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https://www.readbyqxmd.com/read/30092381/quantitative-proteomics-of-psychotrophic-diazotroph-in-response-to-nitrogen-deficiency-and-cold-stress
#1
Deep Chandra Suyal, Saurabh Kumar, Divya Joshi, Ravindra Soni, Reeta Goel
Effective protocols and novel biomarkers are the need of this hour to screen potential cold adapted diazotrophs for sustainable mountain agricultural plans. LC-MS/MS based gel less quantitative proteomics was employed to investigate the metabolic response of Himalayan cold adapted diazotroph Pseudomonas palleroniana N26 (JN055435) for nitrogen deficiency and cold stress. More than 5000 proteins were identified, and 125 of them showed significant difference with a 2-fold or greater change (p < .05) between normal and stress conditions, including 29 up-regulated proteins and 35 down-regulated proteins...
August 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29896173/nifpred-proteome-wide-identification-and-categorization-of-nitrogen-fixation-proteins-of-diaztrophs-based-on-composition-transition-distribution-features-using-support-vector-machine
#2
Prabina K Meher, Tanmaya K Sahu, Jyotilipsa Mohanty, Shachi Gahoi, Supriya Purru, Monendra Grover, Atmakuri R Rao
As inorganic nitrogen compounds are essential for basic building blocks of life (e.g., nucleotides and amino acids), the role of biological nitrogen-fixation (BNF) is indispensible. All nitrogen fixing microbes rely on the same nitrogenase enzyme for nitrogen reduction, which is in fact an enzyme complex consists of as many as 20 genes. However, the occurrence of six genes viz., nifB, nifD, nifE, nifH, nifK , and nifN has been proposed to be essential for a functional nitrogenase enzyme. Therefore, identification of these genes is important to understand the mechanism of BNF as well as to explore the possibilities for improving BNF from agricultural sustainability point of view...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27712144/regulation-of-fixlj-by-hfq-controls-symbiotically-important-genes-in-sinorhizobium-meliloti
#3
Mengsheng Gao, Hahn Nguyen, Isai Salas González, Max Teplitski
The RNA-binding chaperone Hfq plays critical roles in the establishment and functionality of the symbiosis between Sinorhizobium meliloti and its legume hosts. A mutation in hfq reduces symbiotic efficiency resulting in a Fix- phenotype, characterized by the inability of the bacterium to fix nitrogen. At least in part, this is due to the ability of Hfq to regulate the fixLJ operon, which encodes a sensor kinase-response regulator pair that controls expression of the nitrogenase genes. The ability of Hfq to bind fixLJ in vitro and in planta was demonstrated with gel shift and coimmunoprecipitation experiments...
November 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27450089/adaptation-of-the-symbiotic-mesorhizobium-chickpea-relationship-to-phosphate-deficiency-relies-on-reprogramming-of-whole-plant-metabolism
#4
Maryam Nasr Esfahani, Miyako Kusano, Kien Huu Nguyen, Yasuko Watanabe, Chien Van Ha, Kazuki Saito, Saad Sulieman, Luis Herrera-Estrella, L S Tran
Low inorganic phosphate (Pi) availability is a major constraint for efficient nitrogen fixation in legumes, including chickpea. To elucidate the mechanisms involved in nodule acclimation to low Pi availability, two Mesorhizobium-chickpea associations exhibiting differential symbiotic performances, Mesorhizobium ciceri CP-31 (McCP-31)-chickpea and Mesorhizobium mediterranum SWRI9 (MmSWRI9)-chickpea, were comprehensively studied under both control and low Pi conditions. MmSWRI9-chickpea showed a lower symbiotic efficiency under low Pi availability than McCP-31-chickpea as evidenced by reduced growth parameters and down-regulation of nifD and nifK These differences can be attributed to decline in Pi level in MmSWRI9-induced nodules under low Pi stress, which coincided with up-regulation of several key Pi starvation-responsive genes, and accumulation of asparagine in nodules and the levels of identified amino acids in Pi-deficient leaves of MmSWRI9-inoculated plants exceeding the shoot nitrogen requirement during Pi starvation, indicative of nitrogen feedback inhibition...
August 9, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27431195/origin-and-evolution-of-nitrogen-fixation-genes-on-symbiosis-islands-and-plasmid-in-bradyrhizobium
#5
Takashi Okubo, Pongdet Piromyou, Panlada Tittabutr, Neung Teaumroong, Kiwamu Minamisawa
The nitrogen fixation (nif) genes of nodule-forming Bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. The nif genes of rhizobial and non-rhizobial Bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. Based on all codon positions, the phylogenetic tree of concatenated nifD and nifK sequences showed that nifDK on symbiosis islands formed a different clade from nifDK on non-symbiotic loci (located outside of symbiosis islands and plasmids) with elongated branches; however, these genes were located in close proximity, when only the 1st and 2nd codon positions were analyzed...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27407147/the-novel-regulatory-ncrna-nfis-optimizes-nitrogen-fixation-via-base-pairing-with-the-nitrogenase-gene-nifk-mrna-in-pseudomonas-stutzeri-a1501
#6
Yuhua Zhan, Yongliang Yan, Zhiping Deng, Ming Chen, Wei Lu, Chao Lu, Liguo Shang, Zhimin Yang, Wei Zhang, Wei Wang, Yun Li, Qi Ke, Jiasi Lu, Yuquan Xu, Liwen Zhang, Zhihong Xie, Qi Cheng, Claudine Elmerich, Min Lin
Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfq-dependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade...
July 26, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27034220/the-relation-between-n2-fixation-and-h2-metabolism-in-the-marine-filamentous-nonheterocystous-cyanobacterium-lyngbya-aestuarii-ccy-9616-1
#7
Daniela Ferreira, Lucas J Stal, Pedro Moradas-Ferreira, Marta V Mendes, Paula Tamagnini
The marine filamentous nonheterocystous nitrogen-fixing cyanobacterium Lyngbya aestuarii (F. K. Mert.) Liebman ex Gomont CCY 9616 was grown under diazotrophic and nondiazotrophic conditions and under an alternating 16:8 light:dark (L:D) regime. Nitrogenase activity appeared just before the onset of the dark period, reaching its maximum 1-2 h in the dark, subsequently decreasing to zero at the beginning of the following light period. Nitrogenase activity was only detected at low levels of O2 (5%) and when the culture was grown in the absence of combined nitrogen...
August 2009: Journal of Phycology
https://www.readbyqxmd.com/read/26984280/the-nucleolar-protein-nifk-promotes-cancer-progression-via-ck1%C3%AE-%C3%AE-catenin-in-metastasis-and-ki-67-dependent-cell-proliferation
#8
Tsung-Chieh Lin, Chia-Yi Su, Pei-Yu Wu, Tsung-Ching Lai, Wen-An Pan, Yi-Hua Jan, Yu-Chang Chang, Chi-Tai Yeh, Chi-Long Chen, Luo-Ping Ger, Hong-Tai Chang, Chih-Jen Yang, Ming-Shyan Huang, Yu-Peng Liu, Yuan-Feng Lin, John Y-J Shyy, Ming-Daw Tsai, Michael Hsiao
Nucleolar protein interacting with the FHA domain of pKi-67 (NIFK) is a Ki-67-interacting protein. However, its precise function in cancer remains largely uninvestigated. Here we show the clinical significance and metastatic mechanism of NIFK in lung cancer. NIFK expression is clinically associated with poor prognosis and metastasis. Furthermore, NIFK enhances Ki-67-dependent proliferation, and promotes migration, invasion in vitro and metastasis in vivo via downregulation of casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling...
March 17, 2016: ELife
https://www.readbyqxmd.com/read/26897628/using-synthetic-biology-to-increase-nitrogenase-activity
#9
Xin-Xin Li, Qi Liu, Xiao-Meng Liu, Hao-Wen Shi, San-Feng Chen
BACKGROUND: Nitrogen fixation has been established in protokaryotic model Escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) from Paenibacillus sp. WLY78. However, the nitrogenase activity in the recombinant E. coli 78-7 is only 10 % of that observed in wild-type Paenibacillus. Thus, it is necessary to increase nitrogenase activity through synthetic biology. RESULTS: In order to increase nitrogenase activity in heterologous host, a total of 28 selected genes from Paenibacillus sp...
2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/26529540/protein-arginine-methyltransferase-8-tetrameric-structure-and-protein-substrate-specificity
#10
Wei-Chao Lee, Wen-Ling Lin, Tsutomu Matsui, Eric S-W Chen, Tong-You Wade Wei, Wen-Hsuan Lin, Hao Hu, Yujun George Zheng, Ming-Daw Tsai, Meng-Chiao Ho
Type I protein arginine methyltransferases (PRMTs) catalyze asymmetric dimethylation of various proteins, and their dysregulations often correlate with tumorigenesis or developmental deficiency. Recent studies have focused on the in vivo substrate identification and the enzyme mechanism with peptide substrates. However, how PRMTs recognize substrates at the protein level remains unknown. PRMT8 is one of the least characterized type I PRMTs, and its crystal structure has not been reported. Here, we report the crystal structure of the PRMT8:SAH complex, identify a new non-histone protein substrate NIFK, and uncover a previously unknown regulatory region specifically required for recognizing NIFK...
December 29, 2015: Biochemistry
https://www.readbyqxmd.com/read/26309237/analysis-of-phylogeny-and-codon-usage-bias-and-relationship-of-gc-content-amino-acid-composition-with-expression-of-the-structural-nif-genes
#11
Sunil Kanti Mondal, Sudip Kundu, Rabindranath Das, Sujit Roy
Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different...
August 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/25871924/phylogeny-and-evolutionary-genetics-of-frankia-strains-based-on-16s-rrna-and-nifd-k-gene-sequences
#12
Arun Kumar Mishra, Pawan Kumar Singh, Prashant Singh, Anumeha Singh, Satya Shila Singh, Amrita Srivastava, Alok Kumar Srivastava, Hridip Kumar Sarma
16S rRNA and nifD-nifK sequences were used to study the molecular phylogeny and evolutionary genetics of Frankia strains isolated from Hippöphae salicifolia D. Don growing at different altitudes (ecologically classified as riverside and hillside isolates) of the Eastern Himalayan region of North Sikkim, India. Genetic information for the small subunit rRNA (16S rRNA) revealed that the riverside Frankia isolates markedly differed from the hillside isolates suggesting that the riverside isolates are genetically compact...
August 2015: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/25850532/influence-of-different-factors-on-the-nitrogenase-activity-of-the-engineered-escherichia-coli-78-7
#13
Li-hong Zhang, San-feng Chen
The engineered Escherichia coli 78-7 is a derivative of E. coli JM109 carrying a nitrogen fixation (nif) gene cluster composed of nine genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) and its own σ(70)-dependent nif promoter from a gram-positive bacterium Paenibacillus sp. WLY78. The physiological and biochemical characteristics of the engineered E. coli 78-7 were analyzed by using Biolog GEN III MicroPlate, with E. coli JM109 and JM109/pHY300PLK (E. coli JM109 carrying empty vector) as controls...
June 2015: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/25826659/the-rna-recognition-motif-of-nifk-is-required-for-rrna-maturation-during-cell-cycle-progression
#14
Wen-An Pan, Hsin-Yue Tsai, Shun-Chang Wang, Michael Hsiao, Pei-Yu Wu, Ming-Daw Tsai
Ribosome biogenesis governs protein synthesis. NIFK is transactivated by c-Myc, the key regulator of ribosome biogenesis. The biological function of human NIFK is not well established, except that it has been shown to interact with Ki67 and NPM1. Here we report that NIFK is required for cell cycle progression and participates in the ribosome biogenesis via its RNA recognition motif (RRM). We show that silencing of NIFK inhibits cell proliferation through a reversible p53-dependent G1 arrest, possibly by induction of the RPL5/RPL11-mediated nucleolar stress...
2015: RNA Biology
https://www.readbyqxmd.com/read/25400621/phylogeny-and-phylogeography-of-functional-genes-shared-among-seven-terrestrial-subsurface-metagenomes-reveal-n-cycling-and-microbial-evolutionary-relationships
#15
Maggie C Y Lau, Connor Cameron, Cara Magnabosco, C Titus Brown, Faye Schilkey, Sharon Grim, Sarah Hendrickson, Michael Pullin, Barbara Sherwood Lollar, Esta van Heerden, Thomas L Kieft, Tullis C Onstott
Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors...
2014: Frontiers in Microbiology
https://www.readbyqxmd.com/read/25163544/the-genome-of-paenibacillus-sabinae-t27-provides-insight-into-evolution-organization-and-functional-elucidation-of-nif-and-nif-like-genes
#16
Xinxin Li, Zhiping Deng, Zhanzhi Liu, Yongliang Yan, Tianshu Wang, Jianbo Xie, Min Lin, Qi Cheng, Sanfeng Chen
BACKGROUND: Most biological nitrogen fixation is catalyzed by the molybdenum nitrogenase. This enzyme is a complex which contains the MoFe protein encoded by nifDK and the Fe protein encoded by nifH. In addition to nifHDK, nifHDK-like genes were found in some Archaea and Firmicutes, but their function is unclear. RESULTS: We sequenced the genome of Paenibacillus sabinae T27. A total of 4,793 open reading frames were predicted from its 5.27 Mb genome. The genome of P...
2014: BMC Genomics
https://www.readbyqxmd.com/read/25017168/challenges-to-develop-nitrogen-fixing-cereals-by-direct-nif-gene-transfer
#17
REVIEW
Leonardo Curatti, Luis M Rubio
Some regions of the developing world suffer low cereal production yields due to low fertilizer inputs, among other factors. Biological N2 fixation, catalyzed by the prokaryotic enzyme nitrogenase, is an alternative to the use of synthetic N fertilizers. The molybdenum nitrogenase is an O2-labile metalloenzyme composed of the NifDK and NifH proteins, which biosyntheses require a number of nif gene products. A challenging strategy to increase cereal crop productivity in a scenario of low N fertilization is the direct transfer of nif genes into cereals...
August 2014: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/24947137/mechanisms-of-physiological-adjustment-of-n2-fixation-in-cicer-arietinum-l-chickpea-during-early-stages-of-water-deficit-single-or-multi-factor-controls
#18
Maryam Nasr Esfahani, Saad Sulieman, Joachim Schulze, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki, Lam-Son Phan Tran
Drought negatively impacts symbiotic nitrogen fixation (SNF) in Cicer arietinum L. (chickpea), thereby limiting yield potential. Understanding how drought affects chickpea nodulation will enable the development of strategies to biotechnologically engineer chickpea varieties with enhanced SNF under drought conditions. By analyzing carbon and nitrogen metabolism, we studied the mechanisms of physiological adjustment of nitrogen fixation in chickpea plants nodulated with Mesorhizobium ciceri during both drought stress and subsequent recovery...
September 2014: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/24928870/metaproteomic-identification-of-diazotrophic-methanotrophs-and-their-localization-in-root-tissues-of-field-grown-rice-plants
#19
Zhihua Bao, Takashi Okubo, Kengo Kubota, Yasuhiro Kasahara, Hirohito Tsurumaru, Mizue Anda, Seishi Ikeda, Kiwamu Minamisawa
In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp...
August 2014: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/24867636/ki-67-is-a-pp1-interacting-protein-that-organises-the-mitotic-chromosome-periphery
#20
Daniel G Booth, Masatoshi Takagi, Luis Sanchez-Pulido, Elizabeth Petfalski, Giulia Vargiu, Kumiko Samejima, Naoko Imamoto, Chris P Ponting, David Tollervey, William C Earnshaw, Paola Vagnarelli
When the nucleolus disassembles during open mitosis, many nucleolar proteins and RNAs associate with chromosomes, establishing a perichromosomal compartment coating the chromosome periphery. At present nothing is known about the function of this poorly characterised compartment. In this study, we report that the nucleolar protein Ki-67 is required for the assembly of the perichromosomal compartment in human cells. Ki-67 is a cell-cycle regulated protein phosphatase 1-binding protein that is involved in phospho-regulation of the nucleolar protein B23/nucleophosmin...
May 27, 2014: ELife
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