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Journal articles on the topic 'Proteins, Protein, Genes'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Darwish, Kamel, Huiying Li, and Thomas Poulos. "Engineering proteins, subcloning and hyperexpressing oxidoreductase genes." "Protein Engineering, Design and Selection" 4, no. 6 (1991): 701–8. http://dx.doi.org/10.1093/protein/4.6.701.

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2

Darwish, K., H. Li, and T. L. Poulos. "Engineering proteins, subcloning and hyperexpressing xidoreductase genes." "Protein Engineering, Design and Selection" 4, no. 7 (1991): 850. http://dx.doi.org/10.1093/protein/4.7.850.

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3

Neff, Norma F. "Protein splicing: selfish genes invade cellular proteins." Current Opinion in Cell Biology 5, no. 6 (1993): 971–76. http://dx.doi.org/10.1016/0955-0674(93)90079-6.

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4

Yesilirmak, Filiz, and Zehra Sayers. "Heterelogous Expression of Plant Genes." International Journal of Plant Genomics 2009 (August 6, 2009): 1–16. http://dx.doi.org/10.1155/2009/296482.

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Heterologous expression allows the production of plant proteins in an organism which is simpler than the natural source. This technology is widely used for large-scale purification of plant proteins from microorganisms for biochemical and biophysical analyses. Additionally expression in well-defined model organisms provides insights into the functions of proteins in complex pathways. The present review gives an overview of recombinant plant protein production methods using bacteria, yeast, insect cells, and Xenopus laevis oocytes and discusses the advantages of each system for functional studi

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5

Gophna, Uri, and Yanay Ofran. "Lateral acquisition of genes is affected by the friendliness of their products." Proceedings of the National Academy of Sciences 108, no. 1 (2010): 343–48. http://dx.doi.org/10.1073/pnas.1009775108.

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A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few protein–protein interactions. The propensity of proteins to participate in protein–pr

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NG, SEE-KIONG, and SOON-HENG TAN. "DISCOVERING PROTEIN–PROTEIN INTERACTIONS." Journal of Bioinformatics and Computational Biology 01, no. 04 (2004): 711–41. http://dx.doi.org/10.1142/s0219720004000600.

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The ongoing genomics and proteomics efforts have helped identify many new genes and proteins in living organisms. However, simply knowing the existence of genes and proteins does not tell us much about the biological processes in which they participate. Many major biological processes are controlled by protein interaction networks. A comprehensive description of protein–protein interactions is therefore necessary to understand the genetic program of life. In this tutorial, we provide an overview of the various current high-throughput methods for discovering protein–protein interactions, coveri

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Medvedeva, Irina V., Pavel S. Demenkov, and Vladimir A. Ivanisenko. "SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes." Journal of Bioinformatics and Computational Biology 15, no. 02 (2017): 1650044. http://dx.doi.org/10.1142/s021972001650044x.

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Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual project

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8

Kuroda, Hirofumi, Naoki Takahashi, Hiroaki Shimada, Motoaki Seki, Kazuo Shinozaki, and Minami Matsui. "Classification and Expression Analysis of Arabidopsis F-Box-Containing Protein Genes." Plant and Cell Physiology 43, no. 10 (2002): 1073–85. http://dx.doi.org/10.1093/pcp/pcf151.

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Abstract F-box proteins regulate diverse cellular processes, including cell cycle transition, transcriptional regulation and signal transduction, by playing roles in Skp1p-cullin-F-box protein (SCF) complexes or non-SCF complexes. F-box proteins are encoded by a large gene family. Our database search revealed that at least 568 F-box protein genes are present in the Arabidopsisthaliana (Arabidopsis) genome. Domain search analysis using SMART and Pfam-A databases revealed that 67 of the F-box proteins contained Kelch repeats and 29 contained leucine-rich repeats (LRRs). Interestingly only two F-

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Biernat, Jacek, and Hubert Köster. "Expression of synthetic genes coding for completely new, nutritionally rich, artificial proteins." "Protein Engineering, Design and Selection" 1, no. 4 (1987): 353–58. http://dx.doi.org/10.1093/protein/1.4.353.

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10

Chakraborty, Sandip, and David Alvarez-Ponce. "Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks." BioMed Research International 2016 (2016): 1–12. http://dx.doi.org/10.1155/2016/4658506.

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Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins) are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-pr

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11

Liu, Xiao, Xiao Li Geng, and Hong Ling Tang. "Protein Subcellular Localization Feature of Essential/Nonessential Genes in 28 Prokaryotes." Applied Mechanics and Materials 644-650 (September 2014): 5197–201. http://dx.doi.org/10.4028/www.scientific.net/amm.644-650.5197.

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This study aimed to pursue the correlation between essential/nonessential gene and protein subcellular localization. The protein sequences of the essential/nonessential genes of 28 prokaryotes in Database of Essential Genes were analyzed by PSORTb3.0. Results show that proteins of essential genes locate in cytoplasm with relatively high percentage, i.e., in the range of 40% to 55%. Percentages of the proteins of essential genes locate in cytoplasma membrane are lower than that of nonessential genes, which mostly are about 15%. However, the values of proteins of nonessential genes are mostly ab

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12

Chen, Shoukun, Jiawei Li, Yue Liu, and Haifeng Li. "Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon." Plants 8, no. 7 (2019): 188. http://dx.doi.org/10.3390/plants8070188.

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By regulating the pre-mRNA splicing of other genes and themselves, plant serine/arginine-rich (SR) proteins play important roles in development and in response to abiotic stresses. Presently, the functions of most plant SR protein genes remain unclear. Wheat (Triticum aestivum) and Brachypodium distachyon are closely related species. In this study, 40 TaSR and 18 BdSR proteins were identified respectively, and they were classified into seven subfamilies: SR, RS, SCL, RSZ, RS2Z, SC35, and SR45. Similar to Arabidopsis and rice SR protein genes, most TaSR and BdSR protein genes are expressed exte

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13

Hooper, Scott L., and Jeffrey B. Thuma. "Invertebrate Muscles: Muscle Specific Genes and Proteins." Physiological Reviews 85, no. 3 (2005): 1001–60. http://dx.doi.org/10.1152/physrev.00019.2004.

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This is the first of a projected series of canonic reviews covering all invertebrate muscle literature prior to 2005 and covers muscle genes and proteins except those involved in excitation-contraction coupling (e.g., the ryanodine receptor) and those forming ligand- and voltage-dependent channels. Two themes are of primary importance. The first is the evolutionary antiquity of muscle proteins. Actin, myosin, and tropomyosin (at least, the presence of other muscle proteins in these organisms has not been examined) exist in muscle-like cells in Radiata, and almost all muscle proteins are presen

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Biernat, Jacek, Hanne Hasselmann, Bernd Hofer, Nick Kennedy, and Hubert Köster. "The construction and cloning of synthetic genes coding for artificial proteins and expression studies to obtain fusion proteins." "Protein Engineering, Design and Selection" 1, no. 4 (1987): 345–51. http://dx.doi.org/10.1093/protein/1.4.345.

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15

Zeng, W., D. J. Andrew, L. D. Mathies, M. A. Horner, and M. P. Scott. "Ectopic expression and function of the Antp and Scr homeotic genes: the N terminus of the homeodomain is critical to functional specificity." Development 118, no. 2 (1993): 339–52. http://dx.doi.org/10.1242/dev.118.2.339.

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The transcription factors encoded by homeotic genes determine cell fates during development. Each homeotic protein causes cells to follow a distinct pathway, presumably by differentially regulating downstream ‘target’ genes. The homeodomain, the DNA-binding part of homeotic proteins, is necessary for conferring the specificity of each homeotic protein's action. The two Drosophila homeotic proteins encoded by Antennapedia and Sex combs reduced determine cell fates in the epidermis and internal tissues of the posterior head and thorax. Genes encoding chimeric Antp/Scr proteins were introduced in

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16

Brady, Timothy P. "Genes and Protein Synthesis—Updating Our Understanding." American Biology Teacher 80, no. 9 (2018): 642–48. http://dx.doi.org/10.1525/abt.2018.80.9.642.

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That genes are indispensable is indisputable but that they are the source of information for protein synthesis—to the extent reflected by statements such as “genes are blueprints for proteins” or “genomes constitute developmental programs”—is challenged by discoveries such as post-translational modification of protein and alternative splicing.

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Arvidsson, Gustav, and Anthony Wright. "A Protein Intrinsic Disorder Approach for Characterising Differentially Expressed Genes in Transcriptome Data: Analysis of Cell-Adhesion Regulated Gene Expression in Lymphoma Cells." International Journal of Molecular Sciences 19, no. 10 (2018): 3101. http://dx.doi.org/10.3390/ijms19103101.

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Conformational protein properties are coupled to protein functionality and could provide a useful parameter for functional annotation of differentially expressed genes in transcriptome studies. The aim was to determine whether predicted intrinsic protein disorder was differentially associated with proteins encoded by genes that are differentially regulated in lymphoma cells upon interaction with stromal cells, an interaction that occurs in microenvironments, such as lymph nodes that are protective for lymphoma cells during chemotherapy. Intrinsic disorder protein properties were extracted from

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18

Iuga, Mihai, Peter Awram, John F. Nomellini, and John Smit. "Comparison of S-layer secretion genes in freshwater caulobacters." Canadian Journal of Microbiology 50, no. 9 (2004): 751–66. http://dx.doi.org/10.1139/w04-046.

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Our freshwater caulobacter collection contains about 40 strains that are morphologically similar to Caulobacter crescentus. All elaborate a crystalline protein surface (S) layer made up of protein monomers 100–193 kDa in size. We conducted a comparative study of S-layer secretion in 6 strains representing 3 size groups of S-layer proteins: small (100–108 kDa), medium (122–151 kDa), and large (181–193 kDa). All contained genes predicted to encode ATP-binding cassette transporters and membrane fusion proteins highly similar to those of C. crescentus, indicating that the S-layer proteins were all

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19

Wickelgren, I. "Architectural Proteins: Protein Sculptors That Help Turn on Genes." Science 270, no. 5242 (1995): 1587–88. http://dx.doi.org/10.1126/science.270.5242.1587.

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20

Kakizawa, Shigeyuki, Kenro Oshima, Tsutomu Kuboyama, et al. "Cloning and Expression Analysis of Phytoplasma Protein Translocation Genes." Molecular Plant-Microbe Interactions® 14, no. 9 (2001): 1043–50. http://dx.doi.org/10.1094/mpmi.2001.14.9.1043.

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Genes encoding SecA and SecY proteins, essential components of the Sec protein translocation system, were cloned from onion yellows phytoplasma, an unculturable plant pathogenic bacterium. The secA gene consists of 2,505 nucleotides encoding an 835 amino acid protein (95.7 kDa) and shows the highest similarity with SecA of Bacillus subtilis. Anti-SecA rabbit antibody was prepared from a purified partial SecA protein, with a histidine tag expressed in Escherichia coli. Western blot analysis confirmed that SecA protein (approximately 96 kDa) is produced in phytoplasma-infected plants. Immunohist

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21

Shin, Tae-Jin, Kang-Hoon Lee, and Je-Yoel Cho. "Epigenetic Mechanisms of LncRNAs Binding to Protein in Carcinogenesis." Cancers 12, no. 10 (2020): 2925. http://dx.doi.org/10.3390/cancers12102925.

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Epigenetic dysregulation is an important feature for cancer initiation and progression. Long non-coding RNAs (lncRNAs) are transcripts that stably present as RNA forms with no translated protein and have lengths larger than 200 nucleotides. LncRNA can epigenetically regulate either oncogenes or tumor suppressor genes. Nowadays, the combined research of lncRNA plus protein analysis is gaining more attention. LncRNA controls gene expression directly by binding to transcription factors of target genes and indirectly by complexing with other proteins to bind to target proteins and cause protein de

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22

Makarova, Kira S., and Eugene V. Koonin. "Archaeal Ubiquitin-Like Proteins: Functional Versatility and Putative Ancestral Involvement in tRNA Modification Revealed by Comparative Genomic Analysis." Archaea 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/710303.

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The recent discovery of protein modification by SAMPs, ubiquitin-like (Ubl) proteins from the archaeonHaloferax volcanii, prompted a comprehensive comparative-genomic analysis of archaeal Ubl protein genes and the genes for enzymes thought to be functionally associated with Ubl proteins. This analysis showed that most archaea encode members of two major groups of Ubl proteins with theβ-grasp fold, the ThiS and MoaD families, and indicated that the ThiS family genes are rarely linked to genes for thiamine or Mo/W cofactor metabolism enzymes but instead are most often associated with genes for e

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23

Tamura, Masaru, and Toshihiko Shiroishi. "GSDM family genes meet autophagy." Biochemical Journal 469, no. 2 (2015): e5-e7. http://dx.doi.org/10.1042/bj20150558.

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Shi et al. provided a new insight of Gsdm family protein function. They reported that N- and C-terminus domain of Gsdm family protein interact each other. Moreover, the N-terminus domain of Gsdm family proteins has pro-autophagic activity, which is suppressed by the C-terminus domain.

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24

Rahmani, Hossein, Hendrik Blockeel, and Andreas Bender. "Predicting Genes Involved in Human Cancer Using Network Contextual Information." Journal of Integrative Bioinformatics 9, no. 1 (2012): 44–71. http://dx.doi.org/10.1515/jib-2012-210.

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Summary Protein-Protein Interaction (PPI) networks have been widely used for the task of predicting proteins involved in cancer. Previous research has shown that functional information about the protein for which a prediction is made, proximity to specific other proteins in the PPI network, as well as local network structure are informative features in this respect. In this work, we introduce two new types of input features, reflecting additional information: (1) Functional Context: the functions of proteins interacting with the target protein (rather than the protein itself); and (2) Structur

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Calderwood, Michael A., Kavitha Venkatesan, Li Xing, et al. "Epstein–Barr virus and virus human protein interaction maps." Proceedings of the National Academy of Sciences 104, no. 18 (2007): 7606–11. http://dx.doi.org/10.1073/pnas.0702332104.

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A comprehensive mapping of interactions among Epstein–Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence. Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system. Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified. EBV–EBV and EBV–human protein interaction, or “interactome” maps provided a framework for hypothe

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Wang, Dandan, Daixi Li, Guangrong Qin, et al. "The Structural Characterization of Tumor Fusion Genes and Proteins." Computational and Mathematical Methods in Medicine 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/912742.

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Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural pr

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Wires, Emily S., Kathleen A. Trychta, Lacey M. Kennedy, and Brandon K. Harvey. "The Function of KDEL Receptors as UPR Genes in Disease." International Journal of Molecular Sciences 22, no. 11 (2021): 5436. http://dx.doi.org/10.3390/ijms22115436.

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The KDEL receptor retrieval pathway is essential for maintaining resident proteins in the endoplasmic reticulum (ER) lumen. ER resident proteins serve a variety of functions, including protein folding and maturation. Perturbations to the lumenal ER microenvironment, such as calcium depletion, can cause protein misfolding and activation of the unfolded protein response (UPR). Additionally, ER resident proteins are secreted from the cell by overwhelming the KDEL receptor retrieval pathway. Recent data show that KDEL receptors are also activated during the UPR through the IRE1/XBP1 signaling path

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Smithers, Ben, Matt Oates, and Julian Gough. "‘Why genes in pieces?’—revisited." Nucleic Acids Research 47, no. 10 (2019): 4970–73. http://dx.doi.org/10.1093/nar/gkz284.

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Abstract The alignment between the boundaries of protein domains and the boundaries of exons could provide evidence for the evolution of proteins via domain shuffling, but literature in the field has so far struggled to conclusively show this. Here, on larger data sets than previously possible, we do finally show that this phenomenon is indisputably found widely across the eukaryotic tree. In contrast, the alignment between exons and the boundaries of intrinsically disordered regions of proteins is not a general property of eukaryotes. Most interesting of all is the discovery that domain–exon

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29

Weising, Kurt, and Günter Kahl. "Towards an Understanding of Plant Gene Regulation: The Action of Nuclear Factors." Zeitschrift für Naturforschung C 46, no. 1-2 (1991): 1–11. http://dx.doi.org/10.1515/znc-1991-1-202.

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Abstract Over the last decade an intensive research on the regulation of gene expression in viral and animal systems has led to the discovery of cis-acting regulatory sequences, the identification of sequence-specific DNA -binding proteins (trans-acting factors), the characterization of protein domains involved in DNA -protein recognition and binding as well as in protein -protein interactions, and the cloning and sequencing of genes encoding regulatory proteins. The tremendous progress in this field is now being complemented by advances in our understanding of how plant genes are regulated.

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Okkels, Limei Meng, and Peter Andersen. "Protein-Protein Interactions of Proteins from the ESAT-6 Family of Mycobacterium tuberculosis." Journal of Bacteriology 186, no. 8 (2004): 2487–91. http://dx.doi.org/10.1128/jb.186.8.2487-2491.2004.

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ABSTRACT In the present study, we demonstrate that, in analogy with the genes encoding ESAT-6 and CFP-10, the genes rv0287 and rv0288 from the ESAT-6 gene family are cotranscribed. Using Western-Western blotting and protein-print overlay methodologies, we demonstrate that ESAT-6 and CFP-10, as well as the protein pair Rv0288/Rv0287, interact pairwise in a highly specific way. Most notably, the ESAT-6 proteins interact directly with Rv3873, a possible cell envelope component of the ESAT-6 secretion pathway.

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Pollmann, Katrin, Johannes Raff, Michaela Schnorpfeil, Galina Radeva, and Sonja Selenska-Pobell. "Novel surface layer protein genes in Bacillus sphaericus associated with unusual insertion elements." Microbiology 151, no. 9 (2005): 2961–73. http://dx.doi.org/10.1099/mic.0.28201-0.

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The surface layer (S-layer) protein genes of the uranium mining waste pile isolate Bacillus sphaericus JG-A12 and of its relative B. sphaericus NCTC 9602 were analysed. The almost identical N-termini of the two S-layer proteins possess a unique structure, comprising three N-terminal S-layer homologous (SLH) domains. The central parts of the proteins share a high homology and are related to the S-layer proteins of B. sphaericus CCM 2177 and P-1. In contrast, the C-terminal parts of the S-layer proteins of JG-A12 and NCTC 9602 differ significantly between each other. Surprisingly, the C-terminal

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32

KAFI, A. K. M., MITSURU HATTORI, and TAKEAKI OZAWA. "LUCIFERASES FOR THE STUDY OF PROTEIN–PROTEIN INTERACTIONS IN LIVE CELLS AND ANIMALS." Nano LIFE 01, no. 01n02 (2010): 79–87. http://dx.doi.org/10.1142/s1793984410000079.

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Many imaging technologies based on luminescent proteins have proven useful for detecting protein–protein interactions, tracking cells in mice, and monitoring transcriptional regulation of specific genes. Especially, novel bioluminescent proteins have advanced the study of induced protein interactions and protein modification in live cells and animals. This review focuses on recent developments of bioluminescent probes for quantitative evaluation of specific protein–protein interactions and their spatio-temporal imaging by means of split luciferase complementation techniques. From the compariso

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Rosander, Anna, Lars Frykberg, Nora Ausmees, and Peter Müller. "Identification of Extracytoplasmic Proteins in Bradyrhizobium japonicum Using Phage Display." Molecular Plant-Microbe Interactions® 16, no. 8 (2003): 727–37. http://dx.doi.org/10.1094/mpmi.2003.16.8.727.

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A novel gene bank of Bradyrhizobium japonicum USDA110spc4 was constructed using pG3DSS, a phagemid vector designed for detecting genes encoding secreted proteins. In this phagemid, the phage protein III lacks its indigenous signal peptide required for protein secretion, thus recombinant fusion proteins are displayed on the phage surface only if a functional signal peptide is provided by an inserted DNA fragment. In addition, the N-terminal half of protein III has been replaced by a short linker region (the E-tag) that is recognized by a monoclonal antibody, which enables isolation of phages di

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Roberts, M. R., and G. L. de Bruxelles. "Plant 14-3-3 protein families: evidence for isoform-specific functions?" Biochemical Society Transactions 30, no. 4 (2002): 373–78. http://dx.doi.org/10.1042/bst0300373.

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14-3-3 proteins regulate a wide range of target proteins via direct protein-protein interactions. The target-binding domain in 14-3-3 proteins is highly conserved, suggesting similar biochemical properties for all 14-3-3s. However, higher eukaryotes possess multiple 14-3-3 genes, and these genes exhibit diverse patterns of gene expression within any one organism. This tends to suggest specific functions for particular genes. Some biochemical data suggest 14-3-3 isoform-specific protein-protein interactions, whereas other studies conclude that apparent isoform-specificity is the result of diffe

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Tate, P., M. Lee, S. Tweedie, W. C. Skarnes, and W. A. Bickmore. "Capturing novel mouse genes encoding chromosomal and other nuclear proteins." Journal of Cell Science 111, no. 17 (1998): 2575–85. http://dx.doi.org/10.1242/jcs.111.17.2575.

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The burgeoning wealth of gene sequences contrasts with our ignorance of gene function. One route to assigning function is by determining the sub-cellular location of proteins. We describe the identification of mouse genes encoding proteins that are confined to nuclear compartments by splicing endogeneous gene sequences to a promoterless betageo reporter, using a gene trap approach. Mouse ES (embryonic stem) cell lines were identified that express betageo fusions located within sub-nuclear compartments, including chromosomes, the nucleolus and foci containing splicing factors. The sequences of

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Lonie, A., R. D'Andrea, R. Paro, and R. Saint. "Molecular characterisation of the Polycomblike gene of Drosophila melanogaster, a trans-acting negative regulator of homeotic gene expression." Development 120, no. 9 (1994): 2629–36. http://dx.doi.org/10.1242/dev.120.9.2629.

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The Polycomblike gene of Drosophila melanogaster, a member of the Polycomb Group of genes, is required for the correct spatial expression of the homeotic genes of the Antennapaedia and Bithorax Complexes. Mutations in Polycomb Group genes result in ectopic homeotic gene expression, indicating that Polycomb Group proteins maintain the transcriptional repression of specific homeotic genes in specific tissues during development. We report here the isolation and molecular characterisation of the Polycomblike gene. The Polycomblike transcript encodes an 857 amino acid protein with no significant ho

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Åkesson, P., K. H. Schmidt, J. Cooney, and L. Björck. "M1 protein and protein H: IgGFc- and albumin-binding streptococcal surface proteins encoded by adjacent genes." Biochemical Journal 300, no. 3 (1994): 877–86. http://dx.doi.org/10.1042/bj3000877.

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M1 protein and Protein H are surface proteins simultaneously present at the surface of certain strains of Streptococcus pyogenes, important pathogenic bacteria in humans. The present study concerns the structure, protein-binding properties and relationship between these two molecules. The gene encoding M1 protein (emm1) was found immediately upstream of the Protein H gene (sph). Both genes were preceded by a promoter region. Comparison of the sequences revealed a high degree of similarity in the signal peptides, the C repeats located in the central parts of the molecules and in the C-terminal

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Rancurel, Corinne, Mahvash Khosravi, A. Keith Dunker, Pedro R. Romero, and David Karlin. "Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation." Journal of Virology 83, no. 20 (2009): 10719–36. http://dx.doi.org/10.1128/jvi.00595-09.

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ABSTRACT It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called “overprinting.” To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition gl

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Mirzaei, Khaled, Bahman Bahramnejad, Mohammad Hasan Shamsifard, and Wahid Zamani. "In SilicoIdentification, Phylogenetic and Bioinformatic Analysis of Argonaute Genes in Plants." International Journal of Genomics 2014 (2014): 1–17. http://dx.doi.org/10.1155/2014/967461.

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Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Arg

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Perry, B. N., D. Savva, E. Radley, C. J. Skidmore, and R. D. Lovell. "Restriction Fragment Length Polymorphisms in Bovine Milk Protein Genes." Proceedings of the British Society of Animal Production (1972) 1989 (March 1989): 147. http://dx.doi.org/10.1017/s0308229600011375.

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Genetic and technological studies have revealed correlations between different individual, or combinations of, alleles of milk proteins and parameters such as cheese yield, the compositional characteristics of milk and total lactation yield. The kappa casein B allele is better for cheese-making, for example (Table 1): the mutation may alter the mechanism by which this protein stabilises the micelles of the caldum-sensitive caseins against precipitation. When rennin cleaves kappa casein between amino acids 105 and 106 the micelle is destabilised and clotting of milk into curds ensues. Therefore

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Wu, Qitu, and Valley Stewart. "NasFED Proteins Mediate Assimilatory Nitrate and Nitrite Transport in Klebsiella oxytoca(pneumoniae) M5al." Journal of Bacteriology 180, no. 5 (1998): 1311–22. http://dx.doi.org/10.1128/jb.180.5.1311-1322.1998.

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ABSTRACT Klebsiella oxytoca can use nitrate and nitrite as sole nitrogen sources. The enzymes required for nitrate and nitrite assimilation are encoded by the nasFEDCBA operon. We report here the complete nasFED sequence. Sequence comparisons indicate that the nasFED genes encode components of a conventional periplasmic binding protein-dependent transport system consisting of a periplasmic binding protein (NasF), a homodimeric intrinsic membrane protein (NasE), and a homodimeric ATP-binding cassette (ABC) protein (NasD). The NasF protein and the related NrtA and CmpA proteins of cyanobacteria

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Southey-Pillig, Christopher J., David G. Davies, and Karin Sauer. "Characterization of Temporal Protein Production in Pseudomonas aeruginosa Biofilms." Journal of Bacteriology 187, no. 23 (2005): 8114–26. http://dx.doi.org/10.1128/jb.187.23.8114-8126.2005.

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ABSTRACT Phenotypic and genetic evidence supporting the notion of biofilm formation as a developmental process is growing. In the present work, we provide additional support for this hypothesis by identifying the onset of accumulation of biofilm-stage specific proteins during Pseudomonas aeruginosa biofilm maturation and by tracking the abundance of these proteins in planktonic and three biofilm developmental stages. The onset of protein production was found to correlate with the progression of biofilms in developmental stages. Protein identification revealed that proteins with similar functio

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Botelho, João, Paulo Mascarenhas, José João Mendes, and Vanessa Machado. "Network Protein Interaction in Parkinson’s Disease and Periodontitis Interplay: A Preliminary Bioinformatic Analysis." Genes 11, no. 11 (2020): 1385. http://dx.doi.org/10.3390/genes11111385.

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Recent studies supported a clinical association between Parkinson’s disease (PD) and periodontitis. Hence, investigating possible interactions between proteins associated to these two conditions is of interest. In this study, we conducted a protein–protein network interaction analysis with recognized genes encoding proteins with variants strongly associated with PD and periodontitis. Genes of interest were collected via the Genome-Wide Association Studies (GWAS) database. Then, we conducted a protein interaction analysis, using the Search Tool for the Retrieval of Interacting Genes/Proteins (S

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Sakai, Daisuke, and Teruya Komano. "Genes Required for Plasmid R64 Thin-Pilus Biogenesis: Identification and Localization of Products of the pilK, pilM, pilO, pilP, pilR, and pilT Genes." Journal of Bacteriology 184, no. 2 (2002): 444–51. http://dx.doi.org/10.1128/jb.184.2.444-451.2002.

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ABSTRACT We have previously shown that the pilL, pilN, pilQ, pilS, pilU, and pilV genes of plasmid R64 encode outer membrane lipoprotein, secretin, cytoplasmic ATPase, major pilin, prepilin peptidase, and minor pilin, respectively, which are required for thin-pilus formation. In this work, we characterized the products of the remaining essential genes, pilK, pilM, pilO, pilP, pilR, and pilT, with regard to their localization and processing. Overexpression systems containing pilM, pilO, and pilP genes fused with N-terminal glutathione S-transferase (GST) or a His tag were constructed. Overprodu

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Selkoe, Dennis J. "Alzheimer's Disease: Genes, Proteins, and Therapy." Physiological Reviews 81, no. 2 (2001): 741–66. http://dx.doi.org/10.1152/physrev.2001.81.2.741.

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Rapid progress in deciphering the biological mechanism of Alzheimer's disease (AD) has arisen from the application of molecular and cell biology to this complex disorder of the limbic and association cortices. In turn, new insights into fundamental aspects of protein biology have resulted from research on the disease. This beneficial interplay between basic and applied cell biology is well illustrated by advances in understanding the genotype-to-phenotype relationships of familial Alzheimer's disease. All four genes definitively linked to inherited forms of the disease to date have been shown

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Lu, Shaohua, Jing Zhang, Xinlei Lian, et al. "A hidden human proteome encoded by ‘non-coding’ genes." Nucleic Acids Research 47, no. 15 (2019): 8111–25. http://dx.doi.org/10.1093/nar/gkz646.

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Abstract It has been a long debate whether the 98% ‘non-coding’ fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting

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Choe, Keith P., and Kevin Strange. "Genome-wide RNAi screen and in vivo protein aggregation reporters identify degradation of damaged proteins as an essential hypertonic stress response." American Journal of Physiology-Cell Physiology 295, no. 6 (2008): C1488—C1498. http://dx.doi.org/10.1152/ajpcell.00450.2008.

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The damaging effects of hypertonic stress on cellular proteins are poorly defined, and almost nothing is known about the pathways that detect and repair hypertonicity-induced protein damage. To begin addressing these problems, we screened ∼19,000 Caenorhabditis elegans genes by RNA interference (RNAi) feeding and identified 40 that are essential for survival during acute hypertonic stress. Half (20 of 40) of these genes encode proteins that function to detect, transport, and degrade damaged proteins, including components of the ubiquitin-proteasome system, endosomal sorting complexes, and lyso

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Lorenzini, Emily, Alexander Singer, Bhag Singh, et al. "Structure and Protein-Protein Interaction Studies on Chlamydia trachomatis Protein CT670 (YscO Homolog)." Journal of Bacteriology 192, no. 11 (2010): 2746–56. http://dx.doi.org/10.1128/jb.01479-09.

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ABSTRACT Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these prote

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Venkatesh, Jelli, Min-Young Kang, Li Liu, Jin-Kyung Kwon, and Byoung-Cheorl Kang. "F-Box Family Genes, LTSF1 and LTSF2, Regulate Low-Temperature Stress Tolerance in Pepper (Capsicum chinense)." Plants 9, no. 9 (2020): 1186. http://dx.doi.org/10.3390/plants9091186.

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The F-box proteins belong to a family of regulatory proteins that play key roles in the proteasomal degradation of other proteins. Plant F-box proteins are functionally diverse, and the precise roles of many such proteins in growth and development are not known. Previously, two low-temperature-sensitive F-box protein family genes (LTSF1 and LTSF2) were identified as candidates responsible for the sensitivity to low temperatures in the pepper (Capsicum chinense) cultivar ‘sy-2’. In the present study, we showed that the virus-induced gene silencing of these genes stunted plant growth and caused

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Mariño-Ramírez, Leonardo, Jonathan L. Minor, Nicola Reading та James C. Hu. "Identification and Mapping of Self-Assembling Protein Domains Encoded by the Escherichia coli K-12 Genome by Use of λ Repressor Fusions". Journal of Bacteriology 186, № 5 (2004): 1311–19. http://dx.doi.org/10.1128/jb.186.5.1311-1319.2004.

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ABSTRACT Self-assembling proteins and protein fragments encoded by the Escherichia coli genome were identified from E. coli K-12 strain MG1655. Libraries of random DNA fragments cloned into a series of λ repressor fusion vectors were subjected to selection for immunity to infection by phage λ. Survivors were identified by sequencing the ends of the inserts, and the fused protein sequence was inferred from the known genomic sequence. Four hundred sixty-three nonredundant open reading frame-encoded interacting sequence tags (ISTs) were recovered from sequencing 2,089 candidates. These ISTs, whic

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