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https://www.readbyqxmd.com/read/28822280/promiscuity-impersonation-and-accommodation-evolution-of-plant-specialized-metabolism
#1
REVIEW
Bryan J Leong, Robert L Last
Specialized metabolic enzymes and metabolite diversity evolve through a variety of mechanisms including promiscuity, changes in substrate specificity, modifications of gene expression and gene duplication. For example, gene duplication and substrate binding site changes led to the evolution of the glucosinolate biosynthetic enzyme, AtIPMDH1, from a Leu biosynthetic enzyme. BAHD acyltransferases illustrate how enzymatic promiscuity leads to metabolite diversity. The examples 4-coumarate:CoA ligase and aromatic acid methyltransferases illustrate how promiscuity can potentiate the evolution of these specialized metabolic enzymes...
August 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28820425/bioinformatics-analysis-of-phylogeny-and-transcription-of-taa-yuc-auxin-biosynthetic-genes
#2
Axel Poulet, Verena Kriechbaumer
Auxin is a main plant growth hormone crucial in a multitude of developmental processes in plants. Auxin biosynthesis via the tryptophan aminotransferase of arabidopsis (TAA)/YUCCA (YUC) route involving tryptophan aminotransferases and YUC flavin-dependent monooxygenases that produce the auxin indole-3-acetic acid (IAA) from tryptophan is currently the most researched auxin biosynthetic pathway. Previous data showed that, in maize and arabidopsis, TAA/YUC-dependent auxin biosynthesis can be detected in endoplasmic reticulum (ER) microsomal fractions, and a subset of auxin biosynthetic proteins are localized to the ER, mainly due to transmembrane domains (TMD)...
August 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#3
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819320/genome-wide-identification-and-expression-analysis-of-e2-ubiquitin-conjugating-enzymes-in-tomato
#4
Bhaskar Sharma, Tarun Kumar Bhatt
The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818380/molecular-cloning-and-expression-analysis-of-duplicated-polyphenol-oxidase-genes-reveal-their-functional-differentiations-in-sorghum
#5
Song Yan, Sujuan Li, Guowei Zhai, Ping Lu, Hui Deng, Shan Zhu, Renliang Huang, Jianfeng Shao, Yuezhi Tao, Guihua Zou
Polyphenol oxidase (PPO) is believed to play a role in plant growth, reproduction, and resistance to pathogens and pests. PPO causes browning of grains in cereals. In this study, genetic mapping of sorghum grain for phenol color reaction (PHR) was performed using a recombinant inbred line population. Only one locus was detected between SSR markers SM06072 and Xtxp176 on chromosome 6. Two linked orthologous genes (Sb06PPO1 and Sb06PPO2) within the mapped region were discovered and cloned. Transformation experiments using Nipponbare (a PHR negative rice cultivar) showed that Sb06PPO1 from LTR108 and two Sb06PPO2 alleles from both varieties could complement Nipponbare, whereas Sb06PPO1 from 654 could not...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28817404/primary-renal-sarcomas-with-bcor-ccnb3-gene-fusion-a-report-of-2-cases-showing-histologic-overlap-with-clear-cell-sarcoma-of-kidney-suggesting-further-link-between-bcor-related-sarcomas-of-the-kidney-and-soft-tissues
#6
Pedram Argani, Yu-Chien Kao, Lei Zhang, Carlos Bacchi, Andres Matoso, Rita Alaggio, Jonathan I Epstein, Cristina R Antonescu
We report 2 primary renal sarcomas demonstrating BCOR-CCNB3 gene fusions that have recently been identified in undifferentiated round cell sarcomas of bone and soft tissue. These neoplasms occurred in male children aged 11 and 12 years, and both were cystic as a result of entrapment and dilatation of native renal tubules. Both cases were composed of variably cellular bland spindle cells with fine chromatin set in myxoid stroma and separated by a branching capillary vasculature. Both neoplasms demonstrated immunoreactivity for BCOR, cyclin D1, TLE1, and SATB2 in the spindle neoplastic cells and negativity in the prominent capillary vasculature...
August 16, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28817303/chrna7-deletions-are-enriched-in-risperidone-treated-children-and-adolescents
#7
Madelyn A Gillentine, Janson J White, Christopher M Grochowski, James R Lupski, Christian P Schaaf, Chadi A Calarge
OBJECTIVE: Aggression is among the most common indications for referral to child and adolescent mental health services and is often challenging to treat. Understanding the biological underpinnings of aggression could help optimize treatment efficacy. Neuronal nicotinic acetylcholine receptors (nAChRs), specifically the α7 nAChR, encoded by the gene CHRNA7, have been implicated in aggressive behaviors in animal models as well as humans. Copy number variants (CNVs) of CHRNA7 are found in individuals with neuropsychiatric disorders, often with comorbid aggression...
August 17, 2017: Journal of Child and Adolescent Psychopharmacology
https://www.readbyqxmd.com/read/28815513/an-update-on-p2y13-receptor-signalling-and-function
#8
Raquel Pérez-Sen, Rosa Gómez-Villafuertes, Felipe Ortega, Javier Gualix, Esmerilda G Delicado, María Teresa Miras-Portugal
The distribution of nucleotide P2Y receptors across different tissues suggests that they fulfil key roles in a number of physiological and pathological conditions. P2Y13 is one of the latest P2Y receptors identified, a novel member of the Gi-coupled P2Y receptor subfamily that responds to ADP, together with P2Y12 and P2Y14. Pharmacological studies drew attention to this new ADP receptor, with a pharmacology that overlaps that of P2Y12 receptors but with unique features and roles. The P2RY12-14 genes all reside on human chromosome 3 at 3q25...
August 17, 2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28813459/%C3%AE-2-microglobulin-gene-duplication-in-cetartiodactyla-remains-intact-only-in-pigs-and-possibly-confers-selective-advantage-to-the-species
#9
Thong Minh Le, Quy Van Chanh Le, Dung Minh Truong, Hye-Jeong Lee, Min-Kyeung Choi, Hyesun Cho, Hak-Jae Chung, Jin-Hoi Kim, Jeong-Tae Do, Hyuk Song, Chankyu Park
Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1...
2017: PloS One
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#10
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811744/cytogenetic-profile-and-flt3-gene-mutations-of-childhood-acute-lymphoblastic-leukemia
#11
Nawaf Alkhayat, Yasser Elborai, Omer Al Sharif, Mohammad Al Shahrani, Omar Alsuhaibani, Mohammed Awad, Hatem Elghezal, Inesse Ben-Abdallah Bouhajar, Mona Alfaraj, Eman Al Mussaed, Fahad Alabbas, Ghaleb Elyamany
BACKGROUND: Childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent genetic aberrations. The identification of those abnormalities is clinically important because they are considered significant risk-stratifying markers. AIMS: There are insufficient data of cytogenetic profiles in Saudi Arabian patients with childhood ALL leukemia. We have examined a cohort of 110 cases of ALL to determine the cytogenetic profiles and prevalence of FLT3 mutations and analysis of the more frequently observed abnormalities and its correlations to other biologic factors and patient outcomes and to compare our results with previously published results...
2017: Clinical Medicine Insights. Oncology
https://www.readbyqxmd.com/read/28811591/alteration-of-sheep-coat-color-pattern-by-disruption-of-asip-gene-via-crispr-cas9
#12
Xuemei Zhang, Wenrong Li, Chenxi Liu, Xinrong Peng, Jiapeng Lin, Sangang He, Xuejiao Li, Bing Han, Ning Zhang, Yangsheng Wu, Lei Chen, Liqin Wang, MaYila, Juncheng Huang, Mingjun Liu
Coat color is an important characteristic and economic trait in domestic sheep. Aiming at alteration of Chinese merino sheep coat color by genome manipulation, we disrupted sheep agouti signaling protein gene by CRISPR/Cas9. A total of seven indels were identified in 5 of 6 born lambs. Each targeted lamb happened at least two kinds of modifications, and targeted lambs with multiple modifications displayed variety of coat color patterns. Three lambs with 4 bp deletion showed badgerface with black body coat color in two lambs, and brown coat color with light ventral pigmentation in another one...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811188/familial-1p36-3-microduplication-resulting-from-a-1p-9q-non-reciprocal-translocation
#13
Valentine Marquet, Sylvie Bourthoumieu, Amelia Dobrescu, Cécile Laroche-Raynaud, Catherine Yardin
Unlike the 1p36 microdeletion syndrome, which has been extensively described, 1p36 microduplications have rarely been reported. We describe a three years old boy presenting with a severe global developmental delay and a few dysmorphic features. Cytogenetic analyses revealed a maternally inherited 3.35 Mb microduplication of chromosomal band 1p36.3. The maternal grand-father is also carrier of the same chromosomal rearrangement. Interestingly, the duplicated 1p36.3 segment was found to be localized at the telomeric end of the long arms of a chromosome 9, probably deriving from a 1p36...
August 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28810832/genome-wide-analysis-of-basic-helix-loop-helix-bhlh-transcription-factors-in-brachypodium-distachyon
#14
Xin Niu, Yuxiang Guan, Shoukun Chen, Haifeng Li
BACKGROUND: As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS: A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810241/molecular-epidemiology-of-charcot-marie-tooth-disease-in-northern-ostrobothnia-finland-a-population-based-study
#15
Maria Marttila, Laura Kytövuori, Seppo Helisalmi, Mika Kallio, Marjo Laitinen, Mikko Hiltunen, Mikko Kärppä, Kari Majamaa
BACKGROUND: Charcot-Marie-Tooth (CMT) disease is the most common hereditary neuromuscular disorder with a population prevalence of 9.7-82.3/100,000. In this study, we have estimated the prevalence of CMT and its subtypes in Finland and examined the frequency of molecular etiologies. METHODS: A population-based survey included adult patients with peripheral neuropathy from the province of Northern Ostrobothnia, Finland. Secondary causes of peripheral polyneuropathy were excluded and patients with clinical and neurophysiological features pertinent with CMT were included...
August 16, 2017: Neuroepidemiology
https://www.readbyqxmd.com/read/28808695/resolving-multicopy-duplications-de-novo-using-polyploid-phasing
#16
Mark J Chaisson, Sudipto Mukherjee, Sreeram Kannan, Evan E Eichler
While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging frontier in assembly. Segmental duplications are at the same time both gene rich and prone to large structural rearrangements, making the resolution of their sequences important in medical and evolutionary studies. Duplicated sequences that are collapsed in mammalian de novo assemblies are rarely identical; after a sequence is duplicated, it begins to acquire paralog specific variants...
May 2017: Research in Computational Molecular Biology: ... Annual International Conference, RECOMB ...: Proceedings
https://www.readbyqxmd.com/read/28808688/adaptive-mistranslation-accelerates-the-evolution-of-fluconazole-resistance-and-induces-major-genomic-and-gene-expression-alterations-in-candida-albicans
#17
Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R Bezerra, Laura Carreto, Gabriela R Moura, Mónica Bayés, Ivo G Gut, Attila Csikasz-Nagy, Duccio Cavalieri, Judith Berman, Manuel A S Santos
Regulated erroneous protein translation (adaptive mistranslation) increases proteome diversity and produces advantageous phenotypic variability in the human pathogen Candida albicans. It also increases fitness in the presence of fluconazole, but the underlying molecular mechanism is not understood. To address this question, we evolved hypermistranslating and wild-type strains in the absence and presence of fluconazole and compared their fluconazole tolerance and resistance trajectories during evolution. The data show that mistranslation increases tolerance and accelerates the acquisition of resistance to fluconazole...
July 2017: MSphere
https://www.readbyqxmd.com/read/28808129/gene-duplication-in-pseudomonas-aeruginosa-improves-growth-on-adenosine
#18
Jean-Paul Toussaint, Anna Farrell-Sherman, Tamar Perla Feldman, Nicole E Smalley, Amy L Schaefer, E Peter Greenberg, Ajai A Dandekar
The laboratory strain of Pseudomonas aeruginosa, PAO1, activates genes for catabolism of adenosine using quorum sensing (QS). However, this strain is not well-adapted for growth on adenosine, with doubling times greater than 40 h. We previously showed that when PAO1 is grown on adenosine and casein, variants emerge that grow rapidly on adenosine. To understand the mechanism by which this adaptation occurs, we performed whole-genome sequencing of five isolates evolved for rapid growth on adenosine. All five genomes had a gene duplication-amplification (GDA) event covering several genes, including the quorum-regulated nucleoside hydrolase, nuh, and an adenine deaminase encoded by PA0148...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28807900/heart-morphogenesis-gene-regulatory-networks-revealed-by-temporal-expression-analysis
#19
Jonathon T Hill, Bradley Demarest, Megan Smith, Bushra Gorsi, H Joseph Yost
During embryogenesis, the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq time course in zebrafish from 30 hpf to 72 hpf and identified 5,861 genes with altered expression. We then clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis...
August 14, 2017: Development
https://www.readbyqxmd.com/read/28806914/expansion-and-evolutionary-patterns-of-cysteine-rich-peptides-in-plants
#20
Xing Liu, Huping Zhang, Huijun Jiao, Leiting Li, Xin Qiao, Musana Rwalinda Fabrice, Juyou Wu, Shaoling Zhang
BACKGROUND: Cysteine-rich peptides (CRPs) are gaining recognition as regulators of cell-cell communication in plants. RESULTS: We identified 9556 CRPs in 12 plant species and analysed their evolutionary patterns. In most angiosperm plants, whole genome duplication and segmental duplication are the major factors driving the expansion of CRP family member genes, especially signal peptides. About 30% of the CRP genes were found clustered on the chromosomes, except in maize (Zea mays)...
August 14, 2017: BMC Genomics
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