Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.
- MeSH
- ATP-Binding Cassette Transporters genetics MeSH
- Anti-Bacterial Agents pharmacology MeSH
- Bacterial Toxins * MeSH
- Clostridioides difficile * genetics MeSH
- Metagenome MeSH
- Paracoccus * genetics MeSH
- Soil chemistry MeSH
- Metals, Heavy * MeSH
- DNA Transposable Elements MeSH
- Hydrocarbons MeSH
- Publication type
- Journal Article MeSH
Whey, the main by-product obtained from the manufacture of cheese, which contains a very high organic load (mainly due to the lactose content), is not easily degradable and creates concern over environmental issues. Hydrolysis of lactose present in whey and conversion of whey lactose into valuable products such as bioethanol, sweet syrup, and animal feed offers the possibility of whey bioremediation. The increasing need for bioremediation in the dairy industry has compelled researchers to search for a novel source of β-galactosidase with diverse properties. In the present study, the bacterium Paracoccus marcusii KGP producing β-galactosidase was subjected to morphological, biochemical, and probiotic characterisation. The bacterial isolate was found to be non-pathogenic and resistant to low pH (3 and 4), bile salts (0.2%), salt (10%), pepsin (at pH 3), and pancreatin (at pH 8). Further characterisation revealed that the bacteria have a good auto-aggregation ability (40% at 24 h), higher hydrophobicity (chloroform-60%, xylene-50%, and ethyl acetate-40%) and a broad spectrum of antibiotic susceptibility. The highest growth of P. marcusii KGP was achieved at pH 7 and 28 °C, and the yeast extract, galactose, and MgSO4 were the best for the growth of the bacterial cells. The bacterium KGP was able to utilise whey as a substrate for its growth with good β-galactosidase production potential. Furthermore, the β-galactosidase extracted from the isolate KGP could hydrolyse 47% whey lactose efficiently at 50 °C. The study thus reveals the potential application of β-galactosidase from P. marcusii KGP in whey bioremediation.
- MeSH
- Biodegradation, Environmental MeSH
- Dairying MeSH
- Paracoccus * metabolism MeSH
- Probiotics * metabolism MeSH
- Industrial Waste * MeSH
- Whey * microbiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
- MeSH
- Bacteriophages genetics physiology ultrastructure MeSH
- DNA, Bacterial genetics MeSH
- Cryoelectron Microscopy MeSH
- Gene Transfer, Horizontal MeSH
- Gene Expression Regulation, Bacterial MeSH
- Rhodobacter capsulatus genetics virology MeSH
- Siphoviridae genetics physiology ultrastructure MeSH
- Gene Transfer Techniques * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
A new β-galactosidase-producing bacterium KGP, isolated from the Bay of Bengal, was identified as Paracoccus marcusii through morphology, biochemistry and 16S rRNA sequencing. This study is the first report on the production of β-galactosidase from P. marcusii. The medium components for the high yield of β-galactosidase were optimised using response surface methodology (RSM). A set of 17 experiments consisting of three independent variables, viz. yeast extract, galactose and MgSO4, was employed. A second-order polynomial equation was used for the analysis of the response, and the optimum β-galactosidase yield was achieved using 12.5 g/L yeast extract, 12.5 g/L galactose and 12.5 mmol/L MgSO4. The predicted quadratic model was inferred to be significant from the F-value, P value and the lack of fit value. Optimisation of the media components resulted in a ninefold increase (560 Miller units) in β-galactosidase production. Furthermore, the hydrolysis and transgalactosylation efficiency of the crude β-galactosidase was assessed and the results showed that the lactose was successfully hydrolysed and transgalactosylated at an optimum temperature of 40 °C and 50 °C, respectively. Considering the overall yield and productivity, P. marcusii can be considered a candidate for the industrial production of β-galactosidase. This study provides an essential basis for the future production and use of the alkali-tolerant β-galactosidase from P. marcusii KGP.
- MeSH
- beta-Galactosidase metabolism MeSH
- Bioreactors MeSH
- Phylogeny MeSH
- Galactose metabolism MeSH
- Hydrolysis MeSH
- Hydrogen-Ion Concentration MeSH
- Lactose metabolism MeSH
- Oligosaccharides biosynthesis MeSH
- Paracoccus classification genetics isolation & purification metabolism MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Temperature MeSH
- Publication type
- Journal Article MeSH
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
The creamy white to beige, aerobic, non-motile, ovoid to rod-shaped, Gram-stain-negative strain, Cd-10T, was isolated from heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory based on its ability to tolerate CdCl2 in the cultivation medium. In the reconstruction of its phylogeny based on 16S rRNA gene sequences, strain Cd-10T clustered with species of the genera Gemmobacter, Xinfangfangia, Tabrizicola and Rhodobacter within the family Rhodobacteraceae. Its 16S rRNA gene sequence exhibited 96.32 % pairwise similarity to the type strain of Xinfangfangia soli, 95.3 % to that of Gemmobacter intermedius, followed by Tabrizicola fusiformis (95.10 %), Rhodobacter sediminis (94.88 %), Gemmobacter nectariphilus and Rhodobacter capsulatus (both 94.81 %). The major respiratory quinone was Q-10 accompanied by Q-9, the fatty acid profile consisted predominantly of C18 : 1ω7c, C18 : 0, C16 : 0 and C16 : 1ω7c, the major polar lipids were phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and diphosphatidylglycerol. An analysis of the percentage of conserved proteins deduced from draft or complete genomic sequences of strain Cd-10T and representatives of its closest relatives suggested that strain Cd-10T is a member of a novel genus within the Rhodobacteraceae family for which we propose the name Pseudogemmobacter. Strain Cd-10T (=DSM 103618T=NCCB 100645T) is the type strain of Pseudogemmobacter bohemicus gen. nov., sp. nov., the type species of the genus Pseudogemmobacter gen. nov.
- MeSH
- DNA, Bacterial genetics MeSH
- Phospholipids chemistry MeSH
- Phylogeny * MeSH
- Fatty Acids chemistry MeSH
- Sewage microbiology MeSH
- Rhodobacteraceae classification isolation & purification MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Sequence Analysis, DNA MeSH
- Bacterial Typing Techniques MeSH
- Metals, Heavy * MeSH
- Ubiquinone analogs & derivatives chemistry MeSH
- Base Composition MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Pden_5119, annotated as an NADPH-dependent FMN reductase, shows homology to proteins assisting in utilization of alkanesulfonates in other bacteria. Here, we report that inactivation of the pden_5119 gene increased susceptibility to oxidative stress, decreased growth rate and increased growth yield; growth on lower alkanesulfonates as sulfur sources was not specifically influenced. Pden_5119 transcript rose in response to oxidative stressors, respiratory chain inhibitors and terminal oxidase downregulation. Kinetic analysis of a fusion protein suggested a sequential mechanism in which FMN binds first, followed by NADH. The affinity of flavin toward the protein decreased only slightly upon reduction. The observed strong viscosity dependence of kcat demonstrated that reduced FMN formed tends to remain bound to the enzyme where it can be re-oxidized by oxygen or, less efficiently, by various artificial electron acceptors. Stopped flow data were consistent with the enzyme-FMN complex being a functional oxidase that conducts the reduction of oxygen by NADH. Hydrogen peroxide was identified as the main product. As shown by isotope effects, hydride transfer occurs from the pro-S C4 position of the nicotinamide ring and partially limits the overall turnover rate. Collectively, our results point to a role for the Pden_5119 protein in maintaining the cellular redox state.
- MeSH
- Flavin-Adenine Dinucleotide metabolism MeSH
- Flavin Mononucleotide metabolism MeSH
- Flavins metabolism MeSH
- FMN Reductase genetics metabolism MeSH
- NADP MeSH
- NADPH-Ferrihemoprotein Reductase metabolism MeSH
- Oxidation-Reduction MeSH
- Paracoccus denitrificans genetics metabolism MeSH
- Amino Acid Sequence genetics MeSH
- Protein Structure, Tertiary MeSH
- Electron Transport MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Ferric reductase B (FerB) is a flavin mononucleotide (FMN)-containing NAD(P)H:acceptor oxidoreductase structurally close to the Gluconacetobacter hansenii chromate reductase (ChrR). The crystal structure of ChrR was previously determined with a chloride bound proximal to FMN in the vicinity of Arg101, and the authors suggested that the anionic electron acceptors, chromate and uranyl tricarbonate, bind similarly. Here, we identify the corresponding arginine residue in FerB (Arg95) as being important for the reaction of FerB with superoxide. Four mutants at position 95 were prepared and found kinetically to have impaired capacity for superoxide binding. Stopped-flow data for the flavin cofactor showed that the oxidative step is rate limiting for catalytic turnover. The findings are consistent with a role for FerB as a superoxide scavenging contributor.
- MeSH
- Arginine genetics MeSH
- Flavin Mononucleotide chemistry genetics MeSH
- Flavins genetics metabolism MeSH
- FMN Reductase chemistry genetics MeSH
- Catalytic Domain genetics MeSH
- Kinetics MeSH
- Protein Conformation * MeSH
- Crystallography, X-Ray MeSH
- Oxidation-Reduction MeSH
- Oxidoreductases chemistry genetics MeSH
- Paracoccus denitrificans chemistry enzymology MeSH
- Amino Acid Sequence genetics MeSH
- Superoxides metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Aerobic anoxygenic photosynthetic bacteria are an important component of marine microbial communities. They produce energy in light using bacteriochlorophyll a containing photosystems. This extra energy provides an advantage over purely heterotrophic bacteria. One of the most intensively studied AAP bacteria is Dinoroseobacter shibae, a member of the environmentally important Roseobacter clade. Light stimulates its growth and metabolism, but the effect of light intensity remains unclear. Here, we show that an increase in biomass along an irradiance gradient followed the exponential rise to the maximum curve, with saturation at about 300 µmol photons m-2 s-1 , without any inhibition at light intensities up to 600 µmol photons m-2 s-1 . The cells adapted to higher irradiance by reducing pigmentation and increasing the electron transfer rate. This additional energy allowed D. shibae to redirect the metabolism of organic carbon sources such as glucose, leucine, glutamate, acetate and pyruvate toward anabolism, resulting in a twofold increase of their assimilation rates. We provide equations that can be feasibly incorporated into the existing model of D. shibae metabolism to further advance our understanding of the role of photoheterotrophy in the ocean.
- MeSH
- Bacteriochlorophyll A metabolism MeSH
- Biomass MeSH
- Energy Metabolism physiology MeSH
- Photosynthesis physiology MeSH
- Organic Chemicals metabolism MeSH
- Roseobacter metabolism MeSH
- Light MeSH
- Electron Transport physiology MeSH
- Aquatic Organisms metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na+/H+ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.
