussed.

Recent discoveries in the pathways to cobalamin (coenzyme B12) achieved through chemistry and biology

The genetic engineering of Escherichia coli for the over-expression of enzymes of the aerobic and anaerobic pathways to cobalamin has resulted in the in vivo and in vitro biosynthesis of new intermediates and other products that were isolated and characterized using a combination of bioorganic chemistry and high-resolution NMR. Analyses of these products were used to deduct the functions of the enzymes that catalyze their synthesis. CobZ, another enzyme for the synthesis of precorrin-3B of the aerobic pathway, has recently been described, as has been BluB, the enzyme responsible for the oxygen-dependent biosynthesis of dimethylbenzimidazole. In the anaerobic pathway, functions have recently been experimentally confirmed for or assigned to the CbiMNOQ cobalt transport complex, CbiA (a,c side chain amidation), CbiD (C-1 methylation), CbiF (C-11 methylation), CbiG (lactone opening, deacylation), CbiP (b,d,e,g side chain amidation), and CbiT (C-15 methylation, C-12 side chain decarboxylation). The dephosphorylation of adenosylcobalamin-phosphate, catalyzed by CobC, has been proposed as the final step in the biosynthesis of adenosylcobalamin.