The cytochrome c maturation operon is involved in manganese oxidation in Pseudomonas putida GB-1

Molecular response to the influences of Cu(II) and Fe(III) on forming biogenic manganese oxides by Pseudomonas putida MnB1

The biogeochemical cycle of biogenic manganese oxides (BioMnOx) is closely associated with the environmental behavior and fate of various pollutants. It is significantly interfered by many metals, such as Cu and Fe. However, the bacterial molecular responses are not clear. Here, the effects of Cu(II) and Fe(III) on oxidation of manganese by Pseudomonas putida MnB1 and the bacterial molecular response mechanisms have been studied. The bacterial oxidation of manganese were promoted by both Fe(III) and Cu(II) and the final manganese oxidation rate of the Cu(II) group exceeded 16 % that of the Fe(III) group. The results of transcriptome indicated that Cu(II) promoted manganese oxidation by up-regulating the expression levels of multicopper oxidase (MCO) and peroxidase(POD), and by stimulating electron transfer, while Fe(III) promoted this process by accelerating the electron transfer and nitrogen cycling, and activating POD. The protein-protein interaction (PPI) network indicated that the MCO genes (mnxG and mcoA) were directly linked to the copper homeostasis proteins (cusA, cusB, czcC and cusF). Cytochrome c was closely related to the genes related to nitrogen cycling (glnA, glnL, and putA) and electrons transfer (cycO, cycD, nuoA, nuoK, and nuoL), which also promoted manganese oxidation. This study provides a molecular level insight into the oxidation of Mn(II) by Pseudomonas putida MnB1 with Cu(II) and/or Fe(III) ions.

Microbially formed Mn(IV) oxide as a novel adsorbent for removal of Radium

Radioactivity of Ra isotopes in natural waters is of serious concern. Control of 226Ra concentrations in tailings ponds, which store waste from U ore extraction processes, is an important issue in mill tailings management. In this study, we tested microbially formed Mn(IV) oxide as an adsorbent for removal of Ra in water treatment. Biogenic Mn(IV) oxide (BMO) was prepared using a Mn(II)-oxidizing fungus, Coprinopsis urticicola strain Mn-2. First, adsorption experiments of Sr and Ba, as surrogates for Ra, onto BMO were conducted in aqueous NaCl solution at pH 7. Distribution coefficients for Ba and Sr were estimated to be ∼106.5 and ∼104.3 mL/g, respectively. EXAFS analysis indicated that both Sr and Ba adsorbed in inner-sphere complexes on BMO, suggesting that Ra would adsorb in a similar way. From these findings, we expected that BMO would work effectively in removal of Ra from water. Then, BMO was applied to remove Ra from mine water collected from a U mill tailings pond. Just 7.6 mg of BMO removed >98% of the 226Ra from 3 L of mine water, corresponding to a distribution coefficient of 107.4 mL/g for Ra at pH ∼7. The obtained value was convincingly high for practical application of BMO in water treatment. At the same time, the high distribution coefficient indicates that Mn(IV) oxide can be an important carrier and host phase of Ra in the environment.

Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans

Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.

Genome of the epiphytic bacterium Achromobacter denitrificans strain EPI24, isolated from a macroalga located in the Colombian Caribbean

Marine macroalgae are being recognized as reservoirs of biologically active compounds, as their surfaces are susceptible to the colonization of microorganisms which can produce enzymes with a wide range of molecular architectures. Among these bacteria, Achromobacter is responsible for the biosynthesis of laccases. In this research, we performed a bioinformatic pipeline to annotate the sequenced complete genome of the epiphytic bacterium Achromobacter denitrificans strain EPI24, from the macroalgal surface of the Ulva lactuca species; this strain showed laccase activity which has been previously assessed on plate assays. The genome of A. denitrificans strain EPI24 has a size of ∼6.95 Mb, a GC content of 67.33%, and 6,603 protein-coding genes. The functional annotation of the A. denitrificans strain EPI24 genome confirmed the presence of genes encoding for laccases, which could have functional properties of interest in processes such as the biodegradation of phenolic compounds under versatile and efficient conditions.

Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440

The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.

Manganese oxidation counteracts the deleterious effect of low temperatures on biofilm formation in Pseudomonas sp. MOB-449

Mn removal from groundwater by biological sand filter technology is negatively impacted by low temperatures in winter periods. Therefore, the need to study Mn(II)-oxidizing bacteria (MOB) having the potential to oxidize Mn(II) and form biofilms at low temperatures is imperative. These MOB can have potential as inocula for sand filter bioaugmentation strategies to optimize Mn removal during winter periods. We previously showed that a Pseudomonas sp. MOB-449 (MOB-449), isolated from a Mn biofilter, oxidizes Mn(II) in a biofilm-dependent way at low temperatures. In this work, MOB-449 Mn(II) oxidation and growth capacities were evaluated under planktonic and biofilm conditions at different temperatures. At 18°C, MOB-449 showed enhanced biofilm formation due to the addition of Mn(II) to the medium correlating with Mn(II) oxidation, compared to biofilms grown in control medium. Moreover, this enhancement on biofilm formation due to the addition of Mn(II) was only observed at 18°C. At this temperature, Mn(II) oxidation in membrane fractions collected from biofilms was induced by uncoupling oxidative phosphorylation from the electron transport chain with 2,4-Dinitrophenol. In Pseudomonas, a role for c-type cytochrome in Mn(II) oxidation has been demonstrated. Accordingly, transcriptional profiles of all terminal oxidases genes found in MOB-449 showed an induction of cytochrome c terminal oxidases expression mediated by Mn(II) oxidation at 18°C. Finally, heme peroxidase activity assays and MS analysis revealed that PetC, a cytochrome c5, and also CcmE, involved in the cytochrome c biogenesis machinery, are induced at 18°C only in the presence of Mn(II). These results present evidence supporting that cytochromes c and also the cytochrome c terminal oxidases are activated at low temperatures in the presence of Mn(II). Overall, this work demonstrate that in MOB-449 Mn(II) oxidation is activated at low temperatures to gain energy, suggesting that this process is important for survival under adverse environmental conditions and contributing to the understanding of the physiological role of bacterial Mn(II) oxidation.

Biologically mediated abiotic degradation (BMAD) of bisphenol A by manganese-oxidizing bacteria

Bisphenol A (BPA), a chemical of environmental concern, is recalcitrant under anoxic conditions, but is susceptible to oxidative degradation by manganese(IV)-oxide (MnO₂). Microbial Mn(II)-oxidation generates MnO_2-bio; however, BPA degradation in cultures of Mn(II)-oxidizing bacteria has not been explored. We assessed MnO_2-bio-mediated BPA degradation using three Mn(II)-oxidizing bacteria, Roseobacter sp. AzwK-3b, Erythrobacter sp. SD-21, and Pseudomonas putida GB-1. In cultures of all three strains, enhanced BPA degradation was evident in the presence of Mn(II) compared to replicate incubations without Mn(II), suggesting MnO_2-bio mediated BPA degradation. Increased Mn(II) concentrations up to 100 µM resulted in more MnO_2-bio formation but the highest BPA degradation rates were observed with 10 µM Mn(II). Compared to abiotic BPA degradation with 10 μM synthetic MnO₂, live cultures of strain GB-1 amended with 10 μM Mn(II) consumed 9-fold more BPA at about 5-fold higher rates. Growth of strain AzwK-3b was sensitive to BPA and the organism showed increased tolerance against BPA in the presence of Mn(II), suggesting MnO_2-bio alleviated the inhibition by mediating BPA degradation. The findings demonstrate that Mn(II)-oxidizing bacteria contribute to BPA degradation but organism-specific differences exist, and for biologically-mediated-abiotic-degradation (BMAD), Mn-flux, rather than the absolute amount of MnO_2-bio, is the key determinant for oxidation activity.

Manganese in Marine Microbiology

The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn²⁺), a potent oxidant (Mn³⁺) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.

Synthesis, crystal structure from PXRD of a MnII(purp)2complex, interaction with DNA at different temperatures and pH and lack of stimulated ROS formation by the complex

Mn^II(purpurin)₂crystal structure done from PXRD is the second report on hydroxy-9,10-anthraquinone with a 3d-transition metal. DNA binding of complex is better and ROS generation less than purpurin. Complex maintains biological activity of purpurin.

HipH Catalyzes the Hydroxylation of 4-Hydroxyisophthalate to Protocatechuate in 2,4-Xylenol Catabolism by Pseudomonas putida NCIMB 9866

In addition to growing on p-cresol, Pseudomonas putida NCIMB 9866 is the only reported strain capable of aerobically growing on 2,4-xylenol, which is listed as a priority pollutant by the U.S. Environmental Protection Agency. Several enzymes involved in the oxidation of the para-methyl group, as well as the corresponding genes, have previously been reported. The enzyme catalyzing oxidation of the catabolic intermediate 4-hydroxyisophthalate to the ring cleavage substrate protocatechuate was also purified from strain NCIMB 9866, but its genetic determinant is still unavailable. In this study, the gene hipH, encoding 4-hydroxyisophthalate hydroxylase, from strain NCIMB 9866 was cloned by transposon mutagenesis. Purified recombinant HipH-His6 was found to be a dimer protein with a molecular mass of approximately 110 kDa. HipH-His6 catalyzed the hydroxylation of 4-hydroxyisophthalate to protocatechuate with a specific activity of 1.54 U mg(-1) and showed apparent Km values of 11.40 ± 3.05 μM for 4-hydroxyisophthalate with NADPH and 11.23 ± 2.43 μM with NADH and similar Km values for NADPH and NADH (64.31 ± 13.16 and 72.76 ± 12.06 μM, respectively). The identity of protocatechuate generated from 4-hydroxyisophthalate hydroxylation by HipH-His6 has also been confirmed by high-performance liquid chromatography and mass spectrometry. Gene transcriptional analysis, gene knockout, and complementation indicated that hipH is essential for 2,4-xylenol catabolism but not for p-cresol catabolism in this strain. This fills a gap in our understanding of the gene that encodes a critical step in 2,4-xylenol catabolism and also provides another example of biochemical and genetic diversity of microbial catabolism of structurally similar compounds.

Absorption mechanisms of Cu(2+) on a biogenic bixbyite-like Mn2O3 produced by Bacillus CUA isolated from soil

BACKGROUND

Although most reported biogenic Mn oxides are hexagonal birnessites, other types of biogenic Mn oxides also commonly occur in the environment. However, sorption characteristics and underlying mechanisms of the adsorption of heavy-metal ions on these biogenic Mn oxides are still rarely addressed. In this study, the sorption mechanisms of Cu(II) on a low valence biogenic Mn oxide, poorly crystallized bixbyite-like Mn2O3 (α-Mn2O3), were investigated.

RESULTS

The maximum adsorption capacity of Cu(II) onto this biogenic Mn oxide at pH 6.00 was 796 mmol/kg (0.45 mol Cu mol(-1) Mn). The complex structure of adsorbed Cu(II) was constrained using Cu extended X-ray absorption fine structure (EXAFS) analysis, combined with structural parameters of the biogenic Mn oxide with alternately arranged regular and distorted MnO6 octahedra obtained through multiple-FEFF fitting of Mn EXAFS data. The sorbed Cu(II) was found to coordinate with the biogenic Mn oxide particle edges as inner-sphere complexes. At a relatively low Cu(2+) loading (233 mmol/kg, pH 6.00), Cu(II) adsorbed onto the biogenic Mn oxide with two types of coordinated complexes, i.e., (1) coordinated with one regular/distorted MnO6 octahedron as a monodentate-mononuclear complex and (2) with two adjacent MnO6 octahedra as a bidentate-binuclear complex. While, at a relatively high Cu(2+) loading (787 mmol/kg, pH 6.00), only one type of coordinated complex was constrained, the adsorbed Cu(II) coordinated with one regular/distorted MnO6 octahedron as a monodentate-mononuclear complex.

CONCLUSIONS

This research extends further insight into the bacterial Mn(II) oxidation in the environment and serves as a good reference for understanding the interactions between metal ions and biogenic low valence Mn oxides, which are still poorly explored either theoretically or practically.

Beyond iron: non-classical biological functions of bacterial siderophores

Bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. For over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. The importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiotic-resistant bacteria and the need to prevent the global rise of these superbugs. Increasing reports of siderophores functioning in capacities other than iron transport have appeared recently, but reports of "non-classical" siderophore functions have long paralleled those of iron transport. One particular non-classical function of these iron chelators, namely antibiotic activity, was documented before the role of siderophores in iron transport was established. In this Perspective, we present an exposition of past and current work into non-classical functions of siderophores and highlight the directions in which we anticipate that this research is headed. Examples include the ability of siderophores to function as zincophores, chalkophores, and metallophores for a variety of other metals, sequester heavy metal toxins, transport boron, act as signalling molecules, regulate oxidative stress, and provide antibacterial activity.

Manganese (Mn) oxidation increases intracellular Mn in Pseudomonas putida GB-1

Bacterial manganese (Mn) oxidation plays an important role in the global biogeochemical cycling of Mn and other compounds, and the diversity and prevalence of Mn oxidizers have been well established. Despite many hypotheses of why these bacteria may oxidize Mn, the physiological reasons remain elusive. Intracellular Mn levels were determined for Pseudomonas putida GB-1 grown in the presence or absence of Mn by inductively coupled plasma mass spectrometry (ICP-MS). Mn oxidizing wild type P. putida GB-1 had higher intracellular Mn than non Mn oxidizing mutants grown under the same conditions. P. putida GB-1 had a 5 fold increase in intracellular Mn compared to the non Mn oxidizing mutant P. putida GB-1-007 and a 59 fold increase in intracellular Mn compared to P. putida GB-1 ∆2665 ∆2447. The intracellular Mn is primarily associated with the less than 3 kDa fraction, suggesting it is not bound to protein. Protein oxidation levels in Mn oxidizing and non oxidizing cultures were relatively similar, yet Mn oxidation did increase survival of P. putida GB-1 when oxidatively stressed. This study is the first to link Mn oxidation to Mn homeostasis and oxidative stress protection.

Elimination of manganese(II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes

Bacterial manganese(II) oxidation impacts the redox cycling of Mn, other elements, and compounds in the environment; therefore, it is important to understand the mechanisms of and enzymes responsible for Mn(II) oxidation. In several Mn(II)-oxidizing organisms, the identified Mn(II) oxidase belongs to either the multicopper oxidase (MCO) or the heme peroxidase family of proteins. However, the identity of the oxidase in Pseudomonas putida GB-1 has long remained unknown. To identify the P. putida GB-1 oxidase, we searched its genome and found several homologues of known or suspected Mn(II) oxidase-encoding genes (mnxG, mofA, moxA, and mopA). To narrow this list, we assumed that the Mn(II) oxidase gene would be conserved among Mn(II)-oxidizing pseudomonads but not in nonoxidizers and performed a genome comparison to 11 Pseudomonas species. We further assumed that the oxidase gene would be regulated by MnxR, a transcription factor required for Mn(II) oxidation. Two loci met all these criteria: PputGB1_2447, which encodes an MCO homologous to MnxG, and PputGB1_2665, which encodes an MCO with very low homology to MofA. In-frame deletions of each locus resulted in strains that retained some ability to oxidize Mn(II) or Mn(III); loss of oxidation was attained only upon deletion of both genes. These results suggest that PputGB1_2447 and PputGB1_2665 encode two MCOs that are independently capable of oxidizing both Mn(II) and Mn(III). The purpose of this redundancy is unclear; however, differences in oxidation phenotype for the single mutants suggest specialization in function for the two enzymes.

Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida

Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments contaminated with high concentrations of heavy metals and organic contaminants. Pseudomonas putida strains are also found as plant growth-promoting rhizospheric and endophytic bacteria. The genome sequences of several P. putida species have become available and provide a unique tool to study the specific niche adaptation of the various P. putida strains. In this review, we compare the genomes of four P. putida strains: the rhizospheric strain KT2440, the endophytic strain W619, the aromatic hydrocarbon-degrading strain F1 and the manganese-oxidizing strain GB-1. Comparative genomics provided a powerful tool to gain new insights into the adaptation of P. putida to specific lifestyles and environmental niches, and clearly demonstrated that horizontal gene transfer played a key role in this adaptation process, as many of the niche-specific functions were found to be encoded on clearly defined genomic islands.

Identification of a two-component regulatory pathway essential for Mn(II) oxidation in Pseudomonas putida GB-1

Bacterial manganese(II) oxidation has a profound impact on the biogeochemical cycling of Mn and the availability of the trace metals adsorbed to the surfaces of solid Mn(III, IV) oxides. The Mn(II) oxidase enzyme was tentatively identified in Pseudomonas putida GB-1 via transposon mutagenesis: the mutant strain GB-1-007, which fails to oxidize Mn(II), harbors a transposon insertion in the gene cumA. cumA encodes a putative multicopper oxidase (MCO), a class of enzymes implicated in Mn(II) oxidation in other bacterial species. However, we show here that an in-frame deletion of cumA did not affect Mn(II) oxidation. Through complementation analysis of the oxidation defect in GB-1-007 with a cosmid library and subsequent sequencing of candidate genes we show the causative mutation to be a frameshift within the mnxS1 gene that encodes a putative sensor histidine kinase. The frameshift mutation results in a truncated protein lacking the kinase domain. Multicopy expression of mnxS1 restored Mn(II) oxidation to GB-1-007 and in-frame deletion of mnxS1 resulted in a loss of oxidation in the wild-type strain. These results clearly demonstrated that the oxidation defect of GB-1-007 is due to disruption of mnxS1, not cumA::Tn5, and that CumA is not the Mn(II) oxidase. mnxS1 is located upstream of a second sensor histidine kinase gene, mnxS2, and a response regulator gene, mnxR. In-frame deletions of each of these genes also led to the loss of Mn(II) oxidation. Therefore, we conclude that the MnxS1/MnxS2/MnxR two-component regulatory pathway is essential for Mn(II) oxidation in P. putida GB-1.

Iron requirement for Mn(II) oxidation by Leptothrix discophora SS-1

A common form of biocatalysis of Mn(II) oxidation results in the formation of biogenic Mn(III, IV) oxides and is a key reaction in the geochemical cycling of Mn. In this study, we grew the model Mn(II)-oxidizing bacterium Leptothrix discophora SS-1 in media with limited iron (0.1 microM iron/5.8 mM pyruvate) and sufficient iron (0.2 microM iron/5.8 mM pyruvate). The influence of iron on the rate of extracellular Mn(II) oxidation was evaluated. Cultures in which cell growth was limited by iron exhibited reduced abilities to oxidize Mn(II) compared to cultures in medium with sufficient iron. While the extracellular Mn(II)-oxidizing factor (MOF) is thought to be a putative multicopper oxidase, Mn(II) oxidation in the presence of zero added Cu(II) was detected and the decrease in the observed Mn(II) oxidation rate in iron-limited cultures was not relieved when the medium was supplemented with Cu(II). The decline of Mn(II) oxidation under iron-limited conditions was not accompanied by siderophore production and is unlikely to be an artifact of siderophore complex formation with Mn(III). The temporal variations in mofA gene transcript levels under conditions of limited and abundant iron were similar, indicating that iron limitation did not interfere with the transcription of the mofA gene. Our quantitative PCR results provide a step forward in understanding the regulation of Mn(II) oxidation. The mechanistic role of iron in Mn(II) oxidation is uncertain; the data are consistent with a direct requirement for iron as a component of the MOF or an indirect effect of iron resulting from the limitation of one of many cellular functions requiring iron.

Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-Like bacterium

Bacteria belonging to the Roseobacter clade of the alpha-Proteobacteria occupy a wide range of environmental niches and are numerically abundant in coastal waters. Here we reveal that Roseobacter-like bacteria may play a previously unrecognized role in the oxidation and cycling of manganese (Mn) in coastal waters. A diverse array of Mn(II)-oxidizing Roseobacter-like species were isolated from Elkhorn Slough, a coastal estuary adjacent to Monterey Bay in California. One isolate (designated AzwK-3b), in particular, rapidly oxidizes Mn(II) to insoluble Mn(III, IV) oxides. Interestingly, AzwK-3b is 100% identical (at the 16S rRNA gene level) to a previously described Pfiesteria-associated Roseobacter-like bacterium, which is not able to oxidize Mn(II). The rates of manganese(II) oxidation by live cultures and cell-free filtrates are substantially higher when the preparations are incubated in the presence of light. The rates of oxidation by washed cell extracts, however, are light independent. Thus, AzwK-3b invokes two Mn(II) oxidation mechanisms when it is incubated in the presence of light, in contrast to the predominantly direct enzymatic oxidation in the dark. In the presence of light, production of photochemically active metabolites is coupled with initial direct enzymatic Mn(II) oxidation, resulting in higher Mn(II) oxidation rates. Thus, Roseobacter-like bacteria may not only play a previously unrecognized role in Mn(II) oxidation and cycling in coastal surface waters but also induce a novel photooxidation pathway that provides an alternative means of Mn(II) oxidation in the photic zone.

Covalent cofactor attachment to proteins: cytochrome c biogenesis

Haem (Fe-protoporphyrin IX) is a cofactor found in a wide variety of proteins. It confers diverse functions, including electron transfer, the binding and sensing of gases, and many types of catalysis. The majority of cofactors are non-covalently attached to proteins. There are, however, some proteins in which the cofactor binds covalently and one of the major protein classes characterized by covalent cofactor attachment is the c-type cytochromes. The characteristic haem-binding mode of c-type cytochromes requires the formation of two covalent bonds between two cysteine residues in the protein and the two vinyl groups of haem. Haem attachment is a complex post-translational process that, in bacteria such as Escherichia coli, occurs in the periplasmic space and involves the participation of many proteins. Unexpectedly, it has been found that the haem chaperone CcmE (cytochrome c maturation), which is an essential intermediate in the process, also binds haem covalently before transferring the haem to apocytochromes. A single covalent bond is involved and occurs between a haem vinyl group and a histidine residue of CcmE. Several in vitro and in vivo studies have provided insight into the function of this protein and into the overall process of cytochrome c biogenesis.

Geomicrobiology of manganese(II) oxidation

Mn(II)-oxidizing microbes have an integral role in the biogeochemical cycling of manganese, iron, nitrogen, carbon, sulfur, and several nutrients and trace metals. There is great interest in mechanistically understanding these cycles and defining the importance of Mn(II)-oxidizing bacteria in modern and ancient geochemical environments. Linking Mn(II) oxidation to cellular function, although still enigmatic, continues to drive efforts to characterize manganese biomineralization. Recently, complexed-Mn(III) has been shown to be a transient intermediate in Mn(II) oxidation to Mn(IV), suggesting that the reaction might involve a unique multicopper oxidase system capable of a two-electron oxidation of the substrate. In biogenic and abiotic synthesis experiments, the application of synchrotron-based X-ray scattering and spectroscopic techniques has significantly increased our understanding of the oxidation state and relatively amorphous structure (i.e. delta-MnO(2)-like) of biogenic oxides, providing a new blueprint for the structural signature of biogenic Mn oxides.

Overproduction of CcmG and CcmFH(Rc) fully suppresses the c-type cytochrome biogenesis defect of Rhodobacter capsulatus CcmI-null mutants

Gram-negative bacteria like Rhodobacter capsulatus use intertwined pathways to carry out the posttranslational maturation of c-type cytochromes (Cyts). This periplasmic process requires at least 10 essential components for apo-Cyt c chaperoning, thio-oxidoreduction, and the delivery of heme and its covalent ligation. One of these components, CcmI (also called CycH), is thought to act as an apo-Cyt c chaperone. In R. capsulatus, CcmI-null mutants are unable to produce c-type Cyts and thus sustain photosynthetic (Ps) growth. Previously, we have shown that overproduction of the putative heme ligation components CcmF and CcmH(Rc) (also called Ccl1 and Ccl2) can partially bypass the function of CcmI on minimal, but not on enriched, media. Here, we demonstrate that either additional overproduction of CcmG (also called HelX) or hyperproduction of CcmF-CcmH(Rc) is needed to completely overcome the role of CcmI during the biogenesis of c-type Cyts on both minimal and enriched media. These findings indicate that, in the absence of CcmI, interactions between the heme ligation and thioreduction pathways become restricted for sufficient Cyt c production. We therefore suggest that CcmI, along with its apo-Cyt chaperoning function, is also critical for the efficacy of holo-Cyt c formation, possibly via its close interactions with other components performing the final heme ligation steps during Cyt c biogenesis.

Impact of the bacterial type I cytochromecmaturation system on different biological processes

In the alpha-, beta- and gamma-Proteobacteria, the so-called cytochrome c maturation (Ccm) system is known to promote the covalent attachment of the haem to periplasmic apocytochrome c. However, in species of Pseudomonas, Rhizobium, Paracoccus and Legionella, mutations in ccm genes result in phenotypes that cannot be readily explained by the simple loss of a c-type cytochrome. These phenotypes include loss of siderophore production and utilization, reduced abilities to grow in low-iron conditions and in mammalian and protozoan host cells, and alterations in copper sensitivity and manganese oxidation. These various data suggest that Ccm proteins may perform one or more functions in addition to Ccm, which are critical for bacterial physiology and growth. Novel hypotheses that should be explored include the utilization of Ccm-associated haem for processes besides attachment to apocytochrome c, the export of a non-haem compound through the Ccm system, and the negative effects of protoporphyrin IX accumulation.

Microbially influenced corrosion as a model system for the study of metal microbe interactions: a unifying electron transfer hypothesis

The general term biomineralisation refers to biologically induced mineralisation in which an organism modifies its local microenvironment creating conditions such that there is chemical precipitation of mineral phases extracellularly. Most usually this results from an oxidation or reduction carried out by some microbial species, with the formation of a recognised biomineralised product. These reactions play a major role in microbial physiology and ecology, and are of central importance to such engineering consequences as microbial mining and microbially influenced corrosion. This paper will examine metal microbe interactions, both in naturally occurring microbial ecosystems and in two particular cases of biocorrosion, with the objective of putting forward a unifying hypothesis relevant to the understanding of each of these apparently disparate processes.

Identification of a novel Gsp-related pathway required for secretion of the manganese-oxidizing factor of Pseudomonas putida strain GB-1

The manganese-oxidizing factor of Pseudomonas putida strain GB-1 is associated with the outer membrane. One of the systems of protein transport across the outer membrane is the general secretory pathway (Gsp). The gsp genes are called xcp in Pseudomonas species. In a previous study, it was shown that mutation of the prepilin peptidase XcpA and of a homologue of the pseudopilin XcpT inhibited transport of the factor. In the present study, we describe the genomic region flanking the xcpT homologue (designated xcmT1). We show that xcmT1 is part of a two-gene operon that includes an xcpS homologue (designated xcmS). No other xcp-like genes are present in the regions flanking the xcmT1/xcmS cluster. We also characterized the site of transposon insertion of another transport mutant of P. putida GB-1. This insertion appeared to be located in a gene (designated xcmX) possibly encoding another pseudopilin-related protein. This xcmX is clustered with two other xcpT-related genes (designated xcmT2 and xcmT3) on one side and homologues of three csg genes (designated csmE, csmF and csmG) on the other side. The csg genes are involved in production of aggregative fibres in Escherichia coli and Salmonella typhimurium. A search for XcmX homologues revealed that the recently published genome of Ralstonia solanacearum and the unannotated genome of P. putida KT2440 contain comparable gene clusters with xcmX and xcp homologues that are different from the well-described 'regular'xcp/gsp clusters. They do contain xcpR and xcpQ homologues but, for example, homologues of xcpP, Y and Z are lacking. The results suggest a novel Xcp-related system for the transport of manganese-oxidizing enzymes to the cell surface.

Biochemistry, regulation and genomics of haem biosynthesis in prokaryotes

Haems are involved in many cellular processes in prokaryotes and eukaryotes. The biosynthetic pathway leading to haem formation is, with few exceptions, well-conserved, and is controlled in accordance with cellular function. Here, we review the biosynthesis of haem and its regulation in prokaryotes. In addition, we focus on a modification of haem for cytochrome c biogenesis, a complex process that entails both transport between cellular compartments and a specific thioether linkage between the haem moiety and the apoprotein. Finally, a whole genome analysis from 63 prokaryotes indicates intriguing exceptions to the universality of the haem biosynthetic pathway and helps define new frontiers for future study.

The cytochrome c maturation locus of Legionella pneumophila promotes iron assimilation and intracellular infection and contains a strain-specific insertion sequence element

Previously, we obtained a Legionella pneumophila mutant, NU208, that is hypersensitive to iron chelators when grown on standard Legionella media. Here, we demonstrate that NU208 is also impaired for growth in media that simply lack their iron supplement. The mutant was not, however, impaired for the production of legiobactin, the only known L. pneumophila siderophore. Importantly, NU208 was also highly defective for intracellular growth in human U937 cell macrophages and Hartmannella and Acanthamoeba amoebae. The growth defect within macrophages was exacerbated by treatment of the host cells with an iron chelator. Sequence analysis demonstrated that the transposon disruption in NU208 lies within an open reading frame that is highly similar to the cytochrome c maturation gene, ccmC. CcmC is generally recognized for its role in the heme export step of cytochrome biogenesis. Indeed, NU208 lacked cytochrome c. Phenotypic analysis of two additional, independently derived ccmC mutants confirmed that the growth defect in low-iron medium and impaired infectivity were associated with the transposon insertion and not an entirely spontaneous second-site mutation. trans-complementation analysis of NU208 confirmed that L. pneumophila ccmC is required for cytochrome c production, growth under low-iron growth conditions, and at least some forms of intracellular infection. Although ccm genes have recently been implicated in iron assimilation, our data indicate, for the first time, that a ccm gene can be required for bacterial growth in an intracellular niche. Complete sequence analysis of the ccm locus from strain 130b identified the genes ccmA-H. Interestingly, however, we also observed that a 1.8-kb insertion sequence element was positioned between ccmB and ccmC. Southern hybridizations indicated that the open reading frame within this element (ISLp 1) was present in multiple copies in some strains of L. pneumophila but was absent from others. These findings represent the first evidence for a transposable element in Legionella and the first identification of an L. pneumophila strain-specific gene.

Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species

Bacterial spores are renowned for their longevity, ubiquity, and resistance to environmental insults, but virtually nothing is known regarding whether these metabolically dormant structures impact their surrounding chemical environments. In the present study, a number of spore-forming bacteria that produce dormant spores which enzymatically oxidize soluble Mn(II) to insoluble Mn(IV) oxides were isolated from coastal marine sediments. The highly charged and reactive surfaces of biogenic metal oxides dramatically influence the oxidation and sorption of both trace metals and organics in the environment. Prior to this study, the only known Mn(II)-oxidizing sporeformer was the marine Bacillus sp. strain SG-1, an extensively studied bacterium in which Mn(II) oxidation is believed to be catalyzed by a multicopper oxidase, MnxG. Phylogenetic analysis based on 16S rRNA and mnxG sequences obtained from 15 different Mn(II)-oxidizing sporeformers (including SG-1) revealed extensive diversity within the genus Bacillus, with organisms falling into several distinct clusters and lineages. In addition, active Mn(II)-oxidizing proteins of various sizes, as observed in sodium dodecyl sulfate-polyacrylamide electrophoresis gels, were recovered from the outer layers of purified dormant spores of the isolates. These are the first active Mn(II)-oxidizing enzymes identified in spores or gram-positive bacteria. Although extremely resistant to denaturation, the activities of these enzymes were inhibited by azide and o-phenanthroline, consistent with the involvement of multicopper oxidases. Overall, these studies suggest that the commonly held view that bacterial spores are merely inactive structures in the environment should be revised.

Enzymatic manganese(II) oxidation by a marine alpha-proteobacterium

A yellow-pigmented marine bacterium, designated strain SD-21, was isolated from surface sediments of San Diego Bay, San Diego, Calif., based on its ability to oxidize soluble Mn(II) to insoluble Mn(III, IV) oxides. 16S rRNA analysis revealed that this organism was most closely related to members of the genus Erythrobacter, aerobic anoxygenic phototrophic bacteria within the alpha-4 subgroup of the Proteobacteria (alpha-4 Proteobacteria). SD-21, however, has a number of distinguishing phenotypic features relative to Erythrobacter species, including the ability to oxidize Mn(II). During the logarithmic phase of growth, this organism produces Mn(II)-oxidizing factors of approximately 250 and 150 kDa that are heat labile and inhibited by both azide and o-phenanthroline, suggesting the involvement of a metalloenzyme. Although the expression of the Mn(II) oxidase was not dependent on the presence of Mn(II), higher overall growth yields were reached in cultures incubated with Mn(II) in the culture medium. In addition, the rate of Mn(II) oxidation appeared to be slower in cultures grown in the light. This is the first report of Mn(II) oxidation within the alpha-4 Proteobacteria as well as the first Mn(II)-oxidizing proteins identified in a marine gram-negative bacterium.

cumA multicopper oxidase genes from diverse Mn(II)-oxidizing and non-Mn(II)-oxidizing Pseudomonas strains

A multicopper oxidase gene, cumA, required for Mn(II) oxidation was recently identified in Pseudomonas putida strain GB-1. In the present study, degenerate primers based on the putative copper-binding regions of the cumA gene product were used to PCR amplify cumA gene sequences from a variety of Pseudomonas strains, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. The presence of highly conserved cumA gene sequences in several apparently non-Mn(II)-oxidizing Pseudomonas strains suggests that this gene may not be expressed, may not be sufficient alone to confer the ability to oxidize Mn(II), or may have an alternative function in these organisms. Phylogenetic analysis of both CumA and 16S rRNA sequences revealed similar topologies between the respective trees, including the presence of several distinct phylogenetic clusters. Overall, our results indicate that both the cumA gene and the capacity to oxidize Mn(II) occur in phylogenetically diverse Pseudomonas strains.

A putative ECF sigma factor gene, rpol, regulates siderophore production in Rhizobium leguminosarum

A cloned Rhizobium leguminosarum gene, termed rpoI, when transferred to wild-type strains, caused overproduction of the siderophore vicibactin. An rpoI mutant was defective in Fe uptake but was unaffected in symbiotic N2 fixation. The RpoI gene product was similar in sequence to extra-cytoplasmic sigma factors of RNA polymerase. Transcription of rpoI was reduced in cells grown in medium that was replete with Fe.

cumA, a gene encoding a multicopper oxidase, is involved in Mn2+ oxidation in Pseudomonas putida GB-1

Pseudomonas putida GB-1-002 catalyzes the oxidation of Mn2+. Nucleotide sequence analysis of the transposon insertion site of a nonoxidizing mutant revealed a gene (designated cumA) encoding a protein homologous to multicopper oxidases. Addition of Cu2+ increased the Mn2+-oxidizing activity of the P. putida wild type by a factor of approximately 5. The growth rates of the wild type and the mutant were not affected by added Cu2+. A second open reading frame (designated cumB) is located downstream from cumA. Both cumA and cumB probably are part of a single operon. The translation product of cumB was homologous (level of identity, 45%) to that of orf74 of Bradyrhizobium japonicum. A mutation in orf74 resulted in an extended lag phase and lower cell densities. Similar growth-related observations were made for the cumA mutant, suggesting that the cumA mutation may have a polar effect on cumB. This was confirmed by site-specific gene replacement in cumB. The cumB mutation did not affect the Mn2+-oxidizing ability of the organism but resulted in decreased growth. In summary, our data indicate that the multicopper oxidase CumA is involved in the oxidation of Mn2+ and that CumB is required for optimal growth of P. putida GB-1-002.

c-type cytochromes and manganese oxidation in Pseudomonas putida MnB1

Pseudomonas putida MnB1 is an isolate from an Mn oxide-encrusted pipeline that can oxidize Mn(II) to Mn oxides. We used transposon mutagenesis to construct mutants of strain MnB1 that are unable to oxidize manganese, and we characterized some of these mutants. The mutants were divided into three groups: mutants defective in the biogenesis of c-type cytochromes, mutants defective in genes that encode key enzymes of the tricarboxylic acid cycle, and mutants defective in the biosynthesis of tryptophan. The mutants in the first two groups were cytochrome c oxidase negative and did not contain c-type cytochromes. Mn(II) oxidation capability could be recovered in a c-type cytochrome biogenesis-defective mutant by complementation of the mutation.