Meiotic Recombination Between Paralogous RBCSB Genes on Sister Chromatids of Arabidopsis thaliana

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 947-957 ◽  
Author(s):  
John G Jelesko ◽  
Kristy Carter ◽  
Whitney Thompson ◽  
Yuki Kinoshita ◽  
Wilhelm Gruissem
Keyword(s):  
Gene Cluster ◽  
Dna Sequences ◽  
Meiotic Recombination ◽  
Sequence Similarity ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Paralogous Genes ◽  
Chimeric Genes ◽  
Unequal Recombination ◽  
Sister Chromatids

Abstract Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 × 10-6. A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster.

Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

2021 ◽  
pp. gr.275658.121
Author(s):  
Yuyun Zhang ◽  
Zijuan Li ◽  
Yu'e Zhang ◽  
Kande Lin ◽  
Yuan Peng ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Sequence Similarity ◽  
Purifying Selection ◽  
Wheat Genome ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

scholarly journals Molecular Characteristics of Carnivore Protoparvovirus 1 With High Sequence Similarity Between Wild and Domestic Carnivores in Taiwan

2021 ◽  
Author(s):  
Ai-Mei Chang ◽  
Chen-Chih Chen
Keyword(s):  
Dna Sequences ◽  
Gastrointestinal Disease ◽  
Sequence Similarity ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
High Sequence Similarity ◽  
Vp2 Gene ◽  
Pcr Screening ◽  
Wild Carnivores ◽  
Domestic Carnivores

Carnivore protoparvovirus 1 (CPPV-1) is a DNA virus causing gastrointestinal disease and immunosuppression in various terrestrial carnivores. Domestic dogs and cats are considered the primary CPPV-1 reservoirs. The habitat overlaps of wild carnivores and free-roaming dogs increases the threat of CPPV-1 transmission between them. This study explored the CPPV-1 distribution among wild carnivores through PCR screening and compared the DNA sequences of the partial capsid protein (VP2) between wild and domestic carnivores. In total, 181 samples were screened for the CPPV-1 VP2 gene, including 32 masked palm civets (Paguma larvata), 63 Chinese ferret badgers (Melogale moschata), and 86 crab-eating mongooses (Herpestes urva), from 2015 to 2019 in Taiwan. The average prevalence of CPPV-1 was 17.7% (32/181), with the highest prevalence in masked palm civets (37.5%). In addition, a masked palm civet was coinfected with two CPPV-1 strains. Among the 33 partial VP2 gene sequences, 23 were identical to sequences amplified from domestic dogs and cats in Asia and the remaining 10 were identified for the first time. This study demonstrated that CPPV-1 has circulated between domestic and wild carnivores in rural Taiwan. Therefore, further population control and health management of free-roaming domestic carnivores are recommended.

scholarly journals Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations

2007 ◽  
Vol 6 (7) ◽  
pp. 1200-1209 ◽  
Author(s):  
Howard S. Judelson ◽  
Shuji Tani
Keyword(s):  
Phytophthora Infestans ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Transcriptional Regulator ◽  
Hairpin Rna ◽  
High Sequence Similarity ◽  
Genes Encoding ◽  
Cognate Gene ◽  
Chromatin Packing ◽  
Nif Proteins

ABSTRACT Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.

DNA sequences of RAPD fragments in artiodactyls

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 456-458 ◽  
Author(s):  
Silja Kostia ◽  
Jukka Palo ◽  
Sirkka-Liisa Varvio
Keyword(s):  
Dna Sequences ◽  
Sequence Similarity ◽  
Receptor Gene ◽  
Chromosome 2 ◽  
High Sequence Similarity ◽  
Microsatellite Repeats ◽  
Rapd Profile ◽  
Inositol 1,4,5 Trisphosphate ◽  
Trisphosphate Receptor

A bovine RAPD profile, generated by a 10-mer primer, was analysed by sequencing the major fragments. Three of four different fragments showed homologies to previously characterized mammalian sequences. One was 61–66% identical to LINE sequences and another was 78.5% identical to a human chromosome 2 sequence tagged site. The third fragment was 93.1% identical to the human type 2 inositol 1,4,5-trisphosphate receptor gene. This fragment had counterparts in white-tailed deer and reindeer; fragments of slightly different size in these species showed high sequence similarity and the size differences were due to varying numbers of dinucleotide microsatellite repeats inside the fragment. Key words : RAPD, artiodactyls, sequence similarity, microsatellites, type 2 inositol 1,4,5-trisphosphate receptor.

Molecular identification ofAustrobilharziaspecies parasitizingCerithidea cingulata(Gastropoda: Potamididae) from Kuwait Bay

2011 ◽  
Vol 86 (4) ◽  
pp. 470-478 ◽  
Author(s):  
W.Y. Al-Kandari ◽  
S.A. Al-Bustan ◽  
A.M. Isaac ◽  
B.A. George ◽  
B.S. Chandy
Keyword(s):  
Dna Sequences ◽  
Sequence Comparison ◽  
Sequence Similarity ◽  
Morphological Identification ◽  
High Sequence Similarity ◽  
Data Set ◽  
Kuwait Bay ◽  
Causative Agents ◽  
Avian Schistosomes ◽  
Combined Data

AbstractAvian schistosomes belonging to the genusAustrobilharzia(Digenea: Schistosomatidae) are among the causative agents of cercarial dermatitis in humans. In this paper, ribosomal and mitochondrial DNA sequences were used to study schistosome cercariae from Kuwait Bay that have been identified morphologically asAustrobilharziasp. Sequence comparison of the ribosomal DNA (rDNA) 28S and 18S regions of the collected schistosome cercariae with corresponding sequences of other schistosomes in GenBank revealed high sequence similarity. This confirmed the morphological identification of schistosome cercariae from Kuwait Bay as belonging to the genusAustrobilharzia. The finding was further supported by the phylogenetic tree that was constructed based on the combined data set 18S-28S-mitochondrial cytochrome oxidase I (mtCO1) sequences in whichAustrobilharziasp. clustered withA. terrigalensisandA. variglandis. Sequence comparison of theAustrobilharziasp. from Kuwait Bay withA. variglandisandA. terrigalensisbased on mtCO1 showed a variation of 10% and 11%, respectively. Since the sequence variation in the mtCO1 was within the interspecific range among trematodes, it seems that theAustrobilharziaspecies from Kuwait Bay is different from the two species reported in GenBank,A.terrigalensisandA. variglandis.

scholarly journals Structure and Sequence Conservation of hao Cluster Genes of Autotrophic Ammonia-Oxidizing Bacteria: Evidence for Their Evolutionary History

2005 ◽  
Vol 71 (9) ◽  
pp. 5371-5382 ◽  
Author(s):  
David J. Bergmann ◽  
Alan B. Hooper ◽  
Martin G. Klotz
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Molecular Ecology ◽  
Gene Clusters ◽  
Nitrite Reduction ◽  
Divergent Evolution ◽  
Ammonia Oxidizing Bacteria ◽  
High Sequence Similarity ◽  
Hydroxylamine Oxidoreductase ◽  
Transfer Event

ABSTRACT Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c 554; and cycB, cytochrome c m 552. The deduced protein sequences of HAO, c 554, and c m 552 were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c m 552, NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c 554 gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c 554 gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.

scholarly journals Viral Hormones: Expanding Dimensions in Endocrinology

Endocrinology ◽  
2019 ◽  
Vol 160 (9) ◽  
pp. 2165-2179 ◽  
Author(s):  
Qian Huang ◽  
C Ronald Kahn ◽  
Emrah Altindis
Keyword(s):  
Dna Sequences ◽  
Sequence Similarity ◽  
Endocrine System ◽  
Peptide Hormones ◽  
Rna Sequences ◽  
High Sequence Similarity ◽  
In Vivo Models ◽  
Viral Mimicry

AbstractViruses have developed different mechanisms to manipulate their hosts, including the process of viral mimicry in which viruses express important host proteins. Until recently, examples of viral mimicry were limited to mimics of growth factors and immunomodulatory proteins. Using a comprehensive bioinformatics approach, we have shown that viruses possess the DNA/RNA with potential to encode 16 different peptides with high sequence similarity to human peptide hormones and metabolically important regulatory proteins. We have characterized one of these families, the viral insulin/IGF-1–like peptides (VILPs), which we identified in four members of the Iridoviridae family. VILPs can bind to human insulin and IGF-1 receptors and stimulate classic postreceptor signaling pathways. Moreover, VILPs can stimulate glucose uptake in vitro and in vivo and stimulate DNA synthesis. DNA sequences of some VILP-carrying viruses have been identified in the human enteric virome. In addition to VILPs, sequences with homology to 15 other peptide hormones or cytokines can be identified in viral DNA/RNA sequences, some with a very high identity to hormones. Recent data by others has identified a peptide that resembles and mimics α-melanocyte-stimulating hormone’s anti-inflammatory effects in in vitro and in vivo models. Taken together, these studies reveal novel mechanisms of viral and bacterial pathogenesis in which the microbe can directly target or mimic the host endocrine system. These findings also introduce the concept of a system of microbial hormones that provides new insights into the evolution of peptide hormones, as well as potential new roles of microbial hormones in health and disease.

scholarly journals The cylindrospermopsin gene cluster of Aphanizomenon sp. strain 10E6: organization and recombination

Microbiology ◽  
2010 ◽  
Vol 156 (8) ◽  
pp. 2438-2451 ◽  
Author(s):  
Anke Stüken ◽  
Kjetill S. Jakobsen
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Gc Content ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Cylindrospermopsis Raciborskii ◽  
Rrna Gene ◽  
Full Genome Sequencing ◽  
High Sequence Similarity ◽  
Geographical Regions

Cylindrospermopsin (CYN), a potent hepatoxin, occurs in freshwaters worldwide. Several cyanobacterial species produce the toxin, but the producing species vary between geographical regions. Aphanizomenon flos-aquae, a common algae species in temperate fresh and brackish waters, is one of the three well-documented CYN producers in European waters. So far, no genetic information on the CYN genes of this species has been available. Here, we describe the complete CYN gene cluster, including flanking regions from the German Aphanizomenon sp. strain 10E6 using a full genome sequencing approach by 454 pyrosequencing and bioinformatic identification of the gene cluster. In addition, we have sequenced a ∼7 kb fragment covering the genes cyrC (partially), cyrA and cyrB (partially) of the same gene cluster in the CYN-producing Aphanizomenon sp. strains 10E9 and 22D11. Comparisons with the orthologous gene clusters of the Australian Cylindrospermopsis raciborskii strains AWT205 and CS505 and the partial gene cluster of the Israeli Aphanizomenon ovalisporum strain ILC-146 revealed a high gene sequence similarity, but also extensive rearrangements of gene order. The high sequence similarity (generally higher than that of 16S rRNA gene fragments from the same strains), atypical GC-content and signs of transposase activities support the suggestion that the CYN genes have been horizontally transferred.

scholarly journals The Isolation of Pyrroloformamide Congeners and Characterization of Its Biosynthetic Gene Cluster from Streptomyces sp. CB02980 Revealed a Unified Mechanism for Dithiolopyrrolone Biosynthesis

2019 ◽  
Author(s):  
Wenqing Zhou ◽  
Haoyu Liang ◽  
Xiangjing Qin ◽  
Danfeng Cao ◽  
Xiangcheng Zhu ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Biosynthetic Gene Cluster ◽  
Gene Replacement ◽  
Biosynthetic Gene ◽  
High Sequence Similarity ◽  
Bicyclic Structure ◽  
Microbial Natural Products ◽  
Drug Leads

Dithiolopyrrolones are microbial natural products containing a disulfide or thiosulfonate bridge embedded in a unique bicyclic structure. In the current study, two new dithiolopyrrolones, pyrroloformamide C (<b>3</b>) and pyrroloformamide D (<b>4</b>), were isolated from <i>Streptomyces </i>sp. CB02980, together with the known pyrroloformamides <b>1 </b>and <b>2</b>. The biosynthetic gene cluster for pyrroloformamides was identified from <i>S</i>. sp. CB02980, which shared high sequence similarity with those of dithiolopyrrolones, including holomycin and thiolutin. Gene replacement of pyfE, which encodes a non-ribosomal peptide synthetase, abolished the production of <b>1</b>－<b>4</b>. Overexpression of <i>pyfN</i>, a type II thioesterase gene, increased the production of <b>1</b> and <b>2</b>. The structure elucidation and biosynthetic characterization of pyrroloformamides <b>1</b> - <b>4</b> may inspire future efforts to discover new dithiolopyrrolones, which are promising drug leads for the treatment of infectious diseases or cancer.

scholarly journals The Isolation of Pyrroloformamide Congeners and Characterization of Its Biosynthetic Gene Cluster from Streptomyces sp. CB02980 Revealed a Unified Mechanism for Dithiolopyrrolone Biosynthesis

2019 ◽  
Author(s):  
Wenqing Zhou ◽  
Haoyu Liang ◽  
Xiangjing Qin ◽  
Danfeng Cao ◽  
Xiangcheng Zhu ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Biosynthetic Gene Cluster ◽  
Gene Replacement ◽  
Biosynthetic Gene ◽  
High Sequence Similarity ◽  
Bicyclic Structure ◽  
Microbial Natural Products ◽  
Drug Leads

Dithiolopyrrolones are microbial natural products containing a disulfide or thiosulfonate bridge embedded in a unique bicyclic structure. In the current study, two new dithiolopyrrolones, pyrroloformamide C (<b>3</b>) and pyrroloformamide D (<b>4</b>), were isolated from <i>Streptomyces </i>sp. CB02980, together with the known pyrroloformamides <b>1 </b>and <b>2</b>. The biosynthetic gene cluster for pyrroloformamides was identified from <i>S</i>. sp. CB02980, which shared high sequence similarity with those of dithiolopyrrolones, including holomycin and thiolutin. Gene replacement of pyfE, which encodes a non-ribosomal peptide synthetase, abolished the production of <b>1</b>－<b>4</b>. Overexpression of <i>pyfN</i>, a type II thioesterase gene, increased the production of <b>1</b> and <b>2</b>. The structure elucidation and biosynthetic characterization of pyrroloformamides <b>1</b> - <b>4</b> may inspire future efforts to discover new dithiolopyrrolones, which are promising drug leads for the treatment of infectious diseases or cancer.

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