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Journal articles on the topic 'PufM gene'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Salka, Ivette, Vladimíra Moulisová, Michal Koblížek, Günter Jost, Klaus Jürgens, and Matthias Labrenz. "Abundance, Depth Distribution, and Composition of Aerobic Bacteriochlorophyll a-Producing Bacteria in Four Basins of the Central Baltic Sea." Applied and Environmental Microbiology 74, no. 14 (2008): 4398–404. http://dx.doi.org/10.1128/aem.02447-07.

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ABSTRACT The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 × 105 cells ml−1 (11% of total prokaryotes) or 1.0 × 103 CFU ml−1 (9 to 10% of total CFU

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2

Waidner, Lisa A., and David L. Kirchman. "Diversity and Distribution of Ecotypes of the Aerobic Anoxygenic Phototrophy Gene pufM in the Delaware Estuary." Applied and Environmental Microbiology 74, no. 13 (2008): 4012–21. http://dx.doi.org/10.1128/aem.02324-07.

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ABSTRACT The diversity of aerobic anoxygenic phototrophic (AAP) bacteria has been examined in marine habitats, but the types of AAP bacteria in estuarine waters and distribution of ecotypes in any environment are not well known. The goal of this study was to determine the diversity of AAP bacteria in the Delaware estuary and to examine the distribution of select ecotypes using quantitative PCR (qPCR) assays for the pufM gene, which encodes a protein in the light reaction center of AAP bacteria. In PCR libraries from the Delaware River, pufM genes similar to those from Beta- (Rhodoferax-like) o

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3

Achenbach, Laurie A., Jennifer Carey, and Michael T. Madigan. "Photosynthetic and Phylogenetic Primers for Detection of Anoxygenic Phototrophs in Natural Environments." Applied and Environmental Microbiology 67, no. 7 (2001): 2922–26. http://dx.doi.org/10.1128/aem.67.7.2922-2926.2001.

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ABSTRACT Primer sets were designed to target specific 16S ribosomal DNA (rDNA) sequences of photosynthetic bacteria, including the green sulfur bacteria, the green nonsulfur bacteria, and the members of theHeliobacteriaceae (a gram-positive phylum). Due to the phylogenetic diversity of purple sulfur and purple nonsulfur phototrophs, the 16S rDNA gene was not an appropriate target for phylogenetic rDNA primers. Thus, a primer set was designed that targets the pufM gene, encoding the M subunit of the photosynthetic reaction center, which is universally distributed among purple phototrophic bacte

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4

Karr, Elizabeth A., W. Matthew Sattley, Deborah O. Jung, Michael T. Madigan, and Laurie A. Achenbach. "Remarkable Diversity of Phototrophic Purple Bacteria in a Permanently Frozen Antarctic Lake." Applied and Environmental Microbiology 69, no. 8 (2003): 4910–14. http://dx.doi.org/10.1128/aem.69.8.4910-4914.2003.

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ABSTRACT Although anoxygenic photosynthesis is thought to play an important role in the primary productivity of permanently frozen lakes in the Antarctic dry valleys, the bacterial communities responsible for this metabolism remain uncharacterized. Here we report the composition and activity of phototrophic purple bacteria in Lake Fryxell, Antarctica, as determined by analysis of a photosynthesis-specific gene, pufM. The results revealed an extensive diversity and highly stratified distribution of purple nonsulfur bacteria in Lake Fryxell and showed which phylotypes produced pufM transcripts i

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5

Jeanthon, C., D. Boeuf, O. Dahan, et al. "Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea." Biogeosciences Discussions 8, no. 3 (2011): 4421–57. http://dx.doi.org/10.5194/bgd-8-4421-2011.

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Abstract. Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivabl

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Jeanthon, C., D. Boeuf, O. Dahan, et al. "Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea." Biogeosciences 8, no. 7 (2011): 1955–70. http://dx.doi.org/10.5194/bg-8-1955-2011.

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Abstract. Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivabl

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7

Albuquerque, Luciana, João Santos, Pedro Travassos, et al. "Albidovulum inexpectatum gen. nov., sp. nov., a Nonphotosynthetic and Slightly Thermophilic Bacterium from a Marine Hot Spring That Is Very Closely Related to Members of the Photosynthetic Genus Rhodovulum." Applied and Environmental Microbiology 68, no. 9 (2002): 4266–73. http://dx.doi.org/10.1128/aem.68.9.4266-4273.2002.

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ABSTRACT Several bacterial isolates, with an optimum growth temperature of about 50°C, were recovered from the marine hot spring at Ferraria on the island of São Miguel in the Azores. The geothermal water emerged from a porous lava flow and rapidly cooled in contact with seawater except at low tide. The bacterial species represented by strains FRR-10T and FRR-11 was nonpigmented, strictly aerobic, and organotrophic. Several genes, bchZ, pufB, pufA, pufL, or pufM, encoding the photosynthetic reaction center proteins and the core light-harvesting complexes were not detected in these strains. Th

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8

Oz, Aia, Gazalah Sabehi, Michal KoblÃ¯Â¿Â½zek, Ramon Massana, and Oded BÃ¯Â¿Â½jÃ¯Â¿Â½. "Roseobacter-Like Bacteria in Red and Mediterranean Sea Aerobic Anoxygenic Photosynthetic Populations." Applied and Environmental Microbiology 71, no. 1 (2005): 344–53. http://dx.doi.org/10.1128/aem.71.1.344-353.2005.

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ABSTRACT Bacteriochlorophyll a-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the pufM gene identified the existence of α-proteobacteria as well as possible γ-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using pufM as well as the bchX and bchL genes as molecular markers.

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9

Hiraishi, Akira, Nobuyoshi Nagao, Chinatsu Yonekawa, et al. "Distribution of Phototrophic Purple Nonsulfur Bacteria in Massive Blooms in Coastal and Wastewater Ditch Environments." Microorganisms 8, no. 2 (2020): 150. http://dx.doi.org/10.3390/microorganisms8020150.

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The biodiversity of phototrophic purple nonsulfur bacteria (PNSB) in comparison with purple sulfur bacteria (PSB) in colored blooms and microbial mats that developed in coastal mudflats and pools and wastewater ditches was investigated. For this, a combination of photopigment and quinone profiling, pufM gene-targeted quantitative PCR, and pufM gene clone library analysis was used in addition to conventional microscopic and cultivation methods. Red and pink blooms in the coastal environments contained PSB as the major populations, and smaller but significant densities of PNSB, with members of R

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10

Zeng, Yinxin, Peiyan Dong, Zongyun Qiao, and Tianling Zheng. "Diversity of the aerobic anoxygenic phototrophy gene pufM in Arctic and Antarctic coastal seawaters." Acta Oceanologica Sinica 35, no. 6 (2016): 68–77. http://dx.doi.org/10.1007/s13131-016-0877-y.

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11

Okubo, Yoko, Hiroyuki Futamata, and Akira Hiraishi. "Characterization of Phototrophic Purple Nonsulfur Bacteria Forming Colored Microbial Mats in a Swine Wastewater Ditch." Applied and Environmental Microbiology 72, no. 9 (2006): 6225–33. http://dx.doi.org/10.1128/aem.00796-06.

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ABSTRACT The community structure of pink-colored microbial mats naturally occurring in a swine wastewater ditch was studied by culture-independent biomarker and molecular methods as well as by conventional cultivation methods. The wastewater in the ditch contained acetate and propionate as the major carbon nutrients. Thin-section electron microscopy revealed that the microbial mats were dominated by rod-shaped cells containing intracytoplasmic membranes of the lamellar type. Smaller numbers of oval cells with vesicular internal membranes were also found. Spectroscopic analyses of the cell extr

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12

Salka, Ivette, Zuzana Čuperová, Michal Mašín, Michal Koblížek, and Hans-Peter Grossart. "Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes." Environmental Microbiology 13, no. 11 (2011): 2865–75. http://dx.doi.org/10.1111/j.1462-2920.2011.02562.x.

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13

Waidner, Lisa A., and David L. Kirchman. "Aerobic Anoxygenic Phototrophic Bacteria Attached to Particles in Turbid Waters of the Delaware and Chesapeake Estuaries." Applied and Environmental Microbiology 73, no. 12 (2007): 3936–44. http://dx.doi.org/10.1128/aem.00592-07.

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ABSTRACT Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that, if abundant, may be biogeochemically important in the oceans. We used epifluorescence microscopy and quantitative PCR (qPCR) to examine the abundance of these bacteria by enumerating cells with bacteriochlorophyll a (bChl a) and the light-reaction center gene pufM, respectively. In the surface waters of the Delaware estuary, AAP bacteria were abundant, comprising up to 34% of prokaryotes, although the percentage varied greatly with location and season. On average, AAP bacteria made up 12% of the community as me

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14

Hirose, Setsuko, Kenji V. P. Nagashima, Katsumi Matsuura, and Shin Haruta. "Diversity of Purple Phototrophic Bacteria, Inferred from pufM Gene, within Epilithic Biofilm in Tama River, Japan." Microbes and Environments 27, no. 3 (2012): 327–29. http://dx.doi.org/10.1264/jsme2.me11306.

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15

Du, Hailian, Nianzhi Jiao, Yaohua Hu, and Yonghui Zeng. "Real-time PCR for quantification of aerobic anoxygenic phototrophic bacteria based on pufM gene in marine environment." Journal of Experimental Marine Biology and Ecology 329, no. 1 (2006): 113–21. http://dx.doi.org/10.1016/j.jembe.2005.08.009.

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16

Boeuf, Dominique, Matthew T. Cottrell, David L. Kirchman, et al. "Summer community structure of aerobic anoxygenic phototrophic bacteria in the western Arctic Ocean." FEMS microbiology ecology 85, no. 3 (2013): 1–16. https://doi.org/10.1111/1574-6941.12130.

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Aerobic anoxygenic phototrophic (AAP) bacteria are found in a range of aquatic and terrestrial environments, potentially playing unique roles in biogeochemical cycles. Although known to occur in the Arctic Ocean, their ecology and the factors that govern their community structure and distribution in this extreme environment are poorly understood. Here, we examined summer AAP abundance and diversity in the North East Pacific and the Arctic Ocean with emphasis on the southern Beaufort Sea. AAP bacteria comprised up to 10 and 14% of the prokaryotic community in the bottom nepheloid layer and surf

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17

Biebl, Hanno, Brian J. Tindall, Rüdiger Pukall, Heinrich Lünsdorf, Martin Allgaier, and Irene Wagner-Döbler. "Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a." International Journal of Systematic and Evolutionary Microbiology 56, no. 4 (2006): 821–26. http://dx.doi.org/10.1099/ijs.0.63958-0.

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Within a collection of marine strains that were shown to contain the photosynthesis reaction-centre genes pufL and pufM, a novel group of alphaproteobacteria was found and was characterized phenotypically. The 16S rRNA gene sequence data suggested that the strains belonged to the order Rhizobiales and were closest (98·5 % sequence similarity) to the recently described species Hoeflea marina. The cells contained bacteriochlorophyll a and a carotenoid, presumably spheroidenone, in small to medium amounts. Cells of the novel strains were small rods and were motile by means of single polarly inser

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18

Biebl, Hanno, Rüdiger Pukall, Heinrich Lünsdorf, et al. "Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense." International Journal of Systematic and Evolutionary Microbiology 57, no. 5 (2007): 1095–107. http://dx.doi.org/10.1099/ijs.0.64821-0.

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A slightly pink-coloured strain, strain DFL-11T, was isolated from single cells of the marine dinoflagellate Alexandrium lusitanicum and was found to contain the genes encoding two proteins of the photosynthetic reaction centre, pufL and pufM. 16S rRNA gene sequence analysis revealed that the novel strain belonged to the α-2 subgroup of the Proteobacteria and was most closely related to Stappia aggregata (97.7 % similarity), Stappia alba (98.0 %) and Stappia marina (98.0 %). Dark-grown cells of strain DFL-11T contained small amounts of bacteriochlorophyll a (bchl a) and a carotenoid. Cells of

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19

Li, Ai-Hua, and Yu-Guang Zhou. "Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water." International Journal of Systematic and Evolutionary Microbiology 65, Pt_4 (2015): 1199–206. http://dx.doi.org/10.1099/ijs.0.000080.

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Three Gram-staining-negative, strictly aerobic, non-pigmented, non-motile, rod-shaped bacterial strains, SP32T ( = SLM-1T), SR68 ( = SLM-3) and SP95 ( = SLM-2), were isolated from two water samples of a cold-water lake in Xinjiang province, China. Growth was observed at 4–25 °C and pH 6.0–9.0, and optimum growth occurred at 18–20 °C and at pH 7.0–7.5. Phylogenetic analysis of 16S rRNA gene sequences revealed that these isolates belonged to the family Rhodobacteraceae , but formed an evolutionary lineage distinct from other species of this family with validly published names. Strain SP32T showe

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Davenport, Emily J., and Arpita Bose. "Taxonomic Re-Evaluation and Genomic Comparison of Novel Extracellular Electron Uptake-Capable Rhodovulum visakhapatnamense and Rhodovulum sulfidophilum Isolates." Microorganisms 10, no. 6 (2022): 1235. http://dx.doi.org/10.3390/microorganisms10061235.

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Rhodovulum spp. are anoxygenic phototrophic purple bacteria with versatile metabolisms, including the ability to obtain electrons from minerals in their environment to drive photosynthesis, a relatively novel process called phototrophic extracellular electron uptake (pEEU). A total of 15 strains of Rhodovulum sulfidophilum were isolated from a marine estuary to observe these metabolisms in marine phototrophs. One representative strain, Rhodovulum sulfidophilum strain AB26, can perform phototrophic iron oxidation (photoferrotrophy) and couples carbon dioxide fixation to pEEU. Here, we reclassif

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Cottrell, Matthew T., and David L. Kirchman. "Photoheterotrophic Microbes in the Arctic Ocean in Summer and Winter." Applied and Environmental Microbiology 75, no. 15 (2009): 4958–66. http://dx.doi.org/10.1128/aem.00117-09.

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ABSTRACT Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially for high-latitude waters such as the Arctic Ocean, where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examine

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22

Cheng, Ju-E., Pin Su, Zhan-Hong Zhang, et al. "Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods." PLOS ONE 17, no. 7 (2022): e0262517. http://dx.doi.org/10.1371/journal.pone.0262517.

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Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed

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Perreault, Nancy N., Charles W. Greer, Dale T. Andersen, et al. "Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic." Applied and Environmental Microbiology 74, no. 22 (2008): 6898–907. http://dx.doi.org/10.1128/aem.00359-08.

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ABSTRACT The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates conta

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Jiao, N. "Corrigendum to “Real-time PCR for quantification of aerobic anoxygenic phototrophic bacteria based on pufM gene in marine environment" [J. Exp. Mar. Biol. Ecol. 329 (2006) 113-121]." Journal of Experimental Marine Biology and Ecology 342, no. 2 (2007): 332. http://dx.doi.org/10.1016/j.jembe.2006.09.012.

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Wen, Jing, Zhimao Mai, Jie Li, Lin Wang, and Si Zhang. "The Community Structure of Aerobic Anoxygenic Photosynthetic Bacteria in Biocrusts on Tropical Coral Islands and Their Application in Ecological Restoration, South China Sea." Microorganisms 13, no. 6 (2025): 1265. https://doi.org/10.3390/microorganisms13061265.

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Biological soil crusts (referred to as biocrusts) constitute prominent components within the ecosystem of tropical coral islands in the South China Sea, covering approximately 6.25% of the island’s terrestrial surface. Biocrusts are the key to the restoration of the island ecosystem. It is widely acknowledged that phototrophic microorganisms profoundly contribute to biocrust formation and development. They provide fixed carbon and nitrogen and produce exopolysaccharides for the BSC ecosystems. Although aerobic anoxygenic phototrophic bacteria (AAPB) are an important functional group of phototr

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Dedow, Lauren K., and Julia Bailey-Serres. "Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins." Plant and Cell Physiology 60, no. 9 (2019): 1927–38. http://dx.doi.org/10.1093/pcp/pcz072.

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Abstract Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein–RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential

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27

Giebel, Helge-Ansgar, Daniela Kalhoefer, Renate Gahl-Janssen, et al. "Planktomarina temperata gen. nov., sp. nov., belonging to the globally distributed RCA cluster of the marine Roseobacter clade, isolated from the German Wadden Sea." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (2013): 4207–17. http://dx.doi.org/10.1099/ijs.0.053249-0.

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Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter clade-affiliated) cluster (family Rhodobacteraceae , class Alphaproteobacteria ) were obtained from coastal seawater samples. Strain RCA23T was isolated from a 10−7 dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10−3) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcti

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Böhringer, Nils, Maria A. Patras, and Till F. Schäberle. "Heterologous Expression of Pseudouridimycin and Description of the Corresponding Minimal Biosynthetic Gene Cluster." Molecules 26, no. 2 (2021): 510. http://dx.doi.org/10.3390/molecules26020510.

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Pseudouridimycin (PUM) was recently discovered from Streptomyces sp. DSM26212 as a novel bacterial nucleoside analog that competes with UTP for access to the RNA polymerase (RNAP) active site, thereby inhibiting bacterial RNAP by blocking transcription. This represents a novel antibacterial mode of action and it is known that PUM inhibits bacterial RNAP in vitro, inhibits bacterial growth in vitro, and was active in vivo in a mouse infection model of Streptococcus pyogenes peritonitis. The biosynthetic gene cluster (BGC) was previously identified and characterized by knockout experiments. Howe

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Huh, Sung Un. "The Role of Pumilio RNA Binding Protein in Plants." Biomolecules 11, no. 12 (2021): 1851. http://dx.doi.org/10.3390/biom11121851.

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Eukaryotic organisms have a posttranscriptional/translational regulation system for the control of translational efficiency. RNA binding proteins (RBPs) have been known to control target genes. One type of protein, Pumilio (Pum)/Puf family RNA binding proteins, show a specific binding of 3′ untranslational region (3′ UTR) of target mRNA and function as a post-transcriptional/translational regulator in eukaryotic cells. Plant Pum protein is involved in development and biotic/abiotic stresses. Interestingly, Arabidopsis Pum can control target genes in a sequence-specific manner and rRNA processi

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Souza, G. M., A. M. da Silva, and A. Kuspa. "Starvation promotes Dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway." Development 126, no. 14 (1999): 3263–74. http://dx.doi.org/10.1242/dev.126.14.3263.

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When nutrients are depleted, Dictyostelium cells undergo cell cycle arrest and initiate a developmental program that ensures survival. The YakA protein kinase governs this transition by regulating the cell cycle, repressing growth-phase genes and inducing developmental genes. YakA mutants have a shortened cell cycle and do not initiate development. A suppressor of yakA that reverses most of the developmental defects of yakA- cells, but none of their growth defects was identified. The inactivated gene, pufA, encodes a member of the Puf protein family of translational regulators. Upon starvation

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Ramírez, M. R., and R. Cava. "Changes in Fatty Acid Composition of two Muscles from Three Different Iberian × Duroc Genotypes After Refrigerated Storage." Food Science and Technology International 14, no. 2 (2008): 127–37. http://dx.doi.org/10.1177/1082013208091989.

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The changes of the fatty acid (FA) profile of 2 muscles Longissimus dorsi and Biceps femoris from 3 Iberian × Duroc genotypes were studied: GEN1: ♂ Iberian × ♀ Duroc1, GEN2: ♂ Duroc1 × ♀ Iberian; GEN3: ♂ Duroc2 × ♀ Iberian. GEN1 and GEN2 are reciprocal crosses while the difference between GEN2 and GEN3 is the Duroc sire line. The genotype Duroc1 was selected for the production of dry-cured meat products while the genotype Duroc2 was selected for meat production. Longissimus dorsi and Biceps femoris BF from the reciprocal cross showed similar changes in FAs profile after refrigerated storage. H

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Allgaier, Martin, Heike Uphoff, Andreas Felske, and Irene Wagner-Döbler. "Aerobic Anoxygenic Photosynthesis in Roseobacter Clade Bacteria from Diverse Marine Habitats." Applied and Environmental Microbiology 69, no. 9 (2003): 5051–59. http://dx.doi.org/10.1128/aem.69.9.5051-5059.2003.

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ABSTRACT The marine Roseobacter clade comprises several genera of marine bacteria related to the uncultured SAR83 cluster, the second most abundant marine picoplankton lineage. Cultivated representatives of this clade are physiologically heterogeneous, and only some have the capability for aerobic anoxygenic photosynthesis, a process of potentially great ecological importance in the world's oceans. In an attempt to correlate phylogeny with ecology, we investigated the diversity of Roseobacter clade strains from various marine habitats (water samples, biofilms, laminariae, diatoms, and dinoflag

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Andersson, M. Gunnar, and Lage Cerenius. "Pumilio Homologue from Saprolegnia parasitica Specifically Expressed in Undifferentiated Spore Cysts." Eukaryotic Cell 1, no. 1 (2002): 105–11. http://dx.doi.org/10.1128/ec.1.1.105-111.2002.

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ABSTRACT The expression of spore-specific marker transcripts at different stages of the asexual life cycle of Saprolegnia parasitica was analyzed. One of the markers, designated puf1, was found to be expressed transiently upon each of several cycles of zoospore encystment and reemergence. The transcript is induced immediately upon zoospore encystment and is rapidly lost when a cyst is triggered to germinate. In nongerminating cysts, puf1 is maintained until a time point when the cysts can no longer be triggered to germinate and thus have become determined for zoospore reemergence. The results

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Jha, Bhaskar Anand, Abeer Fadda, Clementine Merce, Elisha Mugo, Dorothea Droll, and Christine Clayton. "Depletion of the Trypanosome Pumilio Domain Protein PUF2 or of Some Other Essential Proteins Causes Transcriptome Changes Related to Coding Region Length." Eukaryotic Cell 13, no. 5 (2014): 664–74. http://dx.doi.org/10.1128/ec.00018-14.

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ABSTRACT Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of in vivo RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of

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Sato, Megumi, Kaoru Irie, Yasuyuki Suda, Tomoaki Mizuno, and Kenji Irie. "The RNA-binding protein Puf5 and the HMGB protein Ixr1 contribute to cell cycle progression through the regulation of cell cycle-specific expression of CLB1 in Saccharomyces cerevisiae." PLOS Genetics 18, no. 7 (2022): e1010340. http://dx.doi.org/10.1371/journal.pgen.1010340.

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Puf5, a Puf-family RNA-binding protein, binds to 3´ untranslated region of target mRNAs and negatively regulates their expression in Saccharomyces cerevisiae. The puf5Δ mutant shows pleiotropic phenotypes including a weakened cell wall, a temperature-sensitive growth, and a shorter lifespan. To further analyze a role of Puf5 in cell growth, we searched for a multicopy suppressor of the temperature-sensitive growth of the puf5Δ mutant in this study. We found that overexpression of CLB2 encoding B-type cyclin suppressed the temperature-sensitive growth of the puf5Δ mutant. The puf5Δ clb2Δ double

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Lin, Kaibo, Shikun Zhang, Qinghua Shi, et al. "Essential requirement of mammalian Pumilio family in embryonic development." Molecular Biology of the Cell 29, no. 24 (2018): 2922–32. http://dx.doi.org/10.1091/mbc.e18-06-0369.

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Mouse PUMILIO1 (PUM1) and PUMILIO2 (PUM2) belong to the PUF (Pumilio/FBF) family, a highly conserved RNA binding protein family whose homologues play critical roles in embryonic development and germ line stem cell maintenance in invertebrates. However, their roles in mammalian embryonic development and stem cell maintenance remained largely uncharacterized. Here we report an essential requirement of the Pum gene family in early embryonic development. A loss of both Pum1 and Pum2 genes led to gastrulation failure, resulting in embryo lethality at E8.5. Pum-deficient blastocysts, however, appear

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Smialek, Maciej J., Erkut Ilaslan, Marcin P. Sajek, and Jadwiga Jaruzelska. "Role of PUM RNA-Binding Proteins in Cancer." Cancers 13, no. 1 (2021): 129. http://dx.doi.org/10.3390/cancers13010129.

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Until recently, post-transcriptional gene regulation (PTGR), in contrast to transcriptional regulation, was not extensively explored in cancer, even though it seems to be highly important. PUM proteins are well described in the PTGR of several organisms and contain the PUF RNA-binding domain that recognizes the UGUANAUA motif, located mostly in the 3′ untranslated region (3′UTR) of target mRNAs. Depending on the protein cofactors recruited by PUM proteins, target mRNAs are directed towards translation, repression, activation, degradation, or specific localization. Abnormal profiles of PUM expr

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Jourdan, C., S. Kloiber, A. Nieters, et al. "Gene–PUFA interactions and obesity risk." British Journal of Nutrition 106, no. 8 (2011): 1263–72. http://dx.doi.org/10.1017/s0007114511001541.

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Although there are indications for modulatory effects of PUFA on associations between SNP and obesity risk, scientific evidence in human subjects is still scarce. The present analyses investigated interaction effects between SNP in candidate genes for obesity and PUFA in erythrocyte membranes on obesity risk. Within the second Bavarian Food Consumption Survey (cross-sectional, population-based), 568 adults provided blood samples. Fatty acid composition of erythrocyte membranes was analysed by means of GC. Genotyping was performed for twenty-one genes, including cytokines, adipokines, neurotran

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Kiani, Seyed Jalal, Zohreh Yousefi Ghalejoogh, and Katayoun Samimi-Rad. "Engineered PUF proteins: new flexible toolkits to target the replication of RNA viruses." Future Virology 16, no. 1 (2021): 5–13. http://dx.doi.org/10.2217/fvl-2020-0134.

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Aim: The RNA recognition code of an RNA-binding protein known as Pumilio/FBF (PUF) protein was reprogrammed in order to provide binding to internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome. Materials & methods: The ability of the modified protein to repress IRES-dependent translation was analyzed by dual-luciferase reporter assay, cell viability assay, cell cytotoxicity assay and anti-HCV assay. Results: The modified protein was able to reduce reporter gene expression (>30%) and HCV viral load (>98%) and reduced HCV-induced cytotoxicity to the level observed in un

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Waters, Sinéad M., Gerard S. Coyne, David A. Kenny, David E. MacHugh, and Dermot G. Morris. "Dietary n-3 polyunsaturated fatty acid supplementation alters the expression of genes involved in the control of fertility in the bovine uterine endometrium." Physiological Genomics 44, no. 18 (2012): 878–88. http://dx.doi.org/10.1152/physiolgenomics.00065.2011.

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The potential for dietary supplementation with n-3 polyunsaturated fatty acids (n-3 PUFA) to improve reproductive efficiency in cattle has received much interest. The mechanisms by which n-3 PUFA may affect physiological and biochemical processes in key reproductive tissues are likely to be mediated by significant alterations in gene expression. The objective of this study was to examine the effects of dietary n-3 PUFA supplementation on global uterine endometrial gene expression in cattle. Beef heifers were supplemented with a rumen protected source of either a saturated fatty acid (CON; palm

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FORETZ, Marc, Fabienne FOUFELLE, and Pascal FERRÉ. "Polyunsaturated fatty acids inhibit fatty acid synthase and spot-14-protein gene expression in cultured rat hepatocytes by a peroxidative mechanism." Biochemical Journal 341, no. 2 (1999): 371–76. http://dx.doi.org/10.1042/bj3410371.

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In vivo, polyunsaturated fatty acids (PUFA) inhibit the expression of hepatic genes related to the lipogenic process such as fatty acid synthase and spot-14-protein (S14) genes. In vitro studies have suggested that this was a direct transcriptional effect of PUFA. In hepatocytes, the inhibition of the lipogenic rate by PUFA is not specific, but is linked to a cytotoxic effect due to peroxidative mechanisms. We have investigated whether peroxidation could also explain the inhibitory effect of PUFA on gene expression. Rat hepatocytes were cultured for 24 h with mono-unsaturated or PUFA. PUFA inh

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Tian, Huimin, Haitao Yu, Yiqi Lin, et al. "Association between FADS Gene Expression and Polyunsaturated Fatty Acids in Breast Milk." Nutrients 14, no. 3 (2022): 457. http://dx.doi.org/10.3390/nu14030457.

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Polyunsaturated fatty acid (PUFA) in breast milk provides physiological benefits for offspring and is closely related to endogenous biosynthesis in lactating women. Few studies have addressed the association between fatty acid desaturase (FADS) gene expression patterns and fatty acids in breast milk. This research aimed to explore the differences in PUFA levels among breast milk groups with different levels of FADS gene expression and provide a scientific basis for precision nutrition strategies. A total of 50 healthy women 42–45 days postpartum were included in this study. A basic information

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Rzehak, Peter, Joachim Heinrich, Norman Klopp, et al. "Evidence for an association between genetic variants of the fatty acid desaturase 1 fatty acid desaturase 2 (FADS1 FADS2) gene cluster and the fatty acid composition of erythrocyte membranes." British Journal of Nutrition 101, no. 1 (2008): 20–26. http://dx.doi.org/10.1017/s0007114508992564.

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The present study gives further evidence for the recently found association between variants of the fatty acid desaturase 1 fatty acid desaturase 2 (FADS1 FADS2) gene cluster and PUFA in blood phospholipids and explores this association for cellular fatty acids in erythrocyte membranes. In a subgroup of adults participating in the Bavarian Nutrition Survey II, a cross-sectional population-based study conducted in Bavaria, Germany, allelic variation in three selected loci of the FADS1 FADS2 gene cluster was analysed and used for haplotype construction. Associations with plasma phospholipid PUFA

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Clarke, Steven D. "I. Molecular mechanism for polyunsaturated fatty acid regulation of gene transcription." American Journal of Physiology-Gastrointestinal and Liver Physiology 281, no. 4 (2001): G865—G869. http://dx.doi.org/10.1152/ajpgi.2001.281.4.g865.

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This review addresses the hypothesis that polyunsaturated fatty acids (PUFA), particularly those of the n-3 family, play pivotal roles as “fuel partitioners” in that they direct fatty acids away from triglyceride storage and toward oxidation and they enhance glucose flux to glycogen. In doing this, PUFA may reduce the risk of enhanced cellular apoptosis associated with excessive cellular lipid accumulation. PUFA exert their beneficial effects by upregulating the expression of genes encoding proteins involved in fatty acid oxidation while simultaneously downregulating genes encoding proteins of

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Fulcher, Timothy K., J. Thomas Beatty, and Michael R. Jones. "Demonstration of the Key Role Played by the PufX Protein in the Functional and Structural Organization of Native and Hybrid Bacterial Photosynthetic Core Complexes." Journal of Bacteriology 180, no. 3 (1998): 642–46. http://dx.doi.org/10.1128/jb.180.3.642-646.1998.

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ABSTRACT The role of a component of the bacterial photosystem, the PufX protein, was examined by heterologous expression of thepufX gene from Rhodobacter capsulatus in a strain of R. sphaeroides that lacks the nativepufX gene. The strain of R. sphaeroidescontaining the R. capsulatus PufX protein was capable of efficient transduction of light energy despite a low degree of sequence conservation between the PufX proteins from the two species. The organization of the hybrid reaction center/LH1 photosystem in strains of R. sphaeroides containing the R. capsulatusLH1 antenna complex was affected di

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Marucha, K. Kamanyi, and C. Clayton. "Roles of the Pumilio domain protein PUF3 in Trypanosoma brucei growth and differentiation." Parasitology 147, no. 11 (2020): 1171–83. http://dx.doi.org/10.1017/s003118202000092x.

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AbstractTrypanosomes strongly rely on post-transcriptional mechanisms to control gene expression. Several Opisthokont Pumilio domain proteins are known to suppress expression when bound to mRNAs. The Trypanosoma brucei Pumilio domain protein PUF3 is a cytosolic mRNA-binding protein that suppresses expression when tethered to a reporter mRNA. RNA-binding studies showed that PUF3 preferentially binds to mRNAs with a classical Pumilio-domain recognition motif, UGUA[U/C]AUU. RNA-interference-mediated reduction of PUF3 in bloodstream forms caused a minor growth defect, but the transcriptome was not

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Zhuang, Pan, Xiaohui Liu, Yin Li, et al. "Circulating Fatty Acids and Genetic Predisposition to Type 2 Diabetes: Gene-Nutrient Interaction Analysis." Diabetes Care 45, no. 3 (2022): 564–75. http://dx.doi.org/10.2337/dc21-2048.

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OBJECTIVE To assess the relationship of circulating fatty acids (FA) with risk of type 2 diabetes (T2D) and potential interactions with genetic risk. RESEARCH DESIGN AND METHODS A total of 95,854 participants with complete data on plasma FA from the UK Biobank were enrolled between 2006 and 2010 and were followed up to the end of 2020. Plasma concentrations of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) were analyzed by a high-throughput nuclear magnetic resonance–based biomarker profiling platform. The genetic risk scores (GRS) were

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Macdonald, P. M. "The Drosophila pumilio gene: an unusually long transcription unit and an unusual protein." Development 114, no. 1 (1992): 221–32. http://dx.doi.org/10.1242/dev.114.1.221.

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Specification of the posterior body plan in Drosophila requires the action of a determinant prelocalized to the posterior pole of the embryo. During embryogenesis this determinant appears to move anteriorly in a process dependent on the pumilio (pum) gene. This report describes the cloning and molecular characterization of a cDNA derived from the pum gene, and the analysis of pum mRNA and protein expression during early Drosophila development. The pum gene is unusually large; comparison of genomic and cDNA sequences reveals that the pum transcription unit is at least 160 kb in length. The pum

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Raclot, Thierry, and Hugues Oudart. "Selectivity of fatty acids on lipid metabolism and gene expression." Proceedings of the Nutrition Society 58, no. 3 (1999): 633–46. http://dx.doi.org/10.1017/s002966519900083x.

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Triacylglycerols represent the main form of storage for a wide spectrum of fatty acids. Their utilization first involves mobilization from adipose tissue through lipolysis. The release of individual fatty acids from adipose tissue is selective in vitro and in vivo in animal studies and also in human subjects. Generally, fatty acids are more readily mobilized from fat cells when they are short-chain and unsaturated. This selectivity could affect the storage of individual fatty acids in adipose tissue, and their subsequent supply to tissues. The nature of the dietary fats could affect lipid home

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Clarke, Steven D. "Polyunsaturated fatty acid regulation of gene transcription: a mechanism to improve energy balance and insulin resistance." British Journal of Nutrition 83, S1 (2000): S59—S66. http://dx.doi.org/10.1017/s0007114500000969.

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This review addresses the hypothesis that polyunsaturated fatty acids (PUFA), particularly those of the n-3 family, play essential roles in the maintenance of energy balance and glucose metabolism. The data discussed indicate that dietary PUFA function as fuel partitioners in that they direct glucose toward glycogen storage, and direct fatty acids away from triglyceride synthesis and assimilation and toward fatty acid oxidation. In addition, the n-3 family of PUFA appear to have the unique ability to enhance thermogenesis and thereby reduce the efficiency of body fat deposition. PUFA exert the

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