Life Sciences Commons^™

Dual Activities Of Acc Synthase: Novel Clues Regarding The Molecular Evolution Of Acs Genes, Chang Xu, Bowei Hao, Gongling Sun, Yuanyuan Mei, Lifang Sun, Yunmei Sun, Yibo Wang, Yongyan Zhang, Wei Zhang, Mengyuan Zhang, Yue Zhang, Dan Wang, Zihe Rao, Xin Li, Jeffery Shen, Ning Ning Wang

Life Sciences Faculty Research

Ethylene plays profound roles in plant development. The rate-limiting enzyme of ethylene biosynthesis is 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS), which is generally believed to be a single-activity enzyme evolving from aspartate aminotransferases. Here, we demonstrate that, in addition to catalyzing the conversion of S-adenosyl-methionine to the ethylene precursor ACC, genuine ACSs widely have Cβ-S lyase activity. Two N-terminal motifs, including a glutamine residue, are essential for conferring ACS activity to ACS-like proteins. Motif and activity analyses of ACS-like proteins from plants at different evolutionary stages suggest that the ACC-dependent pathway is uniquely developed in seed plants. A putative catalytic mechanism for …

Complete Genome Sequences Of Cluster A6 And Cluster G1 Mycobacterium Smegmatis Phages Hoot And Jolene, Jon Thompson, Asli Özdemir, Arsen M. Topchyan, Maxwell Torosian, Victoria Z. Thymianos, Angelica Eagle, Juliana Mccormick, Leon Kyle G. Boyles, Azucena A. Benito, Kurt Regner, Christy Strong, Philippos K. Tsourkas

Life Sciences Faculty Research

We present the complete genome sequences of Mycobacterium smegmatis phages Hoot and Jolene, isolated in Las Vegas, NV. The phages were isolated and annotated by students enrolled in an undergraduate research course at the University of Nevada, Las Vegas. Hoot is a cluster A6 mycobacteriophage, while Jolene is in cluster G1.

Deciphering Symbiotic Interactions Of “Candidatus Aenigmarchaeota” With Inferred Horizontal Gene Transfers And Co-Occurrence Networks, Yu-Xian Li, Yang-Zhi Rao, Yan-Ling Qi, Yan-Ni Qu, Ya-Ting Chen, Jian-Yu Jiao, Wen-Sheng Shu, Hongchen Jiang, Brian P. Hedlund, Zheng-Shuang Hua, Wen-Jun Li

Life Sciences Faculty Research

"Candidatus Aenigmarchaeota"("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota"in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota"in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota …

Comparative Genomics Reveals Thermal Adaptation And A High Metabolic Diversity In “Candidatus Bathyarchaeia”, Yan-Ling Qi, Paul N. Evans, Yu-Xian Li, Yang-Zhi Rao, Yan-Ni Qu, Sha Tan, Jian-Yu Jiao, Ya-Ting Chen, Brian P. Hedlund, Wen-Sheng Shu, Zheng-Shuang Hua, Wen Jun Li

Life Sciences Faculty Research

"Candidatus Bathyarchaeia"is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a …

Highly Contiguous Assemblies Of 101 Drosophilid Genomes, Bernard Y. Kim, Jeremy R. Wang, Danny E. Miller, Olga Barmina, Emily Delaney, Ammon Thompson, Aaron A. Comeault, David Peede, Emmanuel R.R. D’Agostino, Julianne Pelaez, Jessica M. Aguilar, Diler Haji, Teruyuki Matsunaga, Ellie E. Armstrong, Molly Zych, Yoshitaka Ogawa, Marina Stamenković-Radak, Mihailo Jelić, Marija Savić Veselinović, Marija Tanasković, Pavle Erić, Jian Jun Gao, Takehiro K. Katoh, Masanori J. Toda, Hideaki Watabe, Masayoshi Watada, Jeremy S. Davis, Leonie C. Moyle, Giulia Manoli, Enrico Bertolini, Vladimír Košťál, R. Scott Hawley, Aya Takahashi, Corbin D. Jones, Donald K. Price, Noah Whiteman, Artyom Kopp, Daniel R. Matute, Dmitri A. Petrov

Life Sciences Faculty Research

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, …

A Screen For Sleep And Starvation Resistance Identifies A Wake-Promoting Role For The Auxiliary Channel Unc79, Kazuma Murakami, Justin Palermo, Bethany A. Stanhope, Allen G. Gibbs, Alex C. Keene

Life Sciences Faculty Research

The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in …

Genomics, Exometabolomics, And Metabolic Probing Reveal Conserved Proteolytic Metabolism Of Thermoflexus Hugenholtzii And Three Candidate Species From China And Japan, Scott C. Thomas, Devon Payne, Kevin O. Tamadonfar, Cale O. Seymour, Jian Yu Jiao, Senthil K. Murugapiran, Dengxun Lai, Rebecca Lau, Benjamin P. Bowen, Leslie P. Silva, Katherine B. Louie, Marcel Huntemann, Alicia Clum, Alex Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, I. Min Chen, Dimitrios Stamatis, T. B.K. Reddy, Ronan O’Malley, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos C. Kyrpides, Tanja Woyke, Emiley Eloe-Fadrosh, Trinity L. Hamilton, Paul Dijkstra, Brian P. Hedlund

Life Sciences Faculty Research

Thermoflexus hugenholtzii JAD2 , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus …

A Whole-Genome Scan For Association With Invasion Success In The Fruit Fly Drosophila Suzukii Using Contrasts Of Allele Frequencies Corrected For Population Structure, Laure Olazcuaga, Anne Loiseau, Hugues Parrinello, Mathilde Paris, Antoine Fraimout, Christelle Guedot, Lauren M. Diepenbrock, Marc Kenis, Jinping Zhang, Xiao Chen, Nicolas Borowiec, Benoit Facon, Heidrun Vogt, Donald K. Price, Heiko Vogel, Benjamin Prud'homme, Arnaud Estoup, Mathieu Gautier

Life Sciences Faculty Research

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic …

Analysis Of Genomic Sequence Data Reveals The Origin And Evolutionary Separation Of Hawaiian Hoary Bat Populations, Corinna A. Pinzari, Lin Kang, Pawel Michalak, Lars S. Jermiin, Donald K. Price, Frank J. Bonaccorso

Life Sciences Faculty Research

We examine the genetic history and population status of Hawaiian hoary bats (Lasiurus semotus), the most isolated bats on Earth, and their relationship to northern hoary bats (Lasiurus cinereus), through whole-genome analysis of single-nucleotide polymorphisms mapped to a de novo-assembled reference genome. Profiles of genomic diversity and divergence indicate that Hawaiian hoary bats are distinct from northern hoary bats, and form a monophyletic group, indicating a single ancestral colonization event 1.34 Ma, followed by substantial divergence between islands beginning 0.51 Ma. Phylogenetic analysis indicates Maui is central to the radiation across the archipelago, with the southward expansion to Hawai‘i and …

Identifying Pleiotropic Snps Associated With Femoral Neck And Heel Bone Mineral Density, Pei He, Xinag-He Ming, Xiao Zhang, Xu Lin, Qiang Zhang, Ri-Li Jiang, Martin R. Schiller, Fei-Yan Deng, Hong-Wen Deng

Life Sciences Faculty Research

Background: Genome-wide association studies (GWASs) routinely identify loci associated with risk factors for osteoporosis. However, GWASs with relatively small sample sizes still lack sufficient power to ascertain the majority of genetic variants with small to modest effect size, which may together truly influence the phenotype. The loci identified only account for a small percentage of the heritability of osteoporosis. This study aims to identify novel genetic loci associated with DXA-derived femoral neck (FNK) bone mineral density (BMD) and quantitative ultrasound of the heel calcaneus estimated BMD (eBMD), and to detect shared/causal variants for the two traits, to assess whether the …

Microrna Profiling In The Weddell Seal Suggests Novel Regulatory Mechanisms Contributing To Diving Adaptation, Luca Penso-Dolfin, Wilfried Haerty, Allyson Hindle, Federica Di Palma

Life Sciences Faculty Research

Background:The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving... (See full abstract in article).

The Bacillus Subtilis K-State Promotes Stationary-Phase Mutagenesis Via Oxidative Damage, Holly A. Martin, Amanda A. Kidman, Jillian Socea, Carmen Vallin, Mario Pedraza-Reyes, Eduardo A. Robleto

Life Sciences Faculty Research

Bacterial cells develop mutations in the absence of cellular division through a process known as stationary-phase or stress-induced mutagenesis. This phenomenon has been studied in a few bacterial models, including Escherichia coli and Bacillus subtilis; however, the underlying mechanisms between these systems differ. For instance, RecA is not required for stationary-phase mutagenesis in B. subtilis like it is in E. coli. In B. subtilis, RecA is essential to the process of genetic transformation in the subpopulation of cells that become naturally competent in conditions of stress. Interestingly, the transcriptional regulator ComK, which controls the development of competence, does influence the …

Magnetosome Gene Duplication As An Important Driver In The Evolution Of Magnetotaxis In The Alphaproteobacteria, Haijian Du, Wenyan Zhang, Wensi Zhang, Weijia Zhang, Hongmiao Pan, Yongxin Pan, Dennis A. Bazylinski, Long-Fei Wu, Tian Xiao, Wei Lin

Life Sciences Faculty Research

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely …

Correction To: Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han

Life Sciences Faculty Research

Following publication of the original article [1], the authors reported errors in Table 2 wherein all “KZFP” in the gene names should be changed to “ZNF”.

Complete Genome Sequences Of Mycobacterium Smegmatis Phages Nihilnomen And Carlyle, Isolated In Las Vegas, Nevada, Alicia Salisbury, Ryan Doss, Astha Mehta, Khadija Bhatti, Ciera Dapra, Audrey Huntsinger, Stephanie Rodriguez, Scott Yacek, Rylee Sandberg, Alexis Gildore, Jacinda Knudtson, Frances Tibayan, Tiannah Ohta, Neha Zafar, Guadalupe Mercado, Alan Le, Natalie Mekhaeel, Justin Willer, Edith Rodrich-Zuniga, Merissa Mcfarland, Kurt Regner, Christy Strong, Phillippos K. Tsourkas

Life Sciences Faculty Research

We present the complete genomes of the Mycobacterium smegmatis phages Carlyle and NihilNomen, isolated from soil in Las Vegas, Nevada. The phages were isolated and annotated by undergraduate students enrolled in the Phage Discovery course offered by the School of Life Sciences at the University of Nevada Las Vegas.

Transcriptome Analyses Of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed With Transposable Elements, Micky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han

Life Sciences Faculty Research

Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. Results: Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated …

Prioritization Of Variants For Investigation Of Genotype-Directed Nutrition In Human Superpopulations, Pascal D. Nilsson, Jacklyn M. Newsome, Henry M. Santos, Martin R. Schiller

Life Sciences Faculty Research

Dietary guidelines recommended by key health agencies are generally designed for a global population. However, ethnicity affects human disease and environment-gene interactions, including nutrient intake. Historically, isolated human populations with different genetic backgrounds have adapted to distinct environments with varying food sources. Ethnicity is relevant to the interaction of food intake with genes and disease susceptibility; yet major health agencies generally do not recommend food and nutrients codified by population genotypes and their frequencies. In this paper, we have consolidated published nutrigenetic variants and examine their frequencies in human superpopulations to prioritize these variants for future investigation of population-specific genotype-directed …

Paired-End Mappability Of Transposable Elements In The Human Genome, Corinne E. Sexton, Mira V. Han

Life Sciences Faculty Research

Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely …

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Research

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment …

Position-Specific Metabolic Probing And Metagenomics Of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities At High Temperatures, Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund

Life Sciences Faculty Research

Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across …

Novel Algorithms For Ldd Motif Search, Peng Xiao, Martin Schiller, Sanguthevar Rajasekaran

Life Sciences Faculty Research

Background: Motifs are crucial patterns that have numerous applications including the identification of transcription factors and their binding sites, composite regulatory patterns, similarity between families of proteins, etc. Several motif models have been proposed in the literature. The (l,d)-motif model is one of these that has been studied widely. However, this model will sometimes report too many spurious motifs than expected. We interpret a motif as a biologically significant entity that is evolutionarily preserved within some distance. It may be highly improbable that the motif undergoes the same number of changes in each of the species. To address this issue, …

The Anti-Sigma Factor Muca Of Pseudomonas Aeruginosa: Dramatic Differences Of A Muca22 Vs. A Δmuca Mutant In Anaerobic Acidified Nitrite Sensitivity Of Planktonic And Biofilm Bacteria In Vitro And During Chronic Murine Lung Infection, Warunya Panmanee, Shengchang Su, Michael J. Schurr, Gee W. Lau, Xiaoting Zhu, Zhaowei Ren, Cameron T. Mcdaniel, Long J. Lu, Dennis E. Ohman, Daniel A. Muruve, Ralph J. Panos, Hongwei D. Yu, Thomas B. Thompson, Boo Shan Tseng, Daniel J. Hassett

Life Sciences Faculty Research

Mucoid mucA22 Pseudomonas aeruginosa (PA) is an opportunistic lung pathogen of cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) patients that is highly sensitive to acidified nitrite (A-NO2-). In this study, we first screened PA mutant strains for sensitivity or resistance to 20 mM A-NO2- under anaerobic conditions that represent the chronic stages of the aforementioned diseases. Mutants found to be sensitive to A-NO2- included PA0964 (pmpR, PQS biosynthesis), PA4455 (probable ABC transporter permease), katA (major catalase, KatA) and rhlR (quorum sensing regulator). In contrast, mutants lacking PA0450 (a putative phosphate transporter) and PA1505 (moaA2) were A-NO2- resistant. However, …

Investigating The Dna-Binding Site For Virb, A Key Transcriptional Regulator Of Shigella Virulence Genes, Using An In Vivo Binding Tool, Monika M.A. Karney, Joy A. Mckenna, Natasha Weatherspoon-Griffin, Alexander D. Karabachev, Makensie E. Millar, Eliese A. Potoceck, Helen J. Wing

Life Sciences Faculty Research

The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivo studies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer …

Complete Genome Sequences Of 18 Paenibacillus Larvae Phages From The Western United States, Bryan D. Merrill, Christopher P. Fajardo, Jared A. Hilton, Ashley M. Payne, Andy T. Ward, Jamison K. Walker, Aziza Dhalai, Cameron Imahara, James Mangohig, Josh Monk, Cristian Pascacio, Padmani Rai, Alicia Salisbury, Kathie Velez, Travis J. Bloomfield, Brett Buhler, Steven G. Duncan, David A. Fuhriman, Josil George, Kiel Graves, Karli Graves, Hunter L. Hill, Michelle Kim, Bradley K. Knabe, Devin B. Ririe, Spencer L. Rogers, Casey Stamereilers, Michael B. Stephenson, Brittian K. Usher, Colton S. Ward, Jacob M. Withers

Life Sciences Faculty Research

We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course at Brigham Young University. The phages were isolated primarily from bee debris and lysogens.

Complete Genome Sequences Of Paenibacillus Larvae Phages Halcyone, Heath, Scottie, And Unity From Las Vegas, Nevada, Diane G. Yost, Carolyn Chang, Lucy Leblanc, Erin Cassin, Ceara Peterman, Padmani Rai, Alicia Salisbury, Nicolas Barroga, Ramiro Cisneros, Joseph Fersini, Jonathan Juste, Juvie Ines, Gabriel Leyva, Dyanne Macalinao, Spencer Muscelli, Gustavo S. Reyes, Heather Rhoden, Rodney Tan, Erika Torres, Krystal Tran, Georgette Uriarte-Valle, Christopher Wallace, Simon Wong, Kevin Ayala-Pineda, Vanessa Cadiz, Tiffany Jeanite, Sophia Nhan, Julianne H. Grose, Christy Strong, Penny S. Amy, Philippos K. Tsourkas

Life Sciences Faculty Research

We present the complete genome sequences of four phages that infect Paenibacillus larvae, the causative agent of American foulbrood disease in honeybees. The phages were isolated from beehives and beeswax products from Las Vegas, Nevada. The genomes are 50 to 55 kbp long and use the “direct terminal repeats” DNA-packaging strategy.

Genomic Analysis Of 48 Paenibacillus Larvae Bacteriophages, Casey Stamereilers, Christopher P. Fajardo, Jamison K. Walker, Katterinne N. Mendez, Eduardo Castro-Nallar, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas

Life Sciences Faculty Research

The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvaephage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes …

Complete Genome Sequences Of Paenibacillus Larvae Phages Bn12, Dragolir, Kiel007, Leyra, Likha, Pagassa, Pbl1c, And Tadhana, Jamison K. Walker, Bryan D. Merrill, Jordan A. Berg, Aziza Dhalai, Douglas W. Dingman, Chris P. Fajardo, Kiel Graves, Hunter L. Hill, Jared A. Hilton, Cameron Imahara, Bradley K. Knabe, James Mangohig, Josh Monk, Heejin Mun, Ashley M. Payne, Alicia Salisbury, Casey Stamereilers, Kathie Velez, Andy T. Ward, Donald P. Breakwell, Julianne H. Grose, Sandra Hope, Philippos K. Tsourkas

Life Sciences Faculty Research

We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA.

Stationary-Phase Mutagenesis In Stressed Bacillus Subtilis Cells Operates By Mfd-Dependent Mutagenic Pathways, Martha Gómez-Marroquín, Holly A. Martin, Amber Pepper, Mary E. Girard, Amanda Kidman, Carmen Vallin, Ronald E. Yasbin, Mario Pedraza-Reyes, Eduardo Robleto

Life Sciences Faculty Research

In replication-limited cells of Bacillus subtilis, Mfd is mutagenic at highly transcribed regions, even in the absence of bulky DNA lesions. However, the mechanism leading to increased mutagenesis through Mfd remains currently unknown. Here, we report that Mfd may promote mutagenesis in nutritionally stressed B. subtilis cells by coordinating error-prone repair events mediated by UvrA, MutY and PolI. Using a point-mutated gene conferring leucine auxotrophy as a genetic marker, it was found that the absence of UvrA reduced the Leu+ revertants and that a second mutation in mfd reduced mutagenesis further. Moreover, the mfd and polA mutants presented low but …

The Human Phosphotyrosine Signaling Network: Evolution And Hotspots Of Hijacking In Cancer., Lei Li, Chabane Tibiche, Cong Fu, Tomonori Kaneko, Michael F. Moran, Martin Schiller, Shawn Shun-Cheng Li, Edwin Wang

Life Sciences Faculty Research

Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK) circuits, each of which consists of a TK writer, a kinase substrate, and a related reader, such as Src homology (SH) 2 domains and pTyr-binding (PTB) domains, comprise the core machinery of the pTyr signaling network. In this study, we analyzed the evolutionary trajectories of 583 literature-derived and 50,000 computationally predicted human TK circuits in 19 representative …

Reducing False-Positive Prediction Of Minimotifs With A Genetic Interaction Filter, Jerlin Camilus Merlin, Sanguthevar Rajasekaran, Tian Mi, Martin Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists.

Methods and Findings

We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target …