Exploring the onset of B12-based mutualisms using a recently evolved Chlamydomonas auxotroph and B12-producing bacteria

Cobalamin (vitamin B₁₂) is a cofactor for essential metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonize the algal phycosphere, forming stable communities that gain preferential access to photosynthate and in return provide compounds such as B₁₂. Extended coexistence can then drive gene loss, leading to greater algal–bacterial interdependence. In this study, we investigate how a recently evolved B₁₂-dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B₁₂ producers, its growth in co-culture was slower than the B₁₂-independent wild-type, suggesting that high bacterial B₁₂ provision may be necessary to favour B₁₂ auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B₁₂ makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B₁₂ release provided an advantage in co-cultures. We hypothesize that, given the right conditions, bacteria that release more B₁₂ may be selected for, particularly if they form close interactions with B₁₂-dependent algae.     

Role of the CarH photoreceptor protein environment in the modulation of cobalamin photochemistry

The photochemistry of cobalamins has recently been found to have biological importance, with the discovery of bacterial photoreceptor proteins, such as CarH and AerR. CarH and AerR, are involved in the light regulation of carotenoid biosynthesis and bacteriochlorophyll biosynthesis, respectively, in bacteria. Experimental transient absorption spectroscopic studies have indicated unusual photochemical behavior of 5′-deoxy-5′-adenosylcobalamin (AdoCbl) in CarH, with excited-state charge separation between cobalt and adenosyl and possible heterolytic cleavage of the Co-adenosyl bond, as opposed to the homolytic cleavage observed in aqueous solution and in many AdoCbl-based enzymes. We employ molecular dynamics and hybrid quantum mechanical/molecular mechanical calculations to obtain a microscopic understanding of the modulation of the excited electronic states of AdoCbl by the CarH protein environment, in contrast to aqueous solution and AdoCbl-based enzymes. Our results indicate a progressive stabilization of the electronic states involving charge transfer (CT) from cobalt/corrin to adenine on changing the environment from gas phase to water to solvated CarH. The solvent exposure of the adenosyl ligand in CarH, the π-stacking interaction between a tryptophan and the adenine moiety, and the hydrogen-bonding interaction between a glutamate and the lower axial ligand of cobalt are found to contribute to the stabilization of the states involving CT to adenine. The combination of these three factors, the latter two of which can be experimentally tested via mutagenesis studies, is absent in an aqueous solvent environment and in AdoCbl-based enzymes. The favored CT from metal and/or corrin to adenine in CarH may promote heterolytic cleavage of the cobalt-adenosyl bond proposed by experimental studies. Overall, this work provides novel, to our knowledge, physical insights into the mechanism of CarH function and directions for future experimental investigations. The fundamental understanding of the mechanism of CarH functioning will serve the development of optogenetic tools based on the new class of B₁₂-dependent photoreceptors.     

Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution

A widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. Vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism''s metabolism to the environment, but this has never been demonstrated directly. Moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic demand for these important micronutrients has significant implications in terms of nutrient acquisition and, in microbial organisms, can affect community composition and metabolic exchange between coexisting species. Here we investigate the origins of vitamin dependence, using an experimental evolution approach with the vitamin B₁₂-independent model green alga Chlamydomonas reinhardtii. In fewer than 500 generations of growth in the presence of vitamin B₁₂, we observe the evolution of a B₁₂-dependent clone that rapidly displaces its ancestor. Genetic characterization of this line reveals a type-II Gulliver-related transposable element integrated into the B₁₂-independent methionine synthase gene (METE), knocking out gene function and fundamentally altering the physiology of the alga.     

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean

Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B₁₂-independent MetE and B₁₂-dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.     

Mechanism of Photoregulated Carotenogenesis in Rhodotorula minuta III. Effect of Certain Nucleic Acid and Protein Inhibitors on Photoinduction of Carotenoid Biosynthesis

Inhibitors of protein and nucleic acid synthesis such as puromycin,cycloheximide, 5-fluorodeoxyuridine and 5-fluorouracil havebeen used to study the dark reactions involved in photoregulationof carotenogenesis in Rhodotorula minuta. The results indicatedthat as already reported in other organisms, carotenogenic enzymesare synthesized first and, in turn, synthesize carotenoids inthe dark. Synthesis of the carotenogenic enzymes was absolutelydependent on oxygen and came to an end within 6 hr at 26?C underaerobic conditions. Photoregulation of this synthesis may occurat the translational level. 5-Fluorodeoxyuridine and 5-fluorouracilacted as chemical inducers of carotenogenesis in Rh. minutagrown in the dark. However, the site of the action of thesechemicals was assumed to be different from that of light, becausethe chemical and light effects on the induction of carotenogenesiswere additive. (Received September 16, 1981; Accepted March 3, 1982)     

Vitamin B12-dependent Methionine Synthetase in Photosynthetic Bacteria Partial Purification and Properties

Vitamin B₁₂-dependent methionine synthetase (N⁵-methyItetrahydrofolate-homocysteine Bi2-methyltransferase; EC 2.1.1.13) was partially purified from two different types of photo-synthetic bacteria, Chromatium D and Rhodospirillum rubrum.

Chromatium D, which does not produce vitamin B₁₂, possessed apomethionine synthetase when grown in the absence of the vitamin. Partially purified apoenzyme was converted to holoenzyme efficiently with CH₃B₁₂ or OHB₁₂. Holo-methionine synthetase was purified 244 fold with 56.4 % recovery from Chromatium D cells grown with vitamin B₁₂ added. The partially purified enzyme required reductants but was only partially dependent on S-adenosylmethionine.

On the other hand, Rsp. rubrum methionine synthetase which was always present as holoenzyme, in contrast with that of Chromatium D, was purified 40 fold with 2.8% recovery. The obtained preparation required S-adenosylmethionine and reductants for the enzyme activity. The optimal pH of Chromatium D enzyme and of Rsp. rubrum enzyme was in the range of 7.5~7.8 and 6.5~6.75, respectively.     

Untersuchungen über die lichtabhängige Carotinoidsynthese

Summary Under anaerobic conditions Fusarium aquaeductuum is able to synthesize carotenogenic enzymes but does not produce pigments. If illumination of the mycelia in the presence of oxygen is followed by an incubation in the dark under N₂ atmosphere, the strictly concurrent formation of the different carotenoids sets off as soon as aerobic conditions are restored. The paraboloidal increase of pigment production possibly indicates that synthesis of carotenogenic enzymes is also resumed. Blocking this enzyme synthesis by addition of cycloheximide leads to a simultaneous and linear increase of each carotenoid portion as soon as oxygen is replenished. This is interpreted to mean that light induces carotenogenic enzymes in a coupled group. On the other hand, our present and earlier results do not support any hypothesis on the existence of a carotenogenic multienzyme complex. The composition of the pigment after carotenoid production has ceased provides evidence for a selective inhibition of the synthesis of individual carotenogenic enzymes. Changes in pigment composition caused by an incubation of the mycelia for 12 h under anaerobic conditions are also reported.     

The effect of antimycin a on carotenogenesis in Verticillium agaricinum

Summary Antimycin A did not induce carotenogenesis in dark grown cultures of V. agaricinum, but total protein was increased. In light, antimycin A did not affect total carotenoids, although protein was slightly increased. The results suggest that antimycin A could not have acted here as an inducer for the synthesis of specific carotenogenic enzymes or by inactivating a repressor as has been suggested for certain bacteria.     

Metabolism of Glutamate in Purple Nonsulfur Bacteria Participation of Vitamin B12

Purple nonsulfur bacteria, Rhodospirillum rubrum and Rhodopseudomonas spheroides were found to possess coenzyme B₁₂-dependent glutamate mutase activity. Cell-free extracts of these bacteria grown on Co²⁺-containing media catalyzed the conversion of glutamate to β-methylaspartate and further to mesaconate. The activity of the cell-free extracts of these organisms cultivated on Co²⁺-deficient media was markedly lower than that of the normal cells. Addition of coenzyme B₁₂ to the former reaction mixture enhanced the mesaconate formation via β-methylaspartate. These results indicate the involvement of coenzyme Independent glutamate mutase of these bacteria in the dissimilation of glutamate to acetyl-CoA and pyruvate through the following pathway.

glutamate→β→methylaspartate→mesaconate→citramalate→→acetyl-CoA, pyruvate On the other hand, a greater part of glutamate was converted to α-hydroxyglutarate and succinate with the cell-free extracts of these photosynthetic bacteria. This fact, taking account of the presence of propionyl-CoA carboxylase in these bacteria, implies the participation of coenzyme B₁₂-dependent (R)-methylmalonyl-CoA mutase in the formation of succinate via the following route.

glutamate→α-ketoglutarate→α-hydroxyglutarate→propionate→propionyl-CoA→(S)-methylmalonyl-CoA→(R)-methylmalonyl-CoA→succinyl-CoA     

Purification and interaction analyses of two human lysosomal vitamin B12 transporters: LMBD1 and ABCD4

Mutations in human LMBRD1 and ABCD4 prevent lysosomal export of vitamin B₁₂ to the cytoplasm, impairing the vitamin B₁₂-dependent enzymes methionine synthase and methylmalonyl-CoA mutase. The gene products of LMBRD1 and ABCD4 are implicated in vitamin B₁₂ transport at the lysosomal membrane and are proposed to act in complex. To address the mechanism for lysosomal vitamin B₁₂ transport, we report the novel recombinant production of LMBD1 and ABCD4 for detailed biophysical analyses. Using blue native PAGE, chemical crosslinking, and size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), we show that both detergent-solubilized LMBD1 and detergent-solubilized ABCD4 form homodimers. To examine the functional binding properties of these proteins, label-free surface plasmon resonance (SPR) provides direct in vitro evidence that: (i) LMBD1 and ABCD4 interact with low nanomolar affinity; and (ii) the cytoplasmic vitamin B₁₂-processing protein MMACHC also interacts with LMBD1 and ABCD4 with low nanomolar affinity. Accordingly, we propose a model whereby membrane-bound LMBD1 and ABCD4 facilitate the vectorial delivery of lysosomal vitamin B₁₂ to cytoplasmic MMACHC, thus preventing cofactor dilution to the cytoplasmic milieu and protecting against inactivating side reactions.     

Vitamin B12-dependent methionine synthesis in Rhizobium meliloti

Methionine, among the various additions to the medium, could only replace cobalt ion or vitamin B₁₂ required for the growth of $\text{Rhizobium meliloti}$. It was demonstrated that there exists a vitamin B₁₂-dependent terminal step in the methionine synthesis, that is, N⁵CH₃-tetrahydrofolate-homocysteine transmethylase, which can also catalyze the methyl transfer from CH₃B₁₂ to homocysteine, in the cell-free extracts of Rhizobium meliloti. These facts seem to indicate that the vitamin B₁₂-dependent pathway to methionine functions mainly among the B₁₂-dependent enzymatic systems in the wild-type symbionts and this is the chief nutritional significance of cobalt.     

Vitamin B12 transport in Escherichia coli K12 does not require the btuE gene of the btuCED operon

Summary Transport of vitamin B₁₂ across the cytoplamic membrane ofEscherichia coli requires the products ofbtuC andbtuD, two genes in thebtuCED operon. The role ofbtuE, the central gene of this operon, was examined. Deletions withinbtuE were constructed by removal of internal restriction fragments and were crossed onto the chromosome by allelic replacement. In-frame deletions that removed 20% or 82% of thebtuE coding region did not affect expression of the distalbtuD gene. These nonpolar deletions had little effect on vitamin B₁₂ binding (whole cells or periplasmic fraction) and transport. They did not affect the utilization of vitamin B₁₂ or other cobalamins for methionine biosynthesis, even in strains with decreased outer membrane transport of vitamin B₁₂. ThebtuE mutations did not impair adenosyl-cobalamin dependent catabolism of ethanolamine or repression ofbtuB expression. Thus, despite its genetic location in the transport operon, thebtuE product plays no essential role in vitamin B₁₂ transport.     

Metabolic engineering of cobalamin (vitamin B12) production in Bacillus megaterium

Cobalamin (vitamin B₁₂) production in Bacillus megaterium has served as a model system for the systematic evaluation of single and multiple directed molecular and genetic optimization strategies. Plasmid and genome-based overexpression of genes involved in vitamin B₁₂ biosynthesis, including cbiX, sirA, modified hemA, the operons hemAXCDBL and cbiXJCDETLFGAcysG^AcbiYbtuR, and the regulatory gene fnr, significantly increased cobalamin production. To reduce flux along the heme branch of the tetrapyrrole pathway, an antisense RNA strategy involving silencing of the hemZ gene encoding coproporphyrinogen III oxidase was successfully employed. Feedback inhibition of the initial enzyme of the tetrapyrrole biosynthesis, HemA, by heme was overcome by stabilized enzyme overproduction. Similarly, the removal of the B₁₂ riboswitch upstream of the cbiXJCDETLFGAcysG^AcbiYbtuR operon and the recombinant production of three different vitamin B₁₂ binding proteins (glutamate mutase GlmS, ribonucleotide triphosphate reductase RtpR and methionine synthase MetH) partly abolished B₁₂-dependent feedback inhibition. All these strategies increased cobalamin production in B. megaterium. Finally, combinations of these strategies enhanced the overall intracellular vitamin B₁₂ concentrations but also reduced the volumetric cellular amounts by placing the organism under metabolic stress.     

The putative coenzyme B12-dependent methylmalonyl-CoA mutase from potatoes is a phosphatase

The reported presence of a coenzyme B₁₂-dependent methylmalonyl-CoA mutase in potatoes has been reexamined. The enzyme converting methylmalonyl-CoA was purified to electrophoretic homogeneity. Examination of the reaction product by ¹H, ³¹P NMR and mass spectrometry revealed that it was methylmalonyl-3′-dephospho-CoA. The phosphatase enzyme needs neither coenzyme B₁₂ nor S-adenosylmethionine as a cofactor.     

Studies on the mechanism of photosystem II photoinhibition I. A two-step degradation of D1-protein

The role of D1-protein in photoinhibition was examined. Photoinhibition of spinach thylakoids at 20°C caused considerable degradation of D1-protein and a parallel loss of variable fluorescence, Q_B-independent electron flow and Q_B-dependent electron flow. The breakdown of D1-protein as well as the loss of variable fluorescence and Q_B-independent electron flow were largely prevented when thylakoids were photoinhibited at 0°C. The Q_B-dependent electron flow markedly decreased under the same conditions. This inactivation may represent the primary event in photoinhibition and could be the result of some modification at the Q_B-site of D1-protein. Evidence for this comes from fluorescence relaxation kinetics following photoinhibition at 0°C which indicate a partial inactivation of Q_A ^--reoxidation. These results support the idea of D1-protein breakdown during photoinhibition as a two step process consisting of an initial inactivation at the Q_B-site of the protein followed by its degradation. The latter is accompanied by the loss of PS II-reaction centre function.Abbreviations Asc ascorbate - p-BQ 1, 4-benzoquinone - DAD diaminodurene - DPC diphenylcarbazide - DQH₂ duroquinole - Fecy ferricyanide - MV methylviologen - Q_A primary quinone acceptor of PS II - Q_B secondary quinone acceptor of PS II - SiMo silicomolybdate