scholarly journals An Additional Regulatory Gene for Actinorhodin Production in Streptomyces lividans Involves a LysR-Type Transcriptional Regulator

1999 ◽  
Vol 181 (14) ◽  
pp. 4353-4364 ◽  
Author(s):  
Oscar H. Martínez-Costa ◽  
Angel J. Martín-Triana ◽  
Eduardo Martínez ◽  
Miguel A. Fernández-Moreno ◽  
Francisco Malpartida
Keyword(s):  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Streptomyces Lividans ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
The Family ◽  
The Right ◽  
Different Sources ◽  
Transcription Expression

The sequence of a 4.8-kbp DNA fragment adjacent to the right-hand end of the actinorhodin biosynthetic (act) cluster downstream of actVB-orf6 from Streptomyces coelicolor A3(2) reveals six complete open reading frames, namedorf7 to orf12. The deduced amino acid sequences from orf7, orf10, and orf11 show significant similarities with the following products in the databases: a putative protein from the S. coelicolor SCP3 plasmid, LysR-type transcriptional regulators, and proteins belonging to the family of short-chain dehydrogenases/reductases, respectively. The deduced product of orf8 reveals low similarities with several methyltransferases from different sources, whileorf9 and orf12 products show no similarities with other known proteins. Disruptions of orf10 andorf11 genes in S. coelicolor appear to have no significant effect on the production of actinorhodin. Nevertheless, disruption or deletion of orf10 in Streptomyces lividans causes actinorhodin overproduction. The introduction of extra copies of orf10 and orf11 genes in anS. coelicolor actIII mutant restores the ability to produce actinorhodin. Transcriptional analysis and DNA footprinting indicate that Orf10 represses its own transcription and regulatesorf11 transcription, expression of which might require the presence of an unknown inducer. No DNA target for Orf10 protein was found within the act cluster.

scholarly journals Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jian Zeng ◽  
Yan Wang ◽  
Ju Zhang ◽  
Shixing Yang ◽  
Wen Zhang
Keyword(s):  
Gc Content ◽  
Cloacal Swab ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Viral Metagenomics ◽  
Toxin Gene ◽  
Microbial Genomes ◽  
The Family ◽  
Zonula Occludens Toxin ◽  
Reference Strains

AbstractMembers of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

scholarly journals Human Herpesvirus 6B Genome Sequence: Coding Content and Comparison with Human Herpesvirus 6A

1999 ◽  
Vol 73 (10) ◽  
pp. 8040-8052 ◽  
Author(s):  
Geraldina Dominguez ◽  
Timothy R. Dambaugh ◽  
Felicia R. Stamey ◽  
Stephen Dewhurst ◽  
Naoki Inoue ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Genome Sequence ◽  
Nucleotide Sequence Identity ◽  
Genomic Sequence ◽  
Human Herpesvirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Sequence Identity ◽  
T Cell Lines ◽  
The Right

ABSTRACT Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.

scholarly journals Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242362
Author(s):  
Xin Feng ◽  
Rui-lian Lai ◽  
Min-xia Gao ◽  
Wen-guang Chen ◽  
Ru-jian Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Viral Genomes ◽  
Relationship Analysis ◽  
The Family ◽  
Novel Variants ◽  
Rapid Amplification

Two distinct closterovirus-like genome sequences (termed AdV-1 v1 and v2) were identified in Actinidia chinensis var. deliciosa ‘Miliang-1’ that had no disease symptoms using high-throughput sequencing. Using overlapping reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends, the genomic sequences of AdV-1 v1 and v2 were confirmed as 17,646 and 18,578 nucleotides in length, respectively. The two complete genomes contained 9 and 15 open reading frames, respectively, coding for proteins having domains typical of Closteroviridae, such as RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h) and coat protein (CP). Sequence analysis showed that the amino acid sequences of RdRp, HSP70h, and CP of the two variants exhibited high similarity (> 80%), while their genomic organization was somewhat different. This suggested that the two viral genomes identified here are variants of the family Closteroviridae in a single kiwifruit host. Furthermore, phylogenetic relationship analysis revealed that the two variants had a closer relationship with the unclassified virus Persimmon virus B (PeVB) and Actinidia virus 1 (AcV-1) than with other members of the family Closteroviridae, as did their genomic organization. It is speculated that the two variants, together with PeVB and AcV-1 belong to a new subfamily of Closteroviridae.

scholarly journals Deletion of a regulatory gene within the cpk gene cluster reveals novel antibacterial activity in Streptomyces coelicolor A3(2)

Microbiology ◽  
2010 ◽  
Vol 156 (8) ◽  
pp. 2343-2353 ◽  
Author(s):  
Marco Gottelt ◽  
Stefan Kol ◽  
Juan Pablo Gomez-Escribano ◽  
Mervyn Bibb ◽  
Eriko Takano
Keyword(s):  
Antibacterial Activity ◽  
Gene Cluster ◽  
Polyketide Synthase ◽  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Feedback Mechanism ◽  
Biologically Active ◽  
Transcriptional Analysis ◽  
Type I ◽  
Negative Feedback Mechanism

Genome sequencing of Streptomyces coelicolor A3(2) revealed an uncharacterized type I polyketide synthase gene cluster (cpk). Here we describe the discovery of a novel antibacterial activity (abCPK) and a yellow-pigmented secondary metabolite (yCPK) after deleting a presumed pathway-specific regulatory gene (scbR2) that encodes a member of the γ-butyrolactone receptor family of proteins and which lies in the cpk gene cluster. Overproduction of yCPK and abCPK in a scbR2 deletion mutant, and the absence of the newly described compounds from cpk deletion mutants, suggest that they are products of the previously orphan cpk biosynthetic pathway in which abCPK is converted into the yellow pigment. Transcriptional analysis suggests that scbR2 may act in a negative feedback mechanism to eventually limit yCPK biosynthesis. The results described here represent a novel approach for the discovery of new, biologically active compounds.

scholarly journals Role of GntR Family Regulatory Gene SCO1678 in Gluconate Metabolism in Streptomyces coelicolor M145

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Olga Tsypik ◽  
Roman Makitrynskyy ◽  
Agnieszka Bera ◽  
Lijiang Song ◽  
Wolfgang Wohlleben ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Functional Characterization ◽  
Bioinformatic Analysis ◽  
Transcriptional Analysis ◽  
Dependent Manner ◽  
Putative Operon

Here we report functional characterization of the Streptomyces coelicolor M145 gene SCO1678, which encodes a GntR-like regulator of the FadR subfamily. Bioinformatic analysis suggested that SCO1678 is part of putative operon (gnt) involved in gluconate metabolism. Combining the results of SCO1678 knockout, transcriptional analysis of gnt operon, and Sco1678 protein-DNA electromobility shift assays, we established that Sco1678 protein controls the gluconate operon. It does so via repression of its transcription from a single promoter located between genes SCO1678 and SCO1679. The knockout also influenced, in a medium-dependent manner, the production of secondary metabolites by S. coelicolor. In comparison to the wild type, on gluconate-containing minimal medium, the SCO1678 mutant produced much less actinorhodin and accumulated a yellow-colored pigment, likely to be the cryptic polyketide coelimycin. Possible links between gluconate metabolism and antibiotic production are discussed.

scholarly journals Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae

2002 ◽  
Vol 83 (12) ◽  
pp. 3131-3138 ◽  
Author(s):  
M. van Munster ◽  
A. M. Dullemans ◽  
M. Verbeek ◽  
J. F. J. M. van den Heuvel ◽  
A. Clérivet ◽  
...  
Keyword(s):  
Rhopalosiphum Padi ◽  
Trialeurodes Vaporariorum ◽  
Aphid Species ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
The Family ◽  
Orf 5 ◽  
Sequence Similarities ◽  
Paralysis Virus ◽  
Reading Frames

The complete nucleotide sequence of the genomic RNA of an aphid-infecting virus, Aphid lethal paralysis virus (ALPV), has been determined. The genome is 9812 nt in length and contains two long open reading frames (ORFs), which are separated by an intergenic region of 163 nt. The first ORF (5′ ORF) is preceded by an untranslated leader sequence of 506 nt, while an untranslated region of 571 nt follows the second ORF (3′ ORF). The deduced amino acid sequences of the 5′ ORF and 3′ ORF products respectively showed similarity to the non-structural and structural proteins of members of the newly recognized genus Cripavirus (family Dicistroviridae). On the basis of the observed sequence similarities and identical genome organization, it is proposed that ALPV belongs to this genus. Phylogenetic analysis showed that ALPV is most closely related to Rhopalosiphum padi virus, and groups in a cluster with Drosophila C virus and Cricket paralysis virus, while the other members of this genus are more distantly related. Infectivity experiments showed that ALPV can not only infect aphid species but is also able to infect the whitefly Trialeurodes vaporariorum, extending its host range to another family of the order Hemiptera.

scholarly journals glkA Is Involved in Glucose Repression of Chitinase Production in Streptomyces lividans

1998 ◽  
Vol 180 (11) ◽  
pp. 2911-2914 ◽  
Author(s):  
Akihiro Saito ◽  
Takeshi Fujii ◽  
Tadakatsu Yoneyama ◽  
Kiyotaka Miyashita
Keyword(s):  
Sole Carbon Source ◽  
Glucose Repression ◽  
Streptomyces Coelicolor ◽  
Streptomyces Lividans ◽  
Transcriptional Analysis ◽  
Copy Number Plasmid ◽  
Low Copy Number ◽  
Chitinase Production ◽  
Dna Fragment ◽  
Glucose Kinase

ABSTRACT Chitinase production in Streptomyces lividans is induced by chitin and repressed in the presence of glucose. A mutant ofS. lividans TK24, strain G015, which was defective in glucose repression of chitinase production, was obtained by screening colonies for zones of clearing on colloidal chitin agar plates containing 1.0% (wt/vol) glucose. The transcriptional analysis ofchiA in G015 with xylE, which encodes catechol 2,3-dioxygenase, as a reporter gene showed that the transcription from the chiA promoter of S. lividans TK24 occurred regardless of the presence of glucose. G015 was resistant to 2-deoxyglucose (2-DOG) and did not utilize glucose as a sole carbon source. When a DNA fragment containing glkA, a gene for glucose kinase, of Streptomyces coelicolor A3(2) was introduced into strain G015 on a low-copy-number plasmid, the sensitivity to 2-DOG, the ability to utilize glucose, and the glucose repression of chitinase production were restored. These results indicate that glkA is involved in glucose repression of chitinase production in S. lividans TK24.

scholarly journals The Mithramycin Gene Cluster of Streptomyces argillaceus Contains a Positive Regulatory Gene and Two Repeated DNA Sequences That Are Located at Both Ends of the Cluster

1999 ◽  
Vol 181 (2) ◽  
pp. 642-647 ◽  
Author(s):  
Felipe Lombó ◽  
Alfredo F. Braña ◽  
Carmen Méndez ◽  
José A. Salas
Keyword(s):  
Gene Cluster ◽  
Dna Sequences ◽  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Regulatory Protein ◽  
Fold Increase ◽  
Open Reading Frames ◽  
Antibiotic Biosynthesis ◽  
Positive Regulators ◽  
Actinorhodin Production

ABSTRACT Sequencing of a 4.3-kb DNA region from the chromosome ofStreptomyces argillaceus, a mithramycin producer, revealed the presence of two open reading frames (ORFs). The first one (orfA) codes for a protein that resembles several transport proteins. The second one (mtmR) codes for a protein similar to positive regulators involved in antibiotic biosynthesis (DnrI, SnoA, ActII-orf4, CcaR, and RedD) belonging to the Streptomycesantibiotic regulatory protein (SARP) family. Both ORFs are separated by a 1.9-kb, apparently noncoding region. Replacement of themtmR region by an antibiotic resistance cassette completely abolished mithramycin biosynthesis. Expression of mtmR in a high-copy-number vector in S. argillaceus caused a 16-fold increase in mithramycin production. The mtmR gene restored actinorhodin production in Streptomyces coelicolor JF1 mutant, in which the actinorhodin-specific activator ActII-orf4 is inactive, and also stimulated actinorhodin production byStreptomyces lividans TK21. A 241-bp region located 1.9 kb upstream of mtmR was found to be repeated approximately 50 kb downstream of mtmR at the other end of the mithramycin gene cluster. A model to explain a possible route for the acquisition of the mithramycin gene cluster by S. argillaceus is proposed.

SYSTEMIC CAUSES OF THE APPEARANCE OF “COBRA EFFECT” IN THE MANAGEMENT OF SOCIO-ECONOMIC DEVELOPMENT

2019 ◽  
Vol 86 (3) ◽  
pp. 51-61
Author(s):  
M. S. Mokiy ◽  
E. K. Borzenko
Keyword(s):  
Economic Development ◽  
Economic System ◽  
Gross National Product ◽  
The Family ◽  
Social And Economic Development ◽  
Socio Economic Development ◽  
Energy Consuming ◽  
The Right ◽  
Goals And Objectives ◽  
Least Energy

The article on the basis of extrapolation of system laws of management of social and economic development illustrates the system reason of the Cobra effect, that is, a situation where, despite the rather attractive goals that managers formulate, the result of the activities of subordinates is opposite to what was intended. The main problem of management is the development of a system of indicators, in which, working on the indicator, employees would change the state in the right direction. The reason for the Cobra effect is the manifestation of systemic patterns of socio-economic development. The main system regularity is the desire of the system for stability and self-preservation. This state of the system is achieved using the least energy-consuming way. It is shown that any worker, realizing system regularities, aspires to stability and self-preservation. Therefore, the employee is always forced to work for achieving the indicator. The article analyzes the manifestation of these laws at the level of enterprises and state. When managers understand these patterns explicitly or covertly, changes in the economic system are moving in the right direction. It is shown that the existing system of target indicators used as indicators to assess the effectiveness of management does not meet the goals and objectives of socio-economic development. At the meso- and macrolevel, absolute, volumetric indicators, such as gross national product and others, reduce the range of benefits to the population. The article defines the vector of change in the system of indicators for assessing the effectiveness of management at the regional and state levels, based on the fact that the key element is the family. At the same time, the targets should be indicators to assess the availability of benefits for households.

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