scholarly journals Ultraconserved non-coding DNA within insect phyla

2019 ◽  
Author(s):  
Thomas Brody ◽  
Amar Yavatkar ◽  
Alexander Kuzin ◽  
Ward F. Odenwald
Keyword(s):  
Genomic Sequence ◽  
Fruit Fly ◽  
Evolutionary Divergence ◽  
Regulatory Sequences ◽  
Phylogenetic Groups ◽  
Conserved Sequences ◽  
Regulatory Interactions ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
Regulatory Dna

AbstractPresence of ultra-conserved sequence elements in vertebrate enhancers suggest that transcription factor regulatory interactions are shared across phylogenetically diverse species. To date evidence for similarly conserved elements among evolutionarily distant insects such as flies, mosquitos, ants and bees, has been elusive. This study has taken advantage of the availability of the assembled genomic sequence of these insects to explore the presence of ultraconserved sequence elements in these phylogenetic groups. To investigate the integrity of fly regulatory sequences across ~100 million years of evolutionary divergence from the fruitfly Drosophila melanogaster, we compared Drosophila non-coding sequences to those of Ceratitis capitata, the Mediterranean fruit fly and Musca domestica, the domestic housefly. Using various alignment techniques, Blastn, Clustal, Blat, EvoPrinter and Needle, we show that many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. We term the sequence elements shared among these species ultraconserved CSBs (uCSBs). The position of the uCSBs with respect to flanking genes is also conserved. The results suggest that CSBs represent the point of interaction of multiple trans-regulators whose functions and interactions are conserved across divergent genera. Blastn alignments also detect putative cis-regulatory sequences shared among evolutionarily distant mosquitos Anopheles gambiae and Culex pipiens and Aedes aegypti. We have also identified conserved sequences shared among bee species. Side by side comparison of bee and ant EvoPrints identify uCSBs shared between the two taxa, as well as more poorly conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in dipterans, mosquitos and bees will lead to a greater understanding of their evolutionary origin and the function of their conserved sequences.

scholarly journals Ultraconserved non-coding DNA within insect phyla

2019 ◽  
Author(s):  
Thomas Brody ◽  
Amar Yavatkar ◽  
Alexander Kuzin ◽  
Ward F. Odenwald
Keyword(s):  
Culex Pipiens ◽  
Genomic Sequence ◽  
Fruit Fly ◽  
Evolutionary Divergence ◽  
Regulatory Sequences ◽  
Coding Sequences ◽  
Regulatory Interactions ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
Regulatory Dna

Abstract Background Presence of ultra-conserved sequence elements in vertebrate enhancers suggest that transcription factor regulatory interactions are shared across phylogenetically diverse species. To date evidence for similarly conserved elements among evolutionarily distant insects such as flies, mosquitos, ants and bees, has been elusive. This study has taken advantage of the availability of the assembled genomic sequence of these insects to explore the presence of ultraconserved sequence elements in these phylogenetic groups.Results To investigate the integrity of fly regulatory sequences across ~100 million years of evolutionary divergence from the fruitfly Drosophila melanogaster , we compared Drosophila non-coding sequences to those of Ceratitis capitata , the Mediterranean fruit fly and Musca domestica , the domestic housefly. Using various alignment techniques, Blastn, Clustal, Blat, EvoPrinter and Needle, we show that many of the conserved sequence blocks (CSBs) that constitute Drosophila cis -regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca . We term the sequence elements shared among these species ultraconserved CSBs (uCSBs). The position of the uCSBs with respect to flanking genes is also conserved. Blastn alignments also detect putative cis -regulatory sequences shared among evolutionarily distant mosquitos Anopheles gambiae and Culex pipiens and Aedes aegypti. We have also identified conserved sequences shared among bee species. Side by side comparison of bee and ant EvoPrints identify uCSBs shared between the two taxa, as well as more poorly conserved CSBs in either one or the other taxon but not in both.Conclusions The results suggest that CSBs represent the point of interaction of multiple trans-regulators whose functions and interactions are conserved across divergent genera. Analysis of uCSBs in dipterans, mosquitos and bees will lead to a greater understanding of their evolutionary origin and the function of their conserved non-coding sequences.

scholarly journals Ultraconserved Non-coding DNA Within Diptera and Hymenoptera

2020 ◽  
Vol 10 (9) ◽  
pp. 3015-3024 ◽  
Author(s):  
Thomas Brody ◽  
Amarendra Yavatkar ◽  
Alexander Kuzin ◽  
Ward F Odenwald
Keyword(s):  
Genomic Sequence ◽  
Mosquito Species ◽  
Phylogenetic Footprinting ◽  
Reference Sequence ◽  
Phylogenetic Groups ◽  
Developmental Genes ◽  
Coding Sequences ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
And Function

Abstract This study has taken advantage of the availability of the assembled genomic sequence of flies, mosquitos, ants and bees to explore the presence of ultraconserved sequence elements in these phylogenetic groups. We compared non-coding sequences found within and flanking Drosophila developmental genes to homologous sequences in Ceratitis capitata and Musca domestica. Many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. Also conserved is the position but not necessarily the orientation of many of these ultraconserved CSBs (uCSBs) with respect to flanking genes. Using the mosquito EvoPrint algorithm, we have also identified uCSBs shared among distantly related mosquito species. Side by side comparison of bee and ant EvoPrints of selected developmental genes identify uCSBs shared between these two Hymenoptera, as well as less conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in these dipterans and Hymenoptera will lead to a greater understanding of their evolutionary origin and function of their conserved non-coding sequences and aid in discovery of core elements of enhancers. This study applies the phylogenetic footprinting program EvoPrinter to detection of ultraconserved non-coding sequence elements in Diptera, including flies and mosquitos, and Hymenoptera, including ants and bees. EvoPrinter outputs an interspecies comparison as a single sequence in terms of the input reference sequence. Ultraconserved sequences flanking known developmental genes were detected in Ceratitis and Musca when compared with Drosophila species, in Aedes and Culex when compared with Anopheles, and between ants and bees. Our methods are useful in detecting and understanding the core evolutionarily hardened sequences required for gene regulation.

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

scholarly journals SAND, a New Protein Family: From Nucleic Acid to Protein Structure and Function Prediction

2001 ◽  
Vol 2 (4) ◽  
pp. 226-235 ◽  
Author(s):  
Amanda Cottage ◽  
Yvonne J. K. Edwards ◽  
Greg Elgar
Keyword(s):  
Genomic Sequence ◽  
Protein Family ◽  
Sequence Motifs ◽  
Est Database ◽  
Computational Tools ◽  
Conserved Sequence ◽  
Conserved Sequence Motifs ◽  
And Function ◽  
New Protein ◽  
Genomic Organisation

As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence fromFugu rubripes, we identified a novel gene,SAND, with significant sequence identity to hypothetical proteins predicted inSaccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, aDrosophila melanogastergene, and mouse and human cDNAs. Here we identify a furtherSANDhomologue in human andArabidopsis thalianaby use of standard computational tools. We describe the genomic organisation ofSANDin these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.

scholarly journals The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers inEnterobacteriaceae

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
W. Ryan Will ◽  
Peter Brzovic ◽  
Isolde Le Trong ◽  
Ronald E. Stenkamp ◽  
Matthew B. Lawrenz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Regulatory Networks ◽  
Antimicrobial Agents ◽  
Efflux Pumps ◽  
Evolutionary Divergence ◽  
Regulatory Sequences ◽  
Emerging Pathogens ◽  
Practical Applications

ABSTRACTGene duplication and subsequent evolutionary divergence have allowed conserved proteins to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive duplication and diversification in bacteria, where they act as environmentally responsive repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many antimicrobial agents. We have performed structural, functional, and genetic analyses of representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral functions, including repression of their own expression and that of divergently transcribed multidrug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, SlyA and RovA have acquired the ability to countersilence horizontally acquired genes, which has greatly facilitated the evolution ofEnterobacteriaceaeby horizontal gene transfer. SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to provide the enhanced levels of expression required for their new role. Moreover, in contrast to MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to acquire new functions as a result of evolutionary divergence of bothcis-regulatory sequences and intransinteractions with modulatory ligands.IMPORTANCEBacteria primarily evolve via horizontal gene transfer, acquiring new traits such as virulence and antibiotic resistance in single transfer events. However, newly acquired genes must be integrated into existing regulatory networks to allow appropriate expression in new hosts. This is accommodated in part by the opposing mechanisms of xenogeneic silencing and countersilencing. An understanding of these mechanisms is necessary to understand the relationship between gene regulation and bacterial evolution. Here we examine the functional evolution of an important lineage of countersilencers belonging to the ancient MarR family of classical transcriptional repressors. We show that although members of the SlyA lineage retain some ancestral features associated with the MarR family, theircis-regulatory sequences have evolved significantly to support their new function. Understanding the mechanistic requirements for countersilencing is critical to understanding the pathoadaptation of emerging pathogens and also has practical applications in synthetic biology.

scholarly journals Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

2008 ◽  
Vol 28 (10) ◽  
pp. 3089-3100 ◽  
Author(s):  
Wayne A. Decatur ◽  
Murray N. Schnare
Keyword(s):  
Large Subunit ◽  
Consensus Sequence ◽  
5S Rrna ◽  
Stem Loop ◽  
Conserved Sequence ◽  
5.8S Rrna ◽  
Sequence Elements ◽  
The Individual ◽  
A Site ◽  
Large Subunit Rrna

ABSTRACT The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Ψs) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Ψ formation in 5S and 5.8S rRNA in which the unassigned Ψs occur. We show that while the formation of the Ψ in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Ψ in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Ψ in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.

scholarly journals Intron 7 conserved sequence elements regulate the splicing of the SMN genes

2009 ◽  
Vol 126 (6) ◽  
pp. 833-841 ◽  
Author(s):  
Jordan T. Gladman ◽  
Dawn S. Chandler
Keyword(s):  
Conserved Sequence ◽  
Sequence Elements
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