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

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.

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

10.1101/227314 ◽

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.

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

10.1101/714766 ◽

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.

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The Possible Common Origin of tRNA and 5S rRNA

Zeitschrift für Naturforschung C ◽

10.1515/znc-1983-5-633 ◽

1983 ◽

Vol 38 (5-6) ◽

pp. 501-504 ◽

Cited By ~ 2

Author(s):

Mária Ujhelyi

Keyword(s):

Common Ancestor ◽

Common Origin ◽

5S Rrna ◽

Mitochondrial Trna ◽

Trna Molecule ◽

The Common

Seryl tRNA (anticodon GCU) from mammalian mitochondria shows in comparison to other mitochondrial tRNAs additional special features differing from the generalized tRNA model. When arranged in the traditional cloverleaf form, eight bases fall within the TΨC loop, and the entire dihydrouridine loop is lacking. This seryl tRNA molecule is therefore shorter than other tRNAs. It was originally thought to represent a mitochondrial analogon of 5 S rRNA and its precise classification is still disputed. The present studies suggest that this mitochondrial tRNA represents a fossil molecule which is related to the common ancestor of the present tRNA and 5 S rRNA molecules.

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Role of the Digestive Gland in Ink Production in Four Species of Sea Hares: An Ultrastructural Comparison

Journal of Marine Biology ◽

10.1155/2013/209496 ◽

2013 ◽

Vol 2013 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Jeffrey S. Prince ◽

Paul Micah Johnson

Keyword(s):

Digestive Gland ◽

Common Ancestor ◽

Aplysia Californica ◽

Digestive Cell ◽

Digestive Cells ◽

Sea Hare ◽

Red Algal ◽

The Common ◽

Algal Chloroplast

The ultrastructure of the digestive gland of several sea hare species that produce different colored ink (Aplysia californicaproduces purple ink,A. julianawhite ink,A. parvulaboth white and purple ink, whileDolabrifera dolabriferaproduces no ink at all) was compared to determine the digestive gland’s role in the diet-derived ink production process. Rhodoplast digestive cells and their digestive vacuoles, the site of digestion of red algal chloroplast (i.e., rhodoplast) inA. californica, were present and had a similar ultrastructure in all four species. Rhodoplast digestive cell vacuoles either contained a whole rhodoplast or fragments of one or were empty. These results suggest that the inability to produce colored ink in some sea hare species is not due to either an absence of appropriate digestive machinery, that is, rhodoplast digestive cells, or an apparent failure of rhodoplast digestive cells to function. These results also propose that the digestive gland structure described herein occurred early in sea hare evolution, at least in the common ancestor to the generaAplysiaandDolabrifera. Our data, however, do not support the hypothesis that the loss of purple inking is a synapomorphy of the white-ink-producing subgenusAplysia.

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Sexual reproduction and genetic exchange in parasitic protists

Parasitology ◽

10.1017/s0031182014001693 ◽

2014 ◽

Vol 142 (S1) ◽

pp. S120-S127 ◽

Cited By ~ 29

Author(s):

GARETH D. WEEDALL ◽

NEIL HALL

Keyword(s):

Life Cycle ◽

Genome Sequencing ◽

Common Ancestor ◽

Life Cycles ◽

Animal Disease ◽

Eukaryotic Evolution ◽

Sequencing Technology ◽

Parasite Reproduction ◽

The Common ◽

Higher Eukaryotes

SUMMARYA key part of the life cycle of an organism is reproduction. For a number of important protist parasites that cause human and animal disease, their sexuality has been a topic of debate for many years. Traditionally, protists were considered to be primitive relatives of the ‘higher’ eukaryotes, which may have diverged prior to the evolution of sex and to reproduce by binary fission. More recent views of eukaryotic evolution suggest that sex, and meiosis, evolved early, possibly in the common ancestor of all eukaryotes. However, detecting sex in these parasites is not straightforward. Recent advances, particularly in genome sequencing technology, have allowed new insights into parasite reproduction. Here, we review the evidence on reproduction in parasitic protists. We discuss protist reproduction in the light of parasitic life cycles and routes of transmission among hosts.

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Genetic variants of the EGFR ligand-binding domain and their association with structural alterations in Arab cancer patients

BMC Research Notes ◽

10.1186/s13104-021-05559-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Maryam Marzouq ◽

Ali Nairouz ◽

Noureddine Ben Khalaf ◽

Sonia Bourguiba-Hachemi ◽

Raed Quaddorah ◽

...

Keyword(s):

Thyroid Cancer ◽

Cancer Patients ◽

Genetic Variants ◽

Growth Factor Receptor ◽

Genomic Analysis ◽

Egfr Ligand ◽

Energetic State ◽

Epidermal Growth ◽

The Common ◽

Heterozygous Form

Abstract Objective This study aimed to identify novel genetic variants in the CR2 extracellular domain of the epidermal growth factor receptor (EGFR) in healthy individuals and patients with six different types of adenocarcinoma, in Arabian peninsula populations. It also aimed to investigate the effects of these variants on the EGFR structure and their eventual relevance to tumorigenesis. Results We detected seven new EGFR genetic variants in 168 cancer patients and 114 controls. A SNP rs374670788 was more frequent in bladder cancer but not significantly associated to. However, a missense mutation (V550M) was significantly associated to colon, ovary, lung, bladder and thyroid cancer samples (p < 0.05). Three mutations (H590R, E602K and T605T) were found in the heterozygous form only in colon cancer patients. Genomic analysis of the synonymous mutation (G632G) showed that the T/A genotype could be associated to thyroid cancer in Arab patients (p < 0.05). An additional novel SNP rs571064657 was observed in control individuals. Computational analysis of the genetic variants revealed a reduction in the stabilization of the EGFR tethered form for both V550M and the common R521K variant with low energetic state (− ∆∆G). Molecular interactions analysis suggested that these mutations might affect the receptor’s function and promote tumorigenesis.

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Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics

Current Genomics ◽

10.2174/1389202922666211130143328 ◽

2021 ◽

Vol 22 ◽

Author(s):

Soma Ghosh ◽

Malathi Bheri ◽

Girdhar K. Pandey

Keyword(s):

Functional Genomics ◽

Protein Kinases ◽

Regulatory Networks ◽

Crop Improvement ◽

Functional Characterization ◽

Genomic Analysis ◽

Major Elements ◽

Model Systems ◽

Plant Responses ◽

Dependent Protein

: Plant systems have developed calcium (Ca2+) signaling as an important mechanism of regulation of stress perception, developmental cues, and responsive gene expression. The post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery involve Ca2+ sensors and responders such as Calmodulin (CaM), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMK), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be the stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

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Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01395-21 ◽

2021 ◽

Author(s):

Satoshi Nakano ◽

Takao Fujisawa ◽

Bin Chang ◽

Yutaka Ito ◽

Hideki Akeda ◽

...

Keyword(s):

Common Ancestor ◽

Sampling Bias ◽

Health Concern ◽

Recent Common Ancestor ◽

Whole Genome ◽

Whole Genome Analysis ◽

Identification Rate ◽

Most Recent Common Ancestor ◽

The Common ◽

The U.S

After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug resistant serotype 19A-ST320 strains became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the U.S. returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the U.S.; therefore, the common ancestor may have originated in the U.S. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates form Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the U.S. before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the U.S. to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the U.S. before being imported into Japan.

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