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Genome mining

Libing Shen, Qili Shi, Wenyuan Wang
The role of genetic components in cancer development is an area of interest for cancer biologists in general. Intriguingly, some genes have both oncogenic and tumor-suppressor functions. In this study, we systematically identified these genes through database search and text mining. We find that most of them are transcription factors or kinases and exhibit dual biological functions, e.g., that they both positively and negatively regulate transcription in cells. Some cancer types such as leukemia are over-represented by them, whereas some common cancer types such as lung cancer are under-represented by them...
March 13, 2018: Oncogenesis
Betina Cecilia Agaras, Andrés Iriarte, Claudio Fabián Valverde
Plant-growth promotion has been linked to the Pseudomonas genus since the beginning of this research field. In this work, we mined the genome of an Argentinean isolate of the recently described species P. donghuensis. Strain SVBP6, isolated from bulk soil of an agricultural plot, showed a broad antifungal activity and several other plant-probiotic activities. As this species has been recently described, and it seems like some plant-growth promoting (PGP) traits do not belong to the classical pseudomonads toolbox, we decide to explore the SVBP6 genome via an bioinformatic approach...
2018: PloS One
Michael Song, Li-Yaung Kuo, Layne Huiet, Kathleen M Pryer, Carl J Rothfels, Fay-Wei Li
PREMISE OF THE STUDY: Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS: We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction...
January 2018: American Journal of Botany
Yi Zhao, Marcus J C Long, Yiran Wang, Sheng Zhang, Yimon Aye
Posttranslational modifications (PTMs) are the lingua franca of cellular communication. Most PTMs are enzyme-orchestrated. However, the reemergence of electrophilic drugs has ushered mining of unconventional/non-enzyme-catalyzed electrophile-signaling pathways. Despite the latest impetus toward harnessing kinetically and functionally privileged cysteines for electrophilic drug design, identifying these sensors remains challenging. Herein, we designed "G-REX"-a technique that allows controlled release of reactive electrophiles in vivo...
February 28, 2018: ACS Central Science
Daisuke Ogawa, Eiji Yamamoto, Toshikazu Ohtani, Noriko Kanno, Hiroshi Tsunematsu, Yasunori Nonoue, Masahiro Yano, Toshio Yamamoto, Jun-Ichi Yonemaru
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan...
March 12, 2018: Scientific Reports
Serina L Robinson, Jonathan P Badalamenti, Anthony G Dodge, Lambros J Tassoulas, Lawrence P Wackett
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla...
March 12, 2018: Environmental Microbiology
Mario Mardirossian, Natacha Pérébaskine, Monica Benincasa, Stefano Gambato, Sven Hofmann, Paul Huter, Claudia Müller, Kai Hilpert, C Axel Innis, Alessandro Tossi, Daniel N Wilson
Proline-rich antimicrobial peptides (PrAMPs) internalize into susceptible bacteria using specific transporters and interfere with protein synthesis and folding. To date, mammalian PrAMPs have so far been identified only in artiodactyls. Since cetaceans are co-phyletic with artiodactyls, we mined the genome of the bottlenose dolphin Tursiops truncatus, leading to the identification of two PrAMPs, Tur1A and Tur1B. Tur1A, which is orthologous to the bovine PrAMP Bac7, is internalized into Escherichia coli, without damaging the membranes, using the inner membrane transporters SbmA and YjiL/MdM...
February 22, 2018: Cell Chemical Biology
Jing Jin, Xiaoyan Yang, Tan Liu, Hua Xiao, Guiyang Wang, Mengjie Zhou, Fawang Liu, Yingtao Zhang, Dong Liu, Minghua Chen, Wei Cheng, Donghui Yang, Ming Ma
Aromatic polyketides from marine actinomycetes have received increasing attention due to their unusual structures and potent bioactivities. Compared to their terrestrial counterparts, marine aromatic polyketides have been less discovered and their structural and biological diversities are far from being fully investigated. In this study, we employed a PCR-based genome mining method to discover aromatic polyketides in our marine bacteria collection. Five new atypical angucyclinones, fluostatins M-Q ( 1 - 5 ) featuring a unique 6-5-6-6 ring skeleton, were discovered from one "positive" Streptomyces sp...
March 9, 2018: Marine Drugs
Kathleen M Scott, John Williams, Cody M B Porter, Sydney Russel, Tara L Harmer, John H Paul, Kirsten M Antonen, Megan K Bridges, Gary J Camper, Christie K Campla, Leila G Casella, Eva Chase, James W Conrad, Mercedez C Cruz, Darren S Dunlap, Laura Duran, Elizabeth M Fahsbender, Dawn B Goldsmith, Ryan F Keeley, Matthew R Kondoff, Breanna I Kussy, Marannda K Lane, Stephanie Lawler, Brittany A Leigh, Courtney Lewis, Lygia M Lostal, Devon Marking, Paola A Mancera, Evan C McClenthan, Emily A McIntyre, Jessica A Mine, Swapnil Modi, Brittney D Moore, William A Morgan, Kaleigh M Nelson, Kimmy N Nguyen, Nicholas Ogburn, David G Parrino, Anangamanjari D Pedapudi, Rebecca P Pelham, Amanda M Preece, Elizabeth A Rampersad, Jason C Richardson, Christina M Rodgers, Brent L Schaffer, Nancy E Sheridan, Michael R Solone, Zachery R Staley, Maki Tabuchi, Ramond J Waide, Pauline W Wanjugi, Suzanne Young, Alicia Clum, Chris Daum, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Natalia Mikhailova, Krishnaveni Palaniappan, Manoj Pillay, T B K Reddy, Nicole Shapiro, Dimitrios Stamatis, Neha Varghese, Tanja Woyke, Rich Boden, Sharyn K Freyermuth, Cheryl A Kerfeld
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes, and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins, and methyl-accepting chemotaxis proteins) despite their small sizes (2...
March 9, 2018: Environmental Microbiology
B K B Lee, C P Gan, J K Chang, J L Tan, M Z Fadlullah, Z A Abdul Rahman, S S Prime, J S Gutkind, C S Liew, T F Khang, A C Tan, S C Cheong
Head and neck cancer (HNC)-derived cell lines represent fundamental models for studying the biological mechanisms underlying cancer development and precision therapies. However, mining the genomic information of HNC cells from available databases requires knowledge on bioinformatics and computational skill sets. Here, we developed a user-friendly web resource for exploring, visualizing, and analyzing genomics information of commonly used HNC cell lines. We populated the current version of GENIPAC with 44 HNC cell lines from 3 studies: ORL Series, OPC-22, and H Series...
March 1, 2018: Journal of Dental Research
Si-Sun Choi, Yohei Katsuyama, Linquan Bai, Zixin Deng, Yasuo Ohnishi, Eung-Soo Kim
The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach...
March 3, 2018: Current Opinion in Microbiology
Yejun Wang, Ming-An Sun, Aaron P White
RNA-Seq has become a routine strategy for genome-wide gene expression comparisons in bacteria. Despite lower resolution in transcript border parsing compared with dRNA-Seq, TSS-EMOTE, Cappable-seq, Term-seq, and others, directional RNA-Seq still illustrates its advantages: low cost, quantification and transcript border analysis with a medium resolution (±10-20 nt). To facilitate mining of directional RNA-Seq datasets especially with respect to transcript structure analysis, we developed a tool, TrBorderExt, which can parse transcript start sites and termination sites accurately in bacteria...
2018: Methods in Molecular Biology
Ramkrishna Kandel, Xiping Yang, Jian Song, Jianping Wang
Lignocellulosic biomass has become an emerging feedstock for second-generation bioethanol production. Sugarcane ( Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features viz. fast growth rate and abilities for high tillering, ratooning, and photosynthesis. Energy cane, an ideal type of sugarcane, has been bred specifically as a biomass crop. In this review, we described (1) biomass potentials of sugarcane and its underlying genetics, (2) challenges associated with biomass improvement such as large and complex genome, narrow gene pool in existing commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass improvement, and (4) mining candidate genes controlling biomass in genomic databases...
2018: Frontiers in Plant Science
Xiao-Jiao Li, Jin-Shu Pang, Yao-Mei Li, Farah Abdirahman Ahmed, Rong-Quan He, Jie Ma, Fu-Chao Ma, Gang Chen
OBJECTIVE: An increasing number of studies have confirmed that survivin (BIRC5) plays essential roles in ovarian cancer. Nevertheless, inconsistent or controversial results exist in some studies. In the present study, we sought to determine the clinical significance of survivin and its potential molecular pathways. METHODS: The correlation between survivin (BIRC5) expression and diagnostic value, prognostic value and clinicopathological features was assessed by meta-analysis with more than 4000 patients from literature, GEO and TCGA...
January 2, 2018: Pathology, Research and Practice
María J León, Tamara Hoffmann, Cristina Sánchez-Porro, Johann Heider, Antonio Ventosa, Erhard Bremer
Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes...
2018: Frontiers in Microbiology
Sung-Ryul Kim, Joie M Ramos, Rona Joy M Hizon, Motoyuki Ashikari, Parminder S Virk, Edgar A Torres, Eero Nissila, Kshirod K Jena
Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3 F2 and BC3 F3 generations...
March 1, 2018: Scientific Reports
Hui-Yeng Y Yap, Nget-Hong Tan, Szu-Ting Ng, Chon-Seng Tan, Shin-Yee Fung
Naturally occurring anti-glycation compounds have drawn much interest in recent years as they show potential in reducing or preventing the risk of chronic complications for diabetic patients. In this study, annotation of the genome-transcriptome data from tiger milk mushroom ( Lignosus rhinocerus , syn. Lignosus rhinocerotis ) to PlantCyc enzymes database identified transcripts that are related to anti-diabetic properties, and these include genes that are involved in carotenoid and abscisic acid biosynthesis as well as genes that code for glyoxalase I, catalase-peroxidases, and superoxide dismutases...
2018: Frontiers in Pharmacology
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao
Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes...
February 27, 2018: Briefings in Bioinformatics
Miao-Chun Fan, Yan-Qing Guo, Li-Ping Zhang, Ya-Min Zhu, Wei-Min Chen, Yan-Bing Lin, Ge-Hong Wei
A novel endophytic bacterium, designated strain HZ10T , was isolated from root nodules of Robinia pseudoacacia growing in a lead-zinc mine in Mianxian County, Shaanxi Province, China. The bacterium was Gram-stain-negative, aerobic, motile, slightly curved- and rod-shaped, methyl red-negative, catalase-positive, and did not produce H2S. Strain HZ10T grew at 4-45 °C (optimum, 25-30 °C), pH 5-9 (optimum, pH 7-8) and 0-1 % (w/v) NaCl. The major fatty acids were identified as C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and the quinone type was Q-8...
February 27, 2018: International Journal of Systematic and Evolutionary Microbiology
Gunter Vogt
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions...
March 2018: Journal of Biosciences
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