scholarly journals MicroRNA clusters integrate evolutionary constraints on expression and target affinities: the miR-6/5/4/286/3/309 cluster in Drosophila leg development

2019 ◽  
Author(s):  
Zhe Qu ◽  
Wing Chung Yiu ◽  
Ho Yin Yip ◽  
Wenyan Nong ◽  
Clare W.C. Yu ◽  
...  
Keyword(s):  
Small Rna Sequencing ◽  
Cell Transfection ◽  
Wild Type ◽  
New Members ◽  
Microrna Targets ◽  
Wild Type Phenotype ◽  
Leg Development ◽  
Microrna Cluster ◽  
Gene Regulatory ◽  
Evolutionary Consequences

AbstractA striking feature of microRNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a microRNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this microRNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of microRNA cluster members were also constructed. Expression of individual microRNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient microRNAs together (miR-5/4/286/3/309) or more recently evolved clustered microRNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed down-regulation of leg patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of microRNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct microRNAs. Considering together the microRNA targets and the evolutionary ages of each microRNA in the cluster demonstrates the importance of microRNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing microRNAs.

scholarly journals Micro-RNA Clusters Integrate Evolutionary Constraints on Expression and Target Affinities: The miR-6/5/4/286/3/309 Cluster in Drosophila

2020 ◽  
Vol 37 (10) ◽  
pp. 2955-2965
Author(s):  
Qu Zhe ◽  
Wing Chung Yiu ◽  
Ho Yin Yip ◽  
Wenyan Nong ◽  
Clare W C Yu ◽  
...  
Keyword(s):  
Micro Rna ◽  
Small Rna Sequencing ◽  
Wild Type ◽  
New Members ◽  
Cluster Evolution ◽  
Rna Targets ◽  
Wild Type Phenotype ◽  
Micro Rnas ◽  
Gene Regulatory ◽  
Evolutionary Consequences

Abstract A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a micro-RNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this micro-RNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of micro-RNA cluster members were also constructed. Expression of individual micro-RNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient micro-RNAs together (miR-5/4/286/3/309) or more recently evolved clustered micro-RNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed downregulation of leg-patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of micro-RNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct micro-RNAs. Considered together, the micro-RNA targets and the evolutionary ages of each micro-RNA in the cluster demonstrate the importance of micro-RNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing micro-RNAs. Key words: micro-RNA, cluster, evolution.

scholarly journals A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks in Drosophila

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Lyu ◽  
Zhongqi Liufu ◽  
Juan Xiao ◽  
Tian Tang
Keyword(s):  
Regulatory Networks ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Target Prediction ◽  
Cell Transfection ◽  
Functional Evolution ◽  
New Members ◽  
New Targets ◽  
Microrna Cluster ◽  
The Common

New miRNAs are evolutionarily important but their functional evolution remains unclear. Here we report that the evolution of a microRNA cluster, mir-972C rewires its downstream regulatory networks in Drosophila. Genomic analysis reveals that mir-972C originated in the common ancestor of Drosophila where it comprises six old miRNAs. It has subsequently recruited six new members in the melanogaster subgroup after evolving for at least 50 million years. Both the young and the old mir-972C members evolved rapidly in seed and non-seed regions. Combining target prediction and cell transfection experiments, we found that the seed and non-seed changes in individual mir-972C members cause extensive target divergence among D. melanogaster, D. simulans, and D. virilis, consistent with the functional evolution of mir-972C reported recently. Intriguingly, the target pool of the cluster as a whole remains relatively conserved. Our results suggest that clustering of young and old miRNAs broadens the target repertoires by acquiring new targets without losing many old ones. This may facilitate the establishment of new miRNAs in existing regulatory networks.

scholarly journals Gene regulatory network rewiring by an adaptively evolving microRNA cluster in Drosophila

2017 ◽  
Author(s):  
Yang Lyu ◽  
Zhongqi Liufu ◽  
Juan Xiao ◽  
Yuxin Chen ◽  
Chung-I Wu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Biological Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
De Novo ◽  
Target Prediction ◽  
New Members ◽  
Microrna Cluster ◽  
Gene Regulatory ◽  
Network Rewiring

AbstractNew miRNAs are evolutionarily important but their impact on existing biological networks remains unclear. We report the evolution of a microRNA cluster, mir-972C, that arose de novo and the subsequently rewired gene regulatory networks in Drosophila. Molecular evolution analyses revealed that mir-972C originated in the common ancestor of Drosophila where it comprises five old miRNAs. It subsequently recruited five new members in the melanogaster subgroup after conservative evolution for at least 50 million years. Population genetics analyses reveal that young and old mir-972C miRNAs evolved rapidly under positive selection in both seed and non-seed regions. Combining target prediction and cell transfection experiments, we find that sequence changes in individual mir-972C members resulted in extensive gene regulatory network divergence among D. melanogaster, D. simulans, and D. virilis, whereas the target pool of the cluster as a whole remains relatively conserved. Our results suggest that clustering of young and old miRNAs at the same locus broadens target repertoires, resulting in the gain of new targets without losing many old ones. This may facilitate the establishment of new miRNAs within existing regulatory networks.

scholarly journals The UDP N-Acetylgalactosamine 4-Epimerase Gene Is Essential for Mesophilic Aeromonas hydrophila Serotype O34 Virulence

2006 ◽  
Vol 74 (1) ◽  
pp. 537-548 ◽  
Author(s):  
Rocío Canals ◽  
Natalia Jiménez ◽  
Silvia Vilches ◽  
Miguel Regué ◽  
Susana Merino ◽  
...  
Keyword(s):  
Aeromonas Hydrophila ◽  
Type Strain ◽  
Wild Type Strain ◽  
Sugar Residue ◽  
Serum Resistance ◽  
Single Mutation ◽  
Wild Type ◽  
O Antigen ◽  
Wild Type Phenotype

ABSTRACT Mesophilic Aeromonas hydrophila strains of serotype O34 typically express smooth lipopolysaccharide (LPS) on their surface. A single mutation in the gene that codes for UDP N-acetylgalactosamine 4-epimerase (gne) confers the O− phenotype (LPS without O-antigen molecules) on a strain in serotypes O18 and O34, but not in serotypes O1 and O2. The gne gene is present in all the mesophilic Aeromonas strains tested. No changes were observed for the LPS core in a gne mutant from A. hydrophila strain AH-3 (serotype O34). O34 antigen LPS contains N-acetylgalactosamine, while no such sugar residue forms part of the LPS core from A. hydrophila AH-3. Some of the pathogenic features of A. hydrophila AH-3 gne mutants are drastically reduced (serum resistance or adhesion to Hep-2 cells), and the gne mutants are less virulent for fish and mice compared to the wild-type strain. Strain AH-3, like other mesophilic Aeromonas strains, possess two kinds of flagella, and the absence of O34 antigen molecules by gne mutation in this strain reduced motility without any effect on the biogenesis of both polar and lateral flagella. The reintroduction of the single wild-type gne gene in the corresponding mutants completely restored the wild-type phenotype (presence of smooth LPS) independently of the O wild-type serotype, restored the virulence of the wild-type strain, and restored motility (either swimming or swarming).

Rescue of the mutant phenotype by reexpression of full-length vinculin in null F9 cells; effects on cell locomotion by domain deleted vinculin

1998 ◽  
Vol 111 (11) ◽  
pp. 1535-1544 ◽  
Author(s):  
W. Xu ◽  
J.L. Coll ◽  
E.D. Adamson
Keyword(s):  
Marked Effect ◽  
Control Cell ◽  
Covalent Attachment ◽  
Tail Domain ◽  
Wild Type ◽  
F9 Cells ◽  
Wild Type Phenotype ◽  
Correct Location ◽  
Low Levels ◽  
Lamellipodia Formation

Vinculin plays a role in signaling between integrins and the actin cytoskeleton. We reported earlier that F9-derived cells lacking vinculin are less spread, less adhesive, and move two times faster than wild-type F9 cells. Expression of intact vinculin in null cells restored all wild-type characteristics. In contrast, expression of the head (90 kDa) fragment exaggerated mutant characteristics, especially locomotion, which was double that of vinculin null cells. Expression of the tail domain also had a marked effect on locomotion in the opposite direction, reducing it to very low levels. The expression of the head plus tail domains together (no covalent attachment) effected a partial rescue towards wild-type phenotype, thus indicating that reexpressed polypeptides may be in their correct location and are interacting normally. Therefore, we conclude that: (1) the head domain is part of the locomotory force of the cell, modulated by the tail, and driven by the integrin/matrix connection; (2) intact vinculin is required for normal regulation of cell behavior, suggesting that vinculin head-tail interactions control cell adhesion, spreading, lamellipodia formation and locomotion.

scholarly journals New Sporulation Loci in Streptomyces coelicolor A3(2)

1999 ◽  
Vol 181 (17) ◽  
pp. 5419-5425 ◽  
Author(s):  
N. Jamie Ryding ◽  
Maureen J. Bibb ◽  
Virginie Molle ◽  
Kim C. Findlay ◽  
Keith F. Chater ◽  
...  
Keyword(s):  
Phase Contrast ◽  
Streptomyces Coelicolor ◽  
Cosmid Library ◽  
Phase Contrast Microscopy ◽  
Wild Type ◽  
Chromosomal Dna ◽  
East Anglia ◽  
Wild Type Phenotype ◽  
Contrast Microscopy ◽  
Spore Pigment

ABSTRACT Sporulation mutants of Streptomyces coelicolor appear white because they are defective in the synthesis of the grey polyketide spore pigment, and such white (whi) mutants had been used to define eight sporulation loci, whiA,whiB, whiD, whiE, whiG,whiH, whiI, and whiJ (K. F. Chater, J. Gen. Microbiol. 72:9–28, 1972; N. J. Ryding, Ph.D. thesis, University of East Anglia, 1995). In an attempt to identify new whi loci, we mutagenized S. coelicolor M145 spores with nitrosoguanidine and identified 770 mutants with colonies ranging from white to medium grey. After excluding unstable strains, we examined the isolates by phase-contrast microscopy and chose 115 whi mutants with clear morphological phenotypes for further study. To exclude mutants representing cloned whi genes, self-transmissible SCP2*-derived plasmids carrying whiA, whiB,whiG, whiH, or whiJ (but notwhiD, whiE, or whiI) were introduced into each mutant by conjugation, and strains in which the wild-type phenotype was restored either partially or completely by any of these plasmids were excluded from further analysis. In an attempt to complement some of the remaining 31 whi mutants, an SCP2* library of wild-type S. coelicolor chromosomal DNA was introduced into 19 of the mutants by conjugation. Clones restoring the wild-type phenotype to 12 of the 19 strains were isolated and found to represent five distinct loci, designated whiK,whiL, whiM, whiN, andwhiO. Each of the five loci was located on the ordered cosmid library: whiL, whiM, whiN, and whiO occupied positions distinct from previously clonedwhi genes; whiK was located on the same cosmid overlap as whiD, but the two loci were shown by complementation to be distinct. The phenotypes resulting from mutations at each of these new loci are described.

scholarly journals Association of intronic DNA methylation and hydroxymethylation alterations in the epigenetic etiology of dilated cardiomyopathy

2019 ◽  
Vol 317 (1) ◽  
pp. H168-H180 ◽  
Author(s):  
Ali M. Tabish ◽  
Mohammed Arif ◽  
Taejeong Song ◽  
Zaher Elbeck ◽  
Richard C. Becker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dilated Cardiomyopathy ◽  
Cardiac Remodeling ◽  
Rna Seq ◽  
Wild Type ◽  
Kegg Pathways ◽  
Wild Type Phenotype ◽  
Gene Expression Levels

In this study, we investigated the role of DNA methylation [5-methylcytosine (5mC)] and 5-hydroxymethylcytosine (5hmC), epigenetic modifications that regulate gene activity, in dilated cardiomyopathy (DCM). A MYBPC3 mutant mouse model of DCM was compared with wild type and used to profile genomic 5mC and 5hmC changes by Chip-seq, and gene expression levels were analyzed by RNA-seq. Both 5mC-altered genes (957) and 5hmC-altered genes (2,022) were identified in DCM hearts. Diverse gene ontology and KEGG pathways were enriched for DCM phenotypes, such as inflammation, tissue fibrosis, cell death, cardiac remodeling, cardiomyocyte growth, and differentiation, as well as sarcomere structure. Hierarchical clustering of mapped genes affected by 5mC and 5hmC clearly differentiated DCM from wild-type phenotype. Based on these data, we propose that genomewide 5mC and 5hmC contents may play a major role in DCM pathogenesis. NEW & NOTEWORTHY Our data demonstrate that development of dilated cardiomyopathy in mice is associated with significant epigenetic changes, specifically in intronic regions, which, when combined with gene expression profiling data, highlight key signaling pathways involved in pathological cardiac remodeling and heart contractile dysfunction.

scholarly journals Heteromeric Interactions among Nucleoid-Associated Bacterial Proteins: Localization of StpA-Stabilizing Regions in H-NS of Escherichia coli

2001 ◽  
Vol 183 (7) ◽  
pp. 2343-2347 ◽  
Author(s):  
Jörgen Johansson ◽  
Sven Eriksson ◽  
Berit Sondén ◽  
Sun Nyunt Wai ◽  
Bernt Eric Uhlin
Keyword(s):  
Escherichia Coli ◽  
Stable Form ◽  
Lon Protease ◽  
Wild Type ◽  
Bacterial Proteins ◽  
Regulatory Systems ◽  
Associated Proteins ◽  
Gene Regulatory

ABSTRACT The nucleoid-associated proteins H-NS and StpA inEscherichia coli bind DNA as oligomers and are implicated in gene regulatory systems. There is evidence for both homomeric and heteromeric H-NS–StpA complexes. The two proteins show differential turnover, and StpA was previously found to be subject to protease-mediated degradation by the Lon protease. We investigated which regions of the H-NS protein are able to prevent degradation of StpA. A set of truncated H-NS derivatives was tested for their ability to mediate StpA stability and to form heteromers in vitro. The data indicate that H-NS interacts with StpA at two regions and that the presence of at least one of the H-NS regions is necessary for StpA stability. Our results also suggest that a proteolytically stable form of StpA, StpAF21C, forms dimers, whereas wild-type StpA in the absence of H-NS predominantly forms tetramers or oligomers, which are more susceptible to proteolysis.

scholarly journals Construction of a Codon-Adapted Nourseotricin-Resistance Marker Gene for Efficient Targeted Gene Deletion in the Mycophenolic Acid Producer Penicillium brevicompactum

2019 ◽  
Vol 5 (4) ◽  
pp. 96
Author(s):  
Yasaman Mahmoudjanlou ◽  
Birgit Hoff ◽  
Ulrich Kück
Keyword(s):  
Mycophenolic Acid ◽  
Marker Gene ◽  
Wild Type ◽  
Resistance Marker ◽  
Subsequent Transformation ◽  
Targeted Gene Deletion ◽  
Filamentous Ascomycete ◽  
Wild Type Phenotype ◽  
Penicillium Brevicompactum ◽  
Resistance Markers

Penicillium brevicompactum is a filamentous ascomycete used in the pharmaceutical industry to produce mycophenolic acid, an immunosuppressant agent. To extend options for genetic engineering of this fungus, we have tested two resistance markers that have not previously been applied to P. brevicompactum. Although a generally available phleomycin resistance marker (ble) was successfully used in DNA-mediated transformation experiments, we were not able to use a commonly applicable nourseothricin resistance cassette (nat1). To circumvent this failure, we constructed a new nat gene, considering the codon bias for P. brevicompactum. We then used this modified nat gene in subsequent transformation experiments for the targeted disruption of two nuclear genes, MAT1-2-1 and flbA. For MAT1-2-1, we obtained deletion strains with a frequency of about 10%. In the case of flbA, the frequency was about 4%, and this disruption strain also showed reduced conidiospore formation. To confirm the deletion, we used ble to reintroduce the wild-type genes. This step restored the wild-type phenotype in the flbA deletion strain, which had a sporulation defect. The successful transformation system described here substantially extends options for genetically manipulating the biotechnologically relevant fungus P. brevicompactum.

scholarly journals Influence of the σB Stress Factor and yxaB, the Gene for a Putative Exopolysaccharide Synthase under σB Control, on Biofilm Formation

2008 ◽  
Vol 190 (10) ◽  
pp. 3546-3556 ◽  
Author(s):  
Krzysztofa Nagórska ◽  
Krzysztof Hinc ◽  
Mark A. Strauch ◽  
Michał Obuchowski
Keyword(s):  
Growth Conditions ◽  
Transcription Unit ◽  
Solid Surfaces ◽  
Regulation Of Transcription ◽  
Partial Recovery ◽  
Wild Type ◽  
Transcription Start ◽  
Glycerate Kinase ◽  
Wild Type Phenotype ◽  
Air Liquid Interface

ABSTRACT Bacillus subtilis forms structured communities of biofilms encased in an exopolysaccharide matrix on solid surfaces and at the air-liquid interface. It is postulated that nonoptimal growth conditions induce this multicellular behavior. We showed that under laboratory conditions a strain deleted for sigB was unable to form a floating pellicle on the surface of a liquid medium. However, overexpression of yxaB, encoding a putative exopolysaccharide synthase, from a p Spac promoter in a sigB-deleted strain resulted in partial recovery of the wild-type phenotype, indicating the participation of the YxaB protein in this multicellular process. We present data concerning the regulation of transcription of genes yxaB and yxaA, encoding a putative glycerate kinase. Both genes are cotranscribed as a single transcription unit from a σA-dependent promoter during vegetative growth of a liquid bacterial culture. The promoter driving transcription of the yxaAB operon is regulated by AbrB. In addition, the second gene in the operon, yxaB, possesses its own promoter, which is recognized by RNA polymerase containing the σB subunit. This transcription start site is used under general stress conditions, resulting in increased expression.

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