scholarly journals Involvement of Vitamin B6Biosynthesis Pathways in the Insecticidal Activity of Photorhabdus luminescens

2016 ◽  
Vol 82 (12) ◽  
pp. 3546-3553 ◽  
Author(s):  
Kazuki Sato ◽  
Toyoshi Yoshiga ◽  
Koichi Hasegawa
Keyword(s):  
Insecticidal Activity ◽  
Genetic Screening ◽  
De Novo ◽  
Entomopathogenic Nematode ◽  
Vitamin B ◽  
Photorhabdus Luminescens ◽  
Content Type ◽  
C Elegans ◽  
Growth Deficiency ◽  
Highly Virulent

ABSTRACTPhotorhabdus luminescensis a Gram-negative entomopathogenic bacterium which symbiotically associates with the entomopathogenic nematodeHeterorhabditis bacteriophora.P. luminescensis highly virulent to many insects and nonsymbiotic nematodes, includingCaenorhabditis elegans. To understand the virulence mechanisms ofP. luminescens, we obtained virulence-deficient and -attenuated mutants againstC. elegansthrough a transposon-mutagenized library. From the genetic screening, we identified thepdxBgene, encoding erythronate-4-phosphate dehydrogenase, as required forde novovitamin B6biosynthesis. Mutation inpdxBcaused growth deficiency ofP. luminescensin nutrient-poor medium, which was restored under nutrient-rich conditions or by supplementation with pyridoxal 5′-phosphate (PLP), an active form of vitamin B6. Supplementation with three other B6vitamers (pyridoxal, pyridoxine, and pyridoxamine) also restored the growth of thepdxBmutant, suggesting the existence of a salvage pathway for vitamin B6biosynthesis inP. luminescens. Moreover, supplementation with PLP restored the virulence-deficient phenotype againstC. elegans. Combining these results with the fact thatpdxBmutation also caused attenuation of insecticidal activity, we concluded that the production of appropriate amounts of vitamin B6is critical forP. luminescenspathogenicity.IMPORTANCEThe Gram-negative entomopathogenic bacteriumPhotorhabdus luminescenssymbiotically associates with the entomopathogenic nematodeHeterorhabditis bacteriophora.P. luminescensis highly virulent to many insects and nonsymbiotic nematodes, includingCaenorhabditis elegans. We have obtained several virulence-deficient and -attenuatedP. luminescensmutants againstC. elegansthrough genetic screening. From the genetic analysis, we present the vitamin B6biosynthetic pathways inP. luminescensthat are important for its insecticidal activity. Mutation inpdxB, encoding erythronate-4-phosphate dehydrogenase and required for thede novovitamin B6biosynthesis pathway, caused virulence deficiency againstC. elegansand growth deficiency ofP. luminescensin nutrient-poor medium. Because such phenotypes were restored under nutrient-rich conditions or by supplementation with B6vitamers, we showed the presence of the two vitamin B6synthetic pathways (de novoand salvage) inP. luminescensand also showed that the ability to produce an appropriate amount of vitamin B6is critical forP. luminescenspathogenicity.

scholarly journals Impact of Vitamin B12on Formation of the Tetrachloroethene Reductive Dehalogenase in Desulfitobacterium hafniense Strain Y51

2012 ◽  
Vol 78 (22) ◽  
pp. 8025-8032 ◽  
Author(s):  
Anika Reinhold ◽  
Martin Westermann ◽  
Jana Seifert ◽  
Martin von Bergen ◽  
Torsten Schubert ◽  
...  
Keyword(s):  
Gene Cluster ◽  
De Novo ◽  
Anaerobic Bacteria ◽  
Vitamin B ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Gene Level ◽  
Desulfitobacterium Hafniense ◽  
Pce Dehalogenase ◽  
The Impact

ABSTRACTCorrinoids are essential cofactors of reductive dehalogenases in anaerobic bacteria. Microorganisms mediating reductive dechlorination as part of their energy metabolism are either capable ofde novocorrinoid biosynthesis (e.g.,Desulfitobacteriumspp.) or dependent on exogenous vitamin B12(e.g.,Dehalococcoidesspp.). In this study, the impact of exogenous vitamin B12(cyanocobalamin) and of tetrachloroethene (PCE) on the synthesis and the subcellular localization of the reductive PCE dehalogenase was investigated in the Gram-positiveDesulfitobacterium hafniensestrain Y51, a bacterium able to synthesize corrinoidsde novo. PCE-depleted cells grown for several subcultivation steps on fumarate as an alternative electron acceptor lost the tetrachloroethene-reductive dehalogenase (PceA) activity by the transposition of thepcegene cluster. In the absence of vitamin B12, a gradual decrease of the PceA activity and protein amount was observed; after 5 subcultivation steps with 10% inoculum, more than 90% of the enzyme activity and of the PceA protein was lost. In the presence of vitamin B12, a significant delay in the decrease of the PceA activity with an ∼90% loss after 20 subcultivation steps was observed. This corresponded to the decrease in thepceAgene level, indicating that exogenous vitamin B12hampered the transposition of thepcegene cluster. In the absence or presence of exogenous vitamin B12, the intracellular corrinoid level decreased in fumarate-grown cells and the PceA precursor formed catalytically inactive, corrinoid-free multiprotein aggregates. The data indicate that exogenous vitamin B12is not incorporated into the PceA precursor, even though it affects the transposition of thepcegene cluster.

scholarly journals Flexible Cobamide Metabolism in Clostridioides (Clostridium) difficile 630 Δerm

2019 ◽  
Vol 202 (2) ◽  
Author(s):  
Amanda N. Shelton ◽  
Xun Lyu ◽  
Michiko E. Taga
Keyword(s):  
De Novo ◽  
Aminolevulinic Acid ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Vitamin B ◽  
Uptake System ◽  
Human Gut ◽  
Content Type ◽  
Clostridioides Difficile

ABSTRACT Clostridioides (Clostridium) difficile is an opportunistic pathogen known for its ability to colonize the human gut under conditions of dysbiosis. Several aspects of its carbon and amino acid metabolism have been investigated, but its cobamide (vitamin B12 and related cofactors) metabolism remains largely unexplored. C. difficile has seven predicted cobamide-dependent pathways encoded in its genome in addition to a nearly complete cobamide biosynthesis pathway and a cobamide uptake system. To address the importance of cobamides to C. difficile, we studied C. difficile 630 Δerm and mutant derivatives under cobamide-dependent conditions in vitro. Our results show that C. difficile can use a surprisingly diverse array of cobamides for methionine and deoxyribonucleotide synthesis and can use alternative metabolites or enzymes, respectively, to bypass these cobamide-dependent processes. C. difficile 630 Δerm produces the cobamide pseudocobalamin when provided the early precursor 5-aminolevulinic acid or the late intermediate cobinamide (Cbi) and produces other cobamides if provided an alternative lower ligand. The ability of C. difficile 630 Δerm to take up cobamides and Cbi at micromolar or lower concentrations requires the transporter BtuFCD. Genomic analysis revealed genetic variations in the btuFCD loci of different C. difficile strains, which may result in differences in the ability to take up cobamides and Cbi. These results together demonstrate that, like other aspects of its physiology, cobamide metabolism in C. difficile is versatile. IMPORTANCE The ability of the opportunistic pathogen Clostridioides difficile to cause disease is closely linked to its propensity to adapt to conditions created by dysbiosis of the human gut microbiota. The cobamide (vitamin B12) metabolism of C. difficile has been underexplored, although it has seven metabolic pathways that are predicted to require cobamide-dependent enzymes. Here, we show that C. difficile cobamide metabolism is versatile, as it can use a surprisingly wide variety of cobamides and has alternative functions that can bypass some of its cobamide requirements. Furthermore, C. difficile does not synthesize cobamides de novo but produces them when given cobamide precursors. A better understanding of C. difficile cobamide metabolism may lead to new strategies to treat and prevent C. difficile-associated disease.

Isolation, bioassay and characterisation of Xenorhabdus sp. SY5, a highly virulent symbiotic bacterium of an entomopathogenic nematode isolated from China

Nematology ◽  
2013 ◽  
Vol 15 (2) ◽  
pp. 153-163 ◽  
Author(s):  
Huan Wang ◽  
Hui Dong ◽  
Haitao Qian ◽  
Runxi Xia ◽  
Bin Cong
Keyword(s):  
Growth Inhibition ◽  
Insecticidal Activity ◽  
Entomopathogenic Nematode ◽  
Symbiotic Bacterium ◽  
Symbiotic Bacteria ◽  
Toxin Gene ◽  
Agricultural Pests ◽  
Bacterial Strains ◽  
Biological Pest Control ◽  
Highly Virulent

The entomopathogenic nematodes (EPN), together with their symbiotic bacteria, are obligate and lethal parasites of insects and are applied as biological approaches to pest management. In this paper, we isolated 122 strains of symbiotic bacteria from 23 EPN isolates that were gathered in various soils containing different vegetations from different regions of China. All these isolated bacterial strains showed oral insecticidal activity and/or growth inhibition to the larvae of Ostrinia furnacalis. Among these strains, Xenorhabdus sp. SY5 exhibited high insecticidal activity to O. furnacalis, Plutella xylostella, Mythimna separata, Laphygma exigua and Tenebrio molitor, all of which are important agricultural pests. Xenorhabdus sp. SY5 was isolated from EPN Steinernema sp. SY5. Through DEAE-52 column chromatography, seven toxins were purified from X. sp. SY5. Bioassay results showed that all seven toxins had, to a certain extent, insecticidal activity and/or growth inhibition to O. furnacalis, T. molitor, P. xylostella, M. separata and L. exigua. Our data also showed that each of these toxins had different insecticidal activity and/or growth inhibition against different insect species. The partial toxin gene sequence of X. sp. SY5 was determined, and its deduced amino acid sequence only showed 75, 66 and 65% identities to homologues of EPN symbiotic bacteria Photorhabdus luminescens, Xenorhabdus nematophila and Yersinia mollaretii, respectively. These results suggested that strain SY5 is a highly virulent EPN symbiotic bacterial strain that has a potential value for biological pest control.

scholarly journals Thermotoga lettingae Can Salvage Cobinamide To Synthesize Vitamin B12

2013 ◽  
Vol 79 (22) ◽  
pp. 7006-7012 ◽  
Author(s):  
Nicholas C. Butzin ◽  
Michael A. Secinaro ◽  
Kristen S. Swithers ◽  
J. Peter Gogarten ◽  
Kenneth M. Noll
Keyword(s):  
Gene Cluster ◽  
Common Ancestor ◽  
De Novo ◽  
Recent Common Ancestor ◽  
Vitamin B ◽  
Ancestral State ◽  
Salvage Pathway ◽  
Content Type ◽  
Most Recent Common Ancestor

ABSTRACTWe recently reported that theThermotogalesacquired the ability to synthesize vitamin B12by acquisition of genes from two distantly related lineages,ArchaeaandFirmicutes(K. S. Swithers et al., Genome Biol. Evol. 4:730–739, 2012). Ancestral state reconstruction suggested that the cobinamide salvage gene cluster was present in theThermotogales' most recent common ancestor. We also predicted thatThermotoga lettingaecould not synthesize B12de novobut could use the cobinamide salvage pathway to synthesize B12. In this study, these hypotheses were tested, and we found thatTt. lettingaedid not synthesize B12de novobut salvaged cobinamide. The growth rate ofTt. lettingaeincreased with the addition of B12or cobinamide to its medium. It synthesized B12when the medium was supplemented with cobinamide, and no B12was detected in cells grown on cobinamide-deficient medium. Upstream of the cobinamide salvage genes is a putative B12riboswitch. In other organisms, B12riboswitches allow for higher transcriptional activity in the absence of B12. WhenTt. lettingaewas grown with no B12, the salvage genes were upregulated compared to cells grown with B12or cobinamide. Another gene cluster with a putative B12riboswitch upstream is thebtuFCDABC transporter, and it showed a transcription pattern similar to that of the cobinamide salvage genes. The BtuF proteins from species that can and cannot salvage cobinamides were shownin vitroto bind both B12and cobinamide. These results suggest thatThermotogalesspecies can use the BtuFCD transporter to import both B12and cobinamide, even if they cannot salvage cobinamide.

Photorhabdus luminescens subsp. noenieputensis subsp. nov., a symbiotic bacterium associated with a novel Heterorhabditis species related to Heterorhabditis indica

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1853-1858 ◽  
Author(s):  
Tiarin Ferreira ◽  
Carol van Reenen ◽  
Sylvie Pagès ◽  
Patrick Tailliez ◽  
Antoinette P. Malan ◽  
...  
Keyword(s):  
Type Species ◽  
Galleria Mellonella ◽  
Entomopathogenic Nematode ◽  
Symbiotic Bacterium ◽  
Tween 20 ◽  
Haemolytic Activity ◽  
Phenotypic Traits ◽  
Photorhabdus Luminescens ◽  
Content Type ◽  
Link Type

The bacterial symbiont AM7T, isolated from a novel entomopathogenic nematode species of the genus Heterorhabditis, displays the main phenotypic traits of the genus Photorhabdus and is highly pathogenic to Galleria mellonella. Phylogenetic analysis based on a multigene approach (16S rRNA, recA, gyrB, dnaN, gltX and infB) confirmed the classification of isolate AM7T within the species Photorhabdus luminescens and revealed its close relatedness to Photorhabdus luminescens subsp. caribbeanensis , P. luminescens subsp. akhurstii and P. luminescens subsp. hainanensis . The five concatenated protein-encoding sequences (4197 nt) of strain AM7T revealed 95.8, 95.4 and 94.9 % nucleotide identity to sequences of P. luminescens subsp. caribbeanensis HG29T, P. luminescens subsp. akhurstii FRG04T and P. luminescens subsp. hainanensis C8404T, respectively. These identity values are less than the threshold of 97 % proposed for classification within one of the existing subspecies of P. luminescens . Unlike other strains described for P. luminescens , strain AM7T produces acid from adonitol, sorbitol and xylitol, assimilates xylitol and has no lipase activity on medium containing Tween 20 or 60. Strain AM7T is differentiated from P. luminescens subsp. caribbeanensis by the assimilation of N-acetylglucosamine and the absence of haemolytic activity. Unlike P. luminescens subsp. akhurstii , strain AM7T does not assimilate mannitol, and it is distinguished from P. luminescens subsp. hainanensis by the assimilation of trehalose and citrate, the inability to produce indole from tryptophan and the presence of acetoin production and urease activity. Strain AM7T ( = ATCC BAA-2407T  = DSM 25462T) belongs to a novel subspecies, and is proposed as the type strain of Photorhabdus luminescens subsp. noenieputensis sp. nov.

scholarly journals Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila

mBio ◽  
2020 ◽  
Vol 11 (6) ◽  
Author(s):  
Kenny C. Mok ◽  
Olga M. Sokolovskaya ◽  
Alexa M. Nicolas ◽  
Zachary F. Hallberg ◽  
Adam Deutschbauer ◽  
...  
Keyword(s):  
De Novo ◽  
Structural Diversity ◽  
Vitamin B ◽  
Human Gut ◽  
Diverse Range ◽  
Content Type ◽  
Akkermansia Muciniphila ◽  
Binding Domains ◽  
Domains Of Life ◽  
Lower Ligand

ABSTRACT The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment. IMPORTANCE Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. Here, we discovered that the beneficial human gut bacterium Akkermansia muciniphila can use a diverse range of cobamides due to its ability to change the cobamide structure via a process termed cobamide remodeling. We identify and characterize the novel enzyme CbiR that is necessary for initiating the cobamide remodeling process. The discovery of this enzyme has implications for understanding the ecological role of A. muciniphila in the gut and the functions of other bacteria that produce this enzyme.

scholarly journals Draft Genome Sequence of Photorhabdus luminescens HIM3 Isolated from an Entomopathogenic Nematode in Agricultural Soils

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Rosalba Salgado-Morales ◽  
Nancy Rivera-Gómez ◽  
Fernando Martínez-Ocampo ◽  
Luis Fernando Lozano-Aguirre Beltrán ◽  
Armando Hernández-Mendoza ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Agricultural Soils ◽  
Entomopathogenic Nematode ◽  
Draft Genome ◽  
Symbiotic Bacterium ◽  
Draft Genome Sequence ◽  
Photorhabdus Luminescens ◽  
Content Type ◽  
Heterorhabditis Indica

ABSTRACT In this work, we report the draft genome sequence of Photorhabdus luminescens strain HIM3, a symbiotic bacterium associated with the entomopathogenic nematode Heterorhabditis indica MOR03, isolated from soil sugarcane in Yautepec, Morelos, Mexico. These bacteria have a G+C content of 42.6% and genome size of 5.47 Mb.

scholarly journals Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 65
Author(s):  
Patricia Haug ◽  
Samuel Koller ◽  
Jordi Maggi ◽  
Elena Lang ◽  
Silke Feil ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Screening ◽  
De Novo ◽  
Efficient Tool ◽  
Sequencing Technologies ◽  
Whole Exome ◽  
Screening And Identification ◽  
High Throughput Dna Sequencing ◽  
New Mutations

Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.

scholarly journals Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica

2013 ◽  
Vol 79 (23) ◽  
pp. 7360-7370 ◽  
Author(s):  
John Seip ◽  
Raymond Jackson ◽  
Hongxian He ◽  
Quinn Zhu ◽  
Seung-Pyo Hong
Keyword(s):  
Yarrowia Lipolytica ◽  
Lipid Accumulation ◽  
Oleaginous Yeast ◽  
De Novo ◽  
Lipid Synthesis ◽  
Omega 3 ◽  
Wild Type ◽  
Content Type ◽  
Reverse Transcription Pcr ◽  
Dry Cell Weight

ABSTRACTIn the oleaginous yeastYarrowia lipolytica,de novolipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase inY. lipolytica. Strains with aY. lipolyticasnf1(Ylsnf1) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into aY. lipolyticastrain engineered to produce omega-3 eicosapentaenoic acid (EPA),Ylsnf1deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of theY. lipolyticaSNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of theYlsnf1mutant identified significantly differentially expressed genes duringde novolipid synthesis and accumulation inY. lipolytica. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.

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