scholarly journals Transcription of Cystathionine β-lyase (MetC) is Repressed by HeuR in Campylobacter jejuni and Methionine Biosynthesis Facilitates Colonocyte Invasion

2021 ◽  
Author(s):  
Brittni R. Kelley ◽  
Sean M. Callahan ◽  
Jeremiah G. Johnson
Keyword(s):  
Campylobacter Jejuni ◽  
Regulatory Protein ◽  
Direct Interaction ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Methionine Biosynthesis ◽  
Promoter Regions ◽  
Susceptible Host ◽  
Transcriptional Regulatory ◽  
In The Wild

A previously identified transcriptional regulator in C. jejuni, termed HeuR, was found to positively regulate heme utilization. Additionally, transcriptomic work demonstrated the putative operons, CJJ81176_1390-1394 and CJJ81176_1214-1217, were upregulated in a HeuR mutant, suggesting HeuR negatively regulates expression of these genes. Because genes within these clusters include a cystathionine β-lyase (metC) and a methionine synthase (metE), it appeared HeuR negatively regulates C. jejuni methionine biosynthesis. To address this, we confirmed mutation of HeuR reproducibly results in metC overexpression under nutrient-replete conditions, but did not affect expression of metE, while metC expression in the wild-type increased to heuR mutant levels during iron-limitation. We subsequently determined that both gene clusters are operonic and demonstrated the direct interaction of HeuR with the predicted promoter regions of these operons. Using DNase-footprinting assays, we were able to show that HeuR specifically binds within the predicted -35 region of the CJJ81176_1390-1394 operon. As predicted based on transcriptional results, the HeuR mutant was able to grow and remain viable in a defined media with and without methionine, but we identified significant impacts on growth and viability in metC and metE mutants. Additionally, we observed decreased adherence, invasion, and persistence of metC and metE mutants when incubated with human colonocytes, while the heuR mutant exhibited increased invasion. Taken together, these results suggest that HeuR regulates methionine biosynthesis in an iron-responsive manner and that the ability to produce methionine is an important factor for adhering to and invading the gastrointestinal tract of a susceptible host. Importance As the leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health. Investigating colonization factors that allow C. jejuni to successfully infect a host furthers our understanding of genes and regulatory elements necessary for virulence. In this study, we have begun to characterize the role of the transcriptional regulatory protein, HeuR, on methionine biosynthesis in C. jejuni. When the ability to synthesize methionine is impaired, detrimental impacts on growth and viability are observed during growth in limited media lacking methionine and/or iron. Additionally, mutations in the methionine biosynthetic pathway result in decreased adhesion, invasion, and intracellular survival of C. jejuni when incubated with human colonocytes, indicating the importance of regulating methionine biosynthesis.

scholarly journals Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Soonkyu Hwang ◽  
Namil Lee ◽  
Donghui Choe ◽  
Yongjae Lee ◽  
Woori Kim ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Transcription Termination ◽  
Gene Clusters ◽  
Streptomyces Clavuligerus ◽  
Regulatory Elements ◽  
Regulation Of Transcription ◽  
Content Type ◽  
Transcriptional Regulatory Elements ◽  
Transcriptional Regulatory ◽  
Posttranscriptional Processing

ABSTRACT Identification of transcriptional regulatory elements in the GC-rich Streptomyces genome is essential for the production of novel biochemicals from secondary metabolite biosynthetic gene clusters (smBGCs). Despite many efforts to understand the regulation of transcription initiation in smBGCs, information on the regulation of transcription termination and posttranscriptional processing remains scarce. In this study, we identified the transcriptional regulatory elements in β-lactam antibiotic-producing Streptomyces clavuligerus ATCC 27064 by determining a total of 1,427 transcript 3′-end positions (TEPs) using the term-seq method. Termination of transcription was governed by three classes of TEPs, of which each displayed unique sequence features. The data integration with transcription start sites and transcriptome data generated 1,648 transcription units (TUs) and 610 transcription unit clusters (TUCs). TU architecture showed that the transcript abundance in TU isoforms of a TUC was potentially affected by the sequence context of their TEPs, suggesting that the regulatory elements of TEPs could control the transcription level in additional layers. We also identified TU features of a xenobiotic response element (XRE) family regulator and DUF397 domain-containing protein, particularly showing the abundance of bidirectional TEPs. Finally, we found that 189 noncoding TUs contained potential cis- and trans-regulatory elements that played a major role in regulating the 5′ and 3′ UTR. These findings highlight the role of transcriptional regulatory elements in transcription termination and posttranscriptional processing in Streptomyces sp. IMPORTANCE Streptomyces sp. is a great source of bioactive secondary metabolites, including antibiotics, antifungal agents, antiparasitic agents, immunosuppressant compounds, and other drugs. Secondary metabolites are synthesized via multistep conversions of the precursor molecules from primary metabolism, governed by multicomplex enzymes from secondary metabolite biosynthetic gene clusters. As their production is closely related with the growth phase and dynamic cellular status in response to various intra- and extracellular signals, complex regulatory systems tightly control the gene expressions related to secondary metabolism. In this study, we determined genome-wide transcript 3′-end positions and transcription units in the β-lactam antibiotic producer Streptomyces clavuligerus ATCC 27064 to elucidate the transcriptional regulatory elements in transcription termination and posttranscriptional processing by integration of multiomics data. These unique features, such as transcript 3′-end sequence, potential riboregulators, and potential 3′-untranslated region (UTR) cis-regulatory elements, can be potentially used to design engineering tools that can regulate the transcript abundance of genes for enhancing secondary metabolite production.

scholarly journals Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information

2021 ◽  
Vol 12 ◽  
Author(s):  
Julian Droste ◽  
Christian Rückert ◽  
Jörn Kalinowski ◽  
Mohamed Belal Hamed ◽  
Jozef Anné ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Regulatory Networks ◽  
Streptomyces Coelicolor ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Streptomyces Lividans ◽  
Model Organisms ◽  
Promoter Regions ◽  
Gene Characterization ◽  
Novel Transcripts

Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5′-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5′ untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5′-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5′-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.

scholarly journals Gene Cloning and Characterization of Multiple Alkane Hydroxylase Systems in Rhodococcus Strains Q15 and NRRL B-16531

2002 ◽  
Vol 68 (12) ◽  
pp. 5933-5942 ◽  
Author(s):  
L. G. Whyte ◽  
T. H. M. Smits ◽  
D. Labbé ◽  
B. Witholt ◽  
C. W. Greer ◽  
...  
Keyword(s):  
Regulatory Protein ◽  
Gene Clusters ◽  
Alkane Hydroxylase ◽  
Hydrophobic Membrane ◽  
Transcriptional Regulatory ◽  
Monooxygenase Gene ◽  
Alkane Monooxygenase ◽  
Membrane Spanning ◽  
Degradative Enzyme

ABSTRACT The alkane hydroxylase systems of two Rhodococcus strains (NRRL B-16531 and Q15, isolated from different geographical locations) were characterized. Both organisms contained at least four alkane monooxygenase gene homologs (alkB1, alkB2, alkB3, and alkB4). In both strains, the alkB1 and alkB2 homologs were part of alk gene clusters, each encoding two rubredoxins (rubA1 and rubA2; rubA3 and rubA4), a putative TetR transcriptional regulatory protein (alkU1; alkU2), and, in the alkB1 cluster, a rubredoxin reductase (rubB). The alkB3 and alkB4 homologs were found as separate genes which were not part of alk gene clusters. Functional heterologous expression of some of the rhodococcal alk genes (alkB2, rubA2, and rubA4 [NRRL B-16531]; alkB2 and rubB [Q15]) was achieved in Escherichia coli and Pseudomonas expression systems. Pseudomonas recombinants containing rhodococcal alkB2 were able to mineralize and grow on C12 to C16 n-alkanes. All rhodococcal alkane monooxygenases possessed the highly conserved eight-histidine motif, including two apparent alkane monooxygenase signature motifs (LQRH[S/A]DHH and NYXEHYG[L/M]), and the six hydrophobic membrane-spanning regions found in all alkane monooxygenases related to the Pseudomonas putida GPo1 alkane monooxygenase. The presence of multiple alkane hydroxylases in the two rhodococcal strains is reminiscent of other multiple-degradative-enzyme systems reported in Rhodococcus.

scholarly journals In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Getachew Bantihun ◽  
Mulugeta Kebede
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Entomopathogenic Fungi ◽  
Metarhizium Anisopliae ◽  
In Silico ◽  
Promoter Region ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Predictive Score ◽  
Promoter Regions

Abstract Background Pest control strategies almost entirely rely on chemical insecticides, which cause environmental problems such as biosphere deterioration and emergence of resistant pests. Bio-pesticide is an alternative approach, which uses organisms such as entomopathogenic fungi, Metarhizium anisopliae, to control pests. Screening such potential organism at a molecular level and understanding their gene regulation mechanism is an important approach to reduce emergence of pesticide resistance and worsening of the biosphere. Understanding promoter regions which play a pivotal role in gene regulation is crucial. In particular, identification of the promoter regions in M. anisopliae Strain ME1 remains poorly understood. To our knowledge, the mitogenome trn gene clusters of M. anisopliae Strain ME1 were not characterized. Here, we used machine learning approach to identify and characterize the promoter regions, regulatory elements, and CpG island densities of 15 protein coding genes of entomopathogenic fungi, M. anisolpliae Strain ME1. Results The current analysis revealed multiple transcription start sites (TSS) for all utilized sequences, except for promoter region genes of Pro-cob and Pro-nad5. With reference to the start codon (ATG), 85.3% of TSS was located above – 500 bp. Based on the standard predictive score at cut off value of 0.8a, the current study revealed 54.7% of predictive score greater than or equal from 0.9 promoter prediction score. Expectation maximization algorithm output identified five candidate motifs. Nonetheless, of all candidate motifs, MtrnI was revealed as the common promoter region motif with a value of 76.9% both in terms of size of binding sites and with an E value of 9.1E−054. Accordingly, we perceived that MtrnI serve as the binding site for tryptophan cluster with P value 0.0044 and C4 type zinc fingers functions as the binding site to regulate gene expression of M. anisopliae Strain ME1. The analysis revealed that mitogenome trn gene clusters of M. anisopliae Strain ME1 showed homologues evolutionary ancestor supported with a bootstrap value of 100%. Conclusion Identified common candidate motifs and binding transcription factors through in silico approach are likely expected to contribute for better understanding of gene expression and strain improvement of M. anisopliae Strain ME1 for its bio-pesticides role.

scholarly journals TworsaMhomologues encode central regulatory elements modulating quorum sensing expression inBurkholderia thailandensis

2017 ◽  
Author(s):  
Servane Le Guillouzer ◽  
Marie-Christine Groleau ◽  
Eric Déziel
Keyword(s):  
Quorum Sensing ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Regulatory Elements ◽  
Burkholderia Thailandensis ◽  
Gene Coding ◽  
Genes Expression ◽  
In The Wild

AbstractThe bacteriumBurkholderia thailandensispossesses three conservedN-acyl-L-homoserine lactone (AHL) quorum sensing (QS) systems designated BtaI1/BtaR1 (QS-1), BtaI2/BtaR2 (QS-2), and BtaI3/BtaR3 (QS-3). These QS-systems are associated with the biosynthesis ofN-octanoyl-homoserine lactone (C8-HSL),N-3-hydroxy-decanoyl-homoserine lactone (3OHC10-HSL), as well asN-3-hydroxy-octanoyl-homoserine lactone (3OHC8-HSL), which are produced by the LuxI-type synthase BtaI1, BtaI2, and BtaI3, and modulated by the LuxR-type transcriptional regulators BtaR1, BtaR2, and BtaR3. BothbtaR1/btaI1andbtaR2/btaI2gene clusters contain an additional gene that is conserved in theBurkholderiagenus, homologous to a gene coding for the negative AHL biosynthesis modulatory protein RsaM originally identified in the phytopathogenPseudomonas fuscovaginae, and hence designatedrsaM1andrsaM2. We have characterized the function of these tworsaMhomologues and demonstrated their involvement in the regulation of AHLs biosynthesis inB. thailandensisstrain E264. We measured the production of C8-HSL, 3OHC10-HSL, and 3OHC8-HSL by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in the wild-type strain and in thersaM1-andrsaM2-mutants, and monitored the transcription ofbtaI1,btaI2, andbtaI3 using chromosomal mini-CTX-luxtranscriptional reporters. The expression ofbtaR1,btaR2, andbtaR3 was also measured by quantitative everse-transcription PCR (qRT-PCR). We demonstrate that the QS-1 system is repressed by RsaM1, whereas RsaM2 principally represses the QS-2 system. We also found that bothrsaM1andrsaM2are QS-controlled, as well as negatively auto-regulated. We conclude that RsaM1 and RsaM2 are an integral part of the QS modulatory circuitry ofB. thailandensis, and play a major role in the hierarchical and homeostatic organization of the QS-1, QS-2, and QS-3 systems.ImportanceQuorum sensing (QS) is a global regulatory mechanism of genes expression depending on bacterial density. QS is commonly involved in the coordination of genes expression associated with the establishment of host-pathogen interactions and acclimatization to the environment. We present the functional characterization of the tworsaMhomologues designatedrsaM1andrsaM2in the regulation of the multiple QS systems coexisting in the non-pathogenic bacteriumBurkholderia thailandensis, widely used as a model system for the study of the pathogenBurkholderia pseudomallei. We found that inactivation of thesersaMhomologues, which are clustered with the other QS genes, profoundly affects the QS regulatory circuity ofB. thailandensis. It is proposed that these genes code for QS repressors and we conclude that they constitute essential regulatory components of the QS modulatory network ofB. thailandensis, and provide additional layers of regulation to modulate the expression of QS-controlled genes, including those encoding virulence/survival factors and linked to environmental adaptation inB. pseudomallei.

scholarly journals Control of Methionine Synthesis and Uptake by MetR and Homocysteine in Streptococcus mutans

2007 ◽  
Vol 189 (19) ◽  
pp. 7032-7044 ◽  
Author(s):  
Brice Sperandio ◽  
Céline Gautier ◽  
Stephen McGovern ◽  
Dusko S. Ehrlich ◽  
Pierre Renault ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Transcriptional Activation ◽  
Gene Clusters ◽  
Common Mechanism ◽  
Methionine Biosynthesis ◽  
Promoter Regions ◽  
Streptococcal Species ◽  
Dna Complex

ABSTRACT MetR (formerly Smu.1225), a regulator of the LysR family, controls key genes for methionine supply in Streptococcus mutans. An S. mutans metR mutant is unable to transport l-methionine and to grow in the absence of this amino acid. Accordingly, MetR activates transcription by binding to the promoter regions of two gene clusters and smu.1487, whose products are involved in methionine biosynthesis (MetEF and Smu.1487) and uptake (AtmBDE). Transcriptional activation by MetR requires the presence of a 17-bp palindromic sequence, the Met box. Base substitutions in the Met box hinder the formation of a MetR-DNA complex and abolish MetR-dependent activation, showing that Met boxes correspond to MetR recognition sites. Activation by MetR occurs in methionine-depleted medium and is rapidly triggered under nonactivating conditions by the addition of homocysteine. This intermediate of methionine biosynthesis increases the affinity of MetR for DNA in vitro and appears to be the MetR coeffector in vivo. Homocysteine plays a crucial role in methionine metabolic gene regulation by controlling MetR activity. A similar mechanism of homocysteine- and MetR-dependent control of methionine biosynthetic genes operates in S. thermophilus. These data suggest a common mechanism for the regulation of the methionine supply in streptococci. However, some streptococcal species are unable to synthesize the homocysteine coeffector. This intriguing feature is discussed in the light of comparative genomics and streptococcal ecology.

scholarly journals TworsaMHomologues Encode Central Regulatory Elements Modulating Quorum Sensing inBurkholderia thailandensis

2018 ◽  
Vol 200 (14) ◽  
Author(s):  
Servane Le Guillouzer ◽  
Marie-Christine Groleau ◽  
Eric Déziel
Keyword(s):  
Quorum Sensing ◽  
Functional Characterization ◽  
Gene Clusters ◽  
Homoserine Lactone ◽  
Regulatory Elements ◽  
Gene Encoding ◽  
Burkholderia Thailandensis ◽  
Content Type ◽  
Reverse Transcription Pcr ◽  
In The Wild

ABSTRACTThe bacteriumBurkholderia thailandensispossesses threeN-acyl-l-homoserine lactone (AHL) quorum sensing (QS) systems designated BtaI1/BtaR1 (QS-1), BtaI2/BtaR2 (QS-2), and BtaI3/BtaR3 (QS-3). These QS systems are associated with the biosynthesis ofN-octanoyl-homoserine lactone (C8-HSL),N-3-hydroxy-decanoyl-homoserine lactone (3OHC10-HSL), andN-3-hydroxy-octanoyl-homoserine lactone (3OHC8-HSL), which are produced by the LuxI-type synthases BtaI1, BtaI2, and BtaI3 and modulated by the LuxR-type transcriptional regulators BtaR1, BtaR2, and BtaR3. ThebtaR1-btaI1andbtaR2-btaI2gene clusters each carry an additional gene encoding a homologue of the QS repressor RsaM originally identified in the phytopathogenPseudomonas fuscovaginaeand thus here namedrsaM1andrsaM2, respectively. We have characterized the functions of these two conservedrsaMhomologues and demonstrated their involvement in the regulation of AHL biosynthesis inB. thailandensisstrain E264. We quantified the production of C8-HSL, 3OHC10-HSL, and 3OHC8-HSL by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in the wild-type strain and in thersaM1andrsaM2mutants, and we monitoredbtaI1,btaI2, andbtaI3expression using chromosomal mini-CTX-luxtranscriptional reporters. The transcription ofbtaR1,btaR2, andbtaR3was also measured by quantitative reverse transcription-PCR (qRT-PCR). We observed that RsaM1 mainly represses the QS-1 system, whereas RsaM2 principally represses the QS-2 system. We also found that bothrsaM1andrsaM2are QS controlled and negatively autoregulated. We conclude that RsaM1 and RsaM2 are an integral part of the QS circuitry ofB. thailandensisand play a major role in the hierarchical and homeostatic organization of the QS-1, QS-2, and QS-3 systems.IMPORTANCEQuorum sensing (QS) is commonly involved in the coordination of gene transcription associated with the establishment of host-pathogen interactions and acclimatization to the environment. We present the functional characterization of tworsaMhomologues in the regulation of the multiple QS systems coexisting in the nonpathogenic bacteriumBurkholderia thailandensis, which is widely used as a model system for the study of the human pathogenBurkholderia pseudomallei. We found that inactivation of thesersaMhomologues, which are clustered with the other QS genes, profoundly affects the QS circuitry ofB. thailandensis. We conclude that they constitute essential regulatory components of the QS modulatory network and provide additional layers of regulation to modulate the transcription of QS-controlled genes, particularly those linked to environmental adaptation.

scholarly journals The Coordinated Upregulated Expression of Genes Involved in MEP, Chlorophyll, Carotenoid and Tocopherol Pathways, Mirrored the Corresponding Metabolite Contents in Rice Leaves during De-Etiolation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1456
Author(s):  
Xin Jin ◽  
Can Baysal ◽  
Margit Drapal ◽  
Yanmin Sheng ◽  
Xin Huang ◽  
...  
Keyword(s):  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Isoprenoid Biosynthesis ◽  
Promoter Regions ◽  
Expression Of Genes ◽  
Coordinated Expression ◽  
Rice Leaves ◽  
Mechanistic Basis ◽  
Phosphate Synthase

Light is an essential regulator of many developmental processes in higher plants. We investigated the effect of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1/2 genes (OsHDR1/2) and isopentenyl diphosphate isomerase 1/2 genes (OsIPPI1/2) on the biosynthesis of chlorophylls, carotenoids, and phytosterols in 14-day-old etiolated rice (Oyza sativa L.) leaves during de-etiolation. However, little is known about the effect of isoprenoid biosynthesis genes on the corresponding metabolites during the de-etiolation of etiolated rice leaves. The results showed that the levels of α-tocopherol were significantly increased in de-etiolated rice leaves. Similar to 1-deoxy-D-xylulose-5-phosphate synthase 3 gene (OsDXS3), both OsDXS1 and OsDXS2 genes encode functional 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activities. Their expression patterns and the synthesis of chlorophyll, carotenoid, and tocopherol metabolites suggested that OsDXS1 is responsible for the biosynthesis of plastidial isoprenoids in de-etiolated rice leaves. The expression analysis of isoprenoid biosynthesis genes revealed that the coordinated expression of the MEP (2-C-methyl-D-erythritol 4-phosphate) pathway, chlorophyll, carotenoid, and tocopherol pathway genes mirrored the changes in the levels of the corresponding metabolites during de-etiolation. The underpinning mechanistic basis of coordinated light-upregulated gene expression was elucidated during the de-etiolation process, specifically the role of light-responsive cis-regulatory motifs in the promoter region of these genes. In silico promoter analysis showed that the light-responsive cis-regulatory elements presented in all the promoter regions of each light-upregulated gene, providing an important link between observed phenotype during de-etiolation and the molecular machinery controlling expression of these genes.

scholarly journals Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marianna Iorio ◽  
Sahar Davatgarbenam ◽  
Stefania Serina ◽  
Paolo Criscenzo ◽  
Mitja M. Zdouc ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Systematic Investigation ◽  
Biosynthetic Gene ◽  
Wild Type ◽  
Bacterial Rna ◽  
Soil Isolate ◽  
Mutant Strains ◽  
In The Wild ◽  
Polymerase Inhibitor

AbstractWe report a metabolomic analysis of Streptomyces sp. ID38640, a soil isolate that produces the bacterial RNA polymerase inhibitor pseudouridimycin. The analysis was performed on the wild type, on three newly constructed and seven previously reported mutant strains disabled in different genes required for pseudouridimycin biosynthesis. The results indicate that Streptomyces sp. ID38640 is able to produce, in addition to lydicamycins and deferroxiamines, as previously reported, also the lassopeptide ulleungdin, the non-ribosomal peptide antipain and the osmoprotectant ectoine. The corresponding biosynthetic gene clusters were readily identified in the strain genome. We also detected the known compound pyridindolol, for which we propose a previously unreported biosynthetic gene cluster, as well as three families of unknown metabolites. Remarkably, the levels of most metabolites varied strongly in the different mutant strains, an observation that enabled detection of metabolites unnoticed in the wild type. Systematic investigation of the accumulated metabolites in the ten different pum mutants identified shed further light on pseudouridimycin biosynthesis. We also show that several Streptomyces strains, able to produce pseudouridimycin, have distinct genetic relationship and metabolic profile with ID38640.

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