scholarly journals Studies towards the production of candicidin by Streptomyces sp. CBMAI 2043

2019 ◽  
Author(s):  
Rodrigo Silva de Oliveira ◽  
Luciana Gonzaga de Oliveira
Keyword(s):  
Gene Cluster ◽  
Genome Sequencing ◽  
Type Strain ◽  
Wild Type Strain ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Pathways ◽  
Wild Type ◽  
Streptomyces Sp ◽  
Cluster A

The aim of this study was to explore two gene clusters from Streptomyces sp. CBMAI 2043. One of them was the candicidin gene cluster, a polyketide annotated form the strain whole genome sequencing. By deleting important genes it is possible to have clues about the biosynthetic pathways and released intermediates. The second gene is a unknown non ribosomal. Using the same approach we expected to ,correlate the gene cluster to the chemical entity. These studies will help to have a better understanding of the whole matabolite profile of the wild type strain.

scholarly journals H-NS Is a Negative Regulator of the Two Hemolysin/Cytotoxin Gene Clusters in Vibrio anguillarum

2013 ◽  
Vol 81 (10) ◽  
pp. 3566-3576 ◽  
Author(s):  
Xiangyu Mou ◽  
Edward J. Spinard ◽  
Maureen V. Driscoll ◽  
Wenjing Zhao ◽  
David R. Nelson
Keyword(s):  
Gene Cluster ◽  
Hemolytic Activity ◽  
Type Strain ◽  
Wild Type Strain ◽  
Vibrio Anguillarum ◽  
Gene Clusters ◽  
Negative Regulator ◽  
Wild Type ◽  
Promoter Regions ◽  
Content Type

ABSTRACTHemolysins produced byVibrio anguillarumhave been implicated in the development of hemorrhagic septicemia during vibriosis, a fatal fish disease. Previously, two hemolysin gene clusters responsible for the hemolysis and cytotoxicity ofV. anguillarumwere identified: thevah1-plpgene cluster and thertxACHBDEgene cluster. In this study, we identified thehnsgene, which encodes the H-NS protein and acts as a negative regulator of both gene clusters. TheV. anguillarumH-NS protein shares strong homology with other bacterial H-NS proteins. Anhnsmutant exhibited increased hemolytic activity and cytotoxicity compared to the wild-type strain. Complementation of thehnsmutation restored hemolytic activity and cytotoxicity levels to nearly wild-type levels. Furthermore, expression ofrtxA,rtxH,rtxB,vah1, andplpincreased in thehnsmutant and decreased in thehns-complemented mutant strain compared to expression in the wild-type strain. Additionally, experiments using DNase I showed that purified recombinant H-NS protected multiple sites in the promoter regions of both gene clusters. Thehnsmutant also exhibited significantly attenuated virulence against rainbow trout. Complementation of thehnsmutation restored virulence to wild-type levels, suggesting that H-NS regulates many genes that affect fitness and virulence. Previously, we showed that HlyU is a positive regulator of expression for both gene clusters. In this study, we demonstrate that upregulation byhlyUishnsdependent, suggesting that H-NS acts to repress or silence both gene clusters and HlyU acts to relieve that repression or silencing.

scholarly journals A Novel CO-Responsive Transcriptional Regulator and Enhanced H2Production by an Engineered Thermococcus onnurineus NA1 Strain

2014 ◽  
Vol 81 (5) ◽  
pp. 1708-1714 ◽  
Author(s):  
Min-Sik Kim ◽  
Ae Ran Choi ◽  
Seong Hyuk Lee ◽  
Hae-Chang Jung ◽  
Seung Seob Bae ◽  
...  
Keyword(s):  
Production Rate ◽  
Gene Cluster ◽  
Type Strain ◽  
Wild Type Strain ◽  
Regulatory System ◽  
Transcriptional Regulator ◽  
Bioreactor Culture ◽  
Wild Type ◽  
Content Type ◽  
Transcriptional Regulatory

ABSTRACTGenome analysis revealed the existence of a putative transcriptional regulatory system governing CO metabolism inThermococcus onnurineusNA1, a carboxydotrophic hydrogenogenic archaeon. The regulatory system is composed of CorQ with a 4-vinyl reductase domain and CorR with a DNA-binding domain of the LysR-type transcriptional regulator family in close proximity to the CO dehydrogenase (CODH) gene cluster. Homologous genes of the CorQR pair were also found in the genomes ofThermococcusspecies and “CandidatusKorarchaeum cryptofilum” OPF8. In-frame deletion of eithercorQorcorRcaused a severe impairment in CO-dependent growth and H2production. WhencorQandcorRdeletion mutants were complemented by introducing thecorQRgenes under the control of a strong promoter, the mRNA and protein levels of the CODH gene were significantly increased in a ΔCorR strain complemented with integratedcorQR(ΔCorR/corQR↑) compared with those in the wild-type strain. In addition, the ΔCorR/corQR↑strain exhibited a much higher H2production rate (5.8-fold) than the wild-type strain in a bioreactor culture. The H2production rate (191.9 mmol liter−1h−1) and the specific H2production rate (249.6 mmol g−1h−1) of this strain were extremely high compared with those of CO-dependent H2-producing prokaryotes reported so far. These results suggest that thecorQRgenes encode a positive regulatory protein pair for the expression of a CODH gene cluster. The study also illustrates that manipulation of the transcriptional regulatory system can improve biological H2production.

scholarly journals Mechanism of PQQ and CoQ10 overproduction in Methylobacterium as revealed by comparative genomic analysis between mutant and wild-type strains

2020 ◽  
Author(s):  
Changle Zhao ◽  
Yinping Wan ◽  
Xiaojie Cao ◽  
Huili Zhang ◽  
Xin Bao
Keyword(s):  
Mutant Strain ◽  
Type Strain ◽  
Wild Type Strain ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Regulation Mechanism ◽  
Whole Genome ◽  
Wild Type ◽  
Coq10 Production

Abstract Background The microbial synthesis of pyrroloquinoline quinone (PQQ) and Coenzyme Q10 (CoQ10) remains the most promising industrial production route. Methylobacterium has been used to generate PQQ and other value-added chemicals from cheap carbon feedstocks.However, the low PQQ and CoQ10 production capacity of the Methylobacterium strains is a major limitation The regulation mechanism for PQQ and CoQ10 biosynthesis in this strain has also not been fully elucidated. Results Methylobacterium sp. CLZ strain was isolated from soil contaminated with chemical wastewater, which can simultaneously produce PQQ, CoQ10, and carotenoids by using cheap methanol as carbon source. We investigated a mutant strain NI91, which increased the PQQ and CoQ10 yield by 72.44% and 59.80%, respectively. Whole-genome sequencing of NI91 and wild-type strain CLZ revealed that both contain a 5.28 Mb chromosome. The comparative genomic analysis and validation study revealed that a significant increase in biomass and PQQ production was associated with the base mutations in the methanol dehydrogenase (MDH) synthesis genes, mxaD and mxaJ. The significant increase in CoQ10 production may be associated with the base mutations in dxs gene, a key gene in the MEP/DOXP pathway. Conclusions A PQQ producing strain that simultaneously produces CoQ10 and carotenoids was selected and after ANI analysis, named as Methylobacterium sp. CLZ. After random mutagenesis of this strain, we obtained NI91 strain, which showed increased production of PQQ and CoQ10. Based on comparative genomic analysis of the whole genome of mutant strain NI91 and wild-type strain CLZ, a total of 270 SNPs and InDels events were detected, which provided a reference for subsequent research. The mutations in mxaD, mxaJ and dxs genes may be related to the high yield of PQQ and CoQ10. These findings will enhance our understanding of the PQQ and CoQ10 over-production mechanism in Methylobacterium sp. NI91 at the genomic level. It will also provide useful clues for strain engineering in order to improve the PQQ and CoQ10 production.

scholarly journals Glycerol Utilization Gene Cluster in Streptomyces clavuligerus

2009 ◽  
Vol 75 (9) ◽  
pp. 2991-2995 ◽  
Author(s):  
Sonia Baños ◽  
Rosario Pérez-Redondo ◽  
Bert Koekman ◽  
Paloma Liras
Keyword(s):  
Clavulanic Acid ◽  
Gene Cluster ◽  
Acid Production ◽  
Type Strain ◽  
Wild Type Strain ◽  
Streptomyces Clavuligerus ◽  
Wild Type ◽  
Glycerol Utilization ◽  
In The Wild

ABSTRACT The Streptomyces clavuligerus ATCC 27064 glycerol cluster gylR-glpF1K1D1 is induced by glycerol but is not affected by glucose. S. clavuligerus growth and clavulanic acid production are stimulated by glycerol, but this does not occur in a glpK1-deleted mutant. Amplification of glpK1D1 results in transformants yielding larger amounts of clavulanic acid in the wild-type strain and in overproducer S. clavuligerus Gap15-7-30 or S. clavuligerus ΔrelA strains.

scholarly journals CO-Dependent H2Production by Genetically Engineered Thermococcus onnurineus NA1

2013 ◽  
Vol 79 (6) ◽  
pp. 2048-2053 ◽  
Author(s):  
Min-Sik Kim ◽  
Seung Seob Bae ◽  
Yun Jae Kim ◽  
Tae Wan Kim ◽  
Jae Kyu Lim ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Strain ◽  
Wild Type Strain ◽  
Specific Activity ◽  
Steel Production ◽  
Transcriptional Analysis ◽  
Bioreactor Culture ◽  
Wild Type ◽  
Steel Mill ◽  
Engineered Strain

ABSTRACTHydrogenogenic CO oxidation (CO + H2O → CO2+ H2) has the potential for H2production as a clean renewable fuel.Thermococcus onnurineusNA1, which grows on CO and produces H2, has a unique gene cluster encoding the carbon monoxide dehydrogenase (CODH) and the hydrogenase. The gene cluster was identified as essential for carboxydotrophic hydrogenogenic metabolism by gene disruption and transcriptional analysis. To develop a strain producing high levels of H2, the gene cluster was placed under the control of a strong promoter. The resulting mutant, MC01, showed 30-fold-higher transcription of the mRNA encoding CODH, hydrogenase, and Na+/H+antiporter and a 1.8-fold-higher specific activity for CO-dependent H2production than did the wild-type strain. The H2production potential of the MC01 mutant in a bioreactor culture was 3.8-fold higher than that of the wild-type strain. The H2production rate of the engineered strain was severalfold higher than those of any other CO-dependent H2-producing prokaryotes studied to date. The engineered strain also possessed high activity for the bioconversion of industrial waste gases created as a by-product during steel production. This work represents the first demonstration of H2production from steel mill waste gas using a carboxydotrophic hydrogenogenic microbe.

scholarly journals Involvement of the XpsN Protein in Formation of the XpsL-XpsM Complex in Xanthomonas campestris pv. campestris Type II Secretion Apparatus

2001 ◽  
Vol 183 (2) ◽  
pp. 528-535 ◽  
Author(s):  
Hsien-Ming Lee ◽  
Shiaw-Wei Tyan ◽  
Wei-Ming Leu ◽  
Ling-Yun Chen ◽  
David Chanhen Chen ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mutant Strain ◽  
Type Strain ◽  
Xanthomonas Campestris ◽  
Wild Type Strain ◽  
Type Ii ◽  
Wild Type ◽  
In The Wild ◽  
Steady State Levels ◽  
Type Gene

ABSTRACT The xps gene cluster is required for the second step of type II protein secretion in Xanthomonas campestrispv. campestris. Deletion of the entire gene cluster caused accumulation of secreted proteins in the periplasm. By analyzing protein abundance in the chromosomal mutant strains, we observed mutual dependence for normal steady-state levels between the XpsL and the XpsM proteins. The XpsL protein was undetectable in total lysate prepared from thexpsM mutant strain, and vice versa. Introduction of the wild-type xpsM gene carried on a plasmid into thexpsM mutant strain was sufficient for reappearance of the XpsL protein, and vice versa. Moreover, both XpsL and XpsM proteins were undetectable in the xpsN mutant strain. They were recovered either by reintroducing the wild-type xpsNgene or by introducing extra copies of wild-type xpsL orxpsM individually. Overproduction of wild-type XpsL and -M proteins simultaneously, but not separately, in the wild-type strain of X. campestris pv. campestris caused inhibition of secretion. Complementation of an xpsL orxpsM mutant strain with a plasmid-borne wild-type gene was inhibited by coexpression of XpsL and XpsM. The presence of the xpsN gene on the plasmid along with thexpsL and the xpsM genes caused more severe inhibition in both cases. Furthermore, complementation of thexpsN mutant strain was also inhibited. In both the wild-type strain and a strain with the xps gene cluster deleted (XC17433), carrying pCPP-LMN, which encodes all three proteins, each protein coprecipitated with the other two upon immunoprecipitation. Expression of pairwise combinations of the three proteins in XC17433 revealed that the XpsL-XpsM and XpsM-XpsN pairs still coprecipitated, whereas the XpsL-XpsN pair no longer coprecipitated.

scholarly journals The Burkholderia contaminans MS14ocfCGene Encodes a Xylosyltransferase for Production of the Antifungal Occidiofungin

2013 ◽  
Vol 79 (9) ◽  
pp. 2899-2905 ◽  
Author(s):  
Kuan-Chih Chen ◽  
Akshaya Ravichandran ◽  
Adam Guerrero ◽  
Peng Deng ◽  
Sonya M. Baird ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Gene Cluster ◽  
Mass Spectroscopy ◽  
Type Strain ◽  
Wild Type Strain ◽  
Activity Level ◽  
Antifungal Compound ◽  
Wild Type ◽  
Content Type ◽  
Burkholderia Contaminans

ABSTRACTBurkholderia contaminansstrain MS14 produces the antifungal compound occidiofungin, which is responsible for significant antifungal activities against a broad range of plant and animal fungal pathogens. Occidiofungin is a cyclic glycolipopeptide made up of eight amino acids and one xylose. A 56-kbocfgene cluster was determined to be essential for occidiofungin production. In this study, theocfCgene, which is located downstream ofocfDand upstream of theocfBgene in theocfgene cluster, was examined. Antifungal activity of theocfCgene mutant MS14KC1 was reduced against the indicator fungusGeotrichum candidumcompared with that of the wild-type strain. Furthermore, the analysis of the protein sequence suggests that theocfCgene encodes a glycosyltransferase. Biochemical analyses using nuclear magnetic resonance (NMR) and mass spectroscopy revealed that theocfCmutant produced the occidiofungin without the xylose. The purifiedocfCmutant MS14KC1 product had a level of bioactivity similar to that of the wild-type product. The revertant MS14KC1-R of theocfCmutant produced the same antifungal activity level on plate assays and the same antifungal compound based on high-performance liquid chromatography (HPLC) and mass spectroscopy analysis as wild-type strain MS14. Collectively, the study demonstrates that theocfCgene encodes a glycosyltransferase responsible to add a xylose to the occidiofungin molecule and that the presence of the xylose is not important for antifungal activity againstCandidaspecies. The finding provides a novel variant for future studies aimed at evaluating its use for inhibiting clinical and agricultural fungi, and the finding could also simplify the chemical synthesis of occidiofungin variants.

scholarly journals The ComQXPA Quorum Sensing System May Play an Important Role in the Synthesis of Bacillomycin D in Bacillus Amyloliquefaciens Q-426

2020 ◽  
Author(s):  
chunshan quan ◽  
liming jin ◽  
wei zhou ◽  
jialu liu ◽  
xian shi ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Quorum Sensing ◽  
Gene Cluster ◽  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Wild Type Strain ◽  
Early Stage ◽  
Tryptophan Residue ◽  
Wild Type ◽  
Bacillomycin D

Abstract Background: Bacillus amyloliquefaciens Q-426 can secrete numerous cyclic lipopeptides that have antifungal and antitumor activities. ComQXPA is a common quorum sensing (QS) system in Bacillus species. Most B. amyloliquefaciens strains are encoding the QS gene cluster comQXPA, however, the biological function of the ComQXPA system in B. amyloliquefaciens has not been well studied. In this study, we identified the comQXPA gene locus and the chemical structure of ComXQ-426 in B. amyloliquefaciens Q-426, and explored the function of ComXQ-426 in regulating lipopeptide production.Results: We identified and analyzed the comQXPA locus in Q-426. The full length of the comQXPA gene cluster was 4,014 bp, including 912 bp of comQ, 165 bp of comX, 2292 bp of comP, and 645 bp of comA. The comQXPA locus belongs to group B, as comQ and comX overlap by only one base pair. ComXQ-426 consists of six amino acids (GGDWKY) that contain a modified tryptophan residue. The antifungal activity of Q426ΔcomX was significantly affected, and almost no antifungal activity was observed, while the antifungal activity of strain Q426ΔcomX /comQX was restored to the same level as that of the wild-type strain. When the ComXQ-426 was added to the culture medium at a final concentration of 8 μg/L at the early stage of the log-phase, the antifungal activity of the wild-type strain Q-426 was significantly improved. Knocking out the comX gene did not affect the growth of the bacteria, however, the strain Q426ΔcomX lost its swimming ability, was unable to form colonies when spread on a solid surface, and could not form biofilms on the interface between the gas and liquid medium.Conclusions: Disruption of the ComPA signaling pathway in the Q-426 strain resulted in significant effects on bacillomycin D production, morphology, and motility.

scholarly journals Local emergence and decline of a SARS-CoV-2 variant with mutations L452R and N501Y in the spike protein

2021 ◽  
Author(s):  
Jan-Philipp Mallm ◽  
Christian Bundschuh ◽  
Heeyoung Kim ◽  
Niklas Weidner ◽  
Simon Steiger ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Type Strain ◽  
Wild Type Strain ◽  
Population Level ◽  
Spike Protein ◽  
Whole Genome ◽  
Wild Type ◽  
Spike Gene ◽  
Mutational Pattern

SummaryVariants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are replacing the initial wild-type strain, jeopardizing current efforts to contain the pandemic. Amino acid exchanges in the spike protein are of particular concern as they can render the virus more transmissible or reduce vaccine efficacy. Here, we conducted whole genome sequencing of SARS-CoV-2 positive samples from the Rhine-Neckar district in Germany during January-March 2021. We detected a total of 166 samples positive for a variant with a distinct mutational pattern in the spike gene comprising L18F, L452R, N501Y, A653V, H655Y, D796Y and G1219V with a later gain of A222V. This variant was designated A.27.RN according to its phylogenetic clade classification. It emerged in parallel with the B.1.1.7 variant, increased to >50% of all SARS-CoV-2 variants by week five. Subsequently it decreased to <10% of all variants by calendar week eight when B.1.1.7 had become the dominant strain. Antibodies induced by BNT162b2 vaccination neutralized A.27.RN but with a two-to-threefold reduced efficacy as compared to the wild-type and B.1.1.7 strains. These observations strongly argue for continuous and comprehensive monitoring of SARS-CoV-2 evolution on a population level.

scholarly journals 4-Chlorobenzoate Uptake in Comamonas sp. Strain DJ-12 Is Mediated by a Tripartite ATP-Independent Periplasmic Transporter

2006 ◽  
Vol 188 (24) ◽  
pp. 8407-8412 ◽  
Author(s):  
Jong-Chan Chae ◽  
Gerben J. Zylstra
Keyword(s):  
Growth Rate ◽  
Gene Cluster ◽  
Type Strain ◽  
Wild Type Strain ◽  
Proton Motive Force ◽  
Significant Inhibition ◽  
Motive Force ◽  
Wild Type ◽  
Knockout Mutant

ABSTRACT The fcb gene cluster involved in the hydrolytic dehalogenation of 4-chlorobenzoate is organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC in Comamonas sp. strain DJ-12. The genes are operonic and inducible with 4-chloro-, 4-iodo-, and 4-bromobenzoate. The fcbT1, fcbT2, and fcbT3 genes encode a transporter in the secondary TRAP (tripartite ATP-independent periplasmic) family. An fcbT1T2T3 knockout mutant shows a much slower growth rate on 4-chlorobenzoate compared to the wild type. 4-Chlorobenzoate is transported into the wild-type strain five times faster than into the fcbT1T2T3 knockout mutant. Transport of 4-chlorobenzoate shows significant inhibition by 4-bromo-, 4-iodo-, and 4-fluorobenzoate and mild inhibition by 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate. Uptake of 4-chlorobenzoate is significantly inhibited by ionophores which collapse the proton motive force.

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