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Journal articles on the topic 'GreA'

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Author: Grafiati

Published: 6 September 2023

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1

Dylewski, Maciej, Llorenç Fernández-Coll, Bożena Bruhn-Olszewska, Carlos Balsalobre, and Katarzyna Potrykus. "Autoregulation of greA Expression Relies on GraL Rather than on greA Promoter Region." International Journal of Molecular Sciences 20, no. 20 (October 22, 2019): 5224. http://dx.doi.org/10.3390/ijms20205224.

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GreA is a well-characterized transcriptional factor that acts primarily by rescuing stalled RNA polymerase complexes, but has also been shown to be the major transcriptional fidelity and proofreading factor, while it inhibits DNA break repair. Regulation of greA gene expression itself is still not well understood. So far, it has been shown that its expression is driven by two overlapping promoters and that greA leader encodes a small RNA (GraL) that is acting in trans on nudE mRNA. It has been also shown that GreA autoinhibits its own expression in vivo. Here, we decided to investigate the inner workings of this autoregulatory loop. Transcriptional fusions with lacZ reporter carrying different modifications (made both to the greA promoter and leader regions) were made to pinpoint the sequences responsible for this autoregulation, while GraL levels were also monitored. Our data indicate that GreA mediated regulation of its own gene expression is dependent on GraL acting in cis (a rare example of dual-action sRNA), rather than on the promoter region. However, a yet unidentified, additional factor seems to participate in this regulation as well. Overall, the GreA/GraL regulatory loop seems to have unique but hard to classify properties.

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2

Gera, Judit. "Ars translationis." Internationale Neerlandistiek 59, no. 1 (February 1, 2021): 81–85. http://dx.doi.org/10.5117/in2021.1.007.grea.

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3

Koulich, Dmitry, Marianna Orlova, Arun Malhotra, Andrej Sali, Seth A. Darst, and Sergei Borukhov. "Domain Organization ofEscherichia coliTranscript Cleavage Factors GreA and GreB." Journal of Biological Chemistry 272, no. 11 (March 14, 1997): 7201–10. http://dx.doi.org/10.1074/jbc.272.11.7201.

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4

Stepanova, Ekaterina, Jookyung Lee, Maria Ozerova, Ekaterina Semenova, Kirill Datsenko, Barry L. Wanner, Konstantin Severinov, and Sergei Borukhov. "Analysis of Promoter Targets for Escherichia coli Transcription Elongation Factor GreA In Vivo and In Vitro." Journal of Bacteriology 189, no. 24 (August 31, 2007): 8772–85. http://dx.doi.org/10.1128/jb.00911-07.

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ABSTRACT Transcription elongation factor GreA induces nucleolytic activity of bacterial RNA polymerase (RNAP). In vitro, transcript cleavage by GreA contributes to transcription efficiency by (i) suppressing pauses and arrests, (ii) stimulating RNAP promoter escape, and (iii) enhancing transcription fidelity. However, it is unclear which of these functions is (are) most relevant in vivo. By comparing global gene expression profiles of Escherichia coli strains lacking Gre factors and strains expressing either the wild type (wt) or a functionally inactive GreA mutant, we identified genes that are potential targets of GreA action. Data analysis revealed that in the presence of chromosomally expressed GreA, 19 genes are upregulated; an additional 105 genes are activated upon overexpression of the wt but not the mutant GreA. Primer extension reactions with selected transcription units confirmed the gene array data. The most prominent stimulatory effect (threefold to about sixfold) of GreA was observed for genes of ribosomal protein operons and the tna operon, suggesting that transcript cleavage by GreA contributes to optimal expression levels of these genes in vivo. In vitro transcription assays indicated that the stimulatory effect of GreA upon the transcription of these genes is mostly due to increased RNAP recycling due to facilitated promoter escape. We propose that transcript cleavage during early stages of initiation is thus the main in vivo function of GreA. Surprisingly, the presence of the wt GreA also led to the decreased transcription of many genes. The mechanism of this effect is unknown and may be indirect.

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5

Marr, Michael T., and Jeffrey W. Roberts. "Function of Transcription Cleavage Factors GreA and GreB at a Regulatory Pause Site." Molecular Cell 6, no. 6 (December 2000): 1275–85. http://dx.doi.org/10.1016/s1097-2765(00)00126-x.

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6

Dylewski, Maciej, Monika Ćwiklińska, and Katarzyna Potrykus. "A search for the in trans role of GraL, an Escherichia coli small RNA*." Acta Biochimica Polonica 65, no. 1 (May 27, 2018): 141–49. http://dx.doi.org/10.18388/abp.2017_2562.

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Small RNA are very important post-transcriptional regulators in both, bacteria and eukaryotes. One of such sRNA is GraL, encoded in the greA leader region and conserved among enteric bacteria. Here, we conducted a bioinformatics search for GraL’s targets in trans and validated our findings in vivo by constructing fusions of probable targets with lacZ and measuring their activity when GraL was overexpressed. Only one target's activity (nudE) decreased under those conditions and was thus selected for further analysis. In the absence of GraL and greA, the nudE::lacZ fusion's β-galactosidase activity was increased. However, a similar effect was also visible in the strain deleted only for greA. Furthermore, overproduction of GreA alone increased the nudE::lacZ fusion’s activity as well. This suggests existence of complex regulatory loop-like interactions between GreA, GraL and nudE mRNA. To further dissect this relationship, we performed in vitro EMSA experiments employing GraL and nudE mRNA. However, stable GraL-nudE complexes were not detected, even though the detectable amount of unbound GraL decreased as increasing amounts of nudE mRNA were added. Interestingly, GraL is being bound by Hfq, but nudE easily displaces it. We also conducted a search for genes that are synthetic lethal when deleted along with GraL. This revealed 40 genes that are rendered essential by GraL deletion, however, they are involved in many different cellular processes and no clear correlation was found. The obtained data suggest that GraL's mechanism of action is non-canonical, unique and requires further research.

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7

Mustaev, Arkady, Christal L. Vitiello, and Max E. Gottesman. "Probing the structure of Nun transcription arrest factor bound to RNA polymerase." Proceedings of the National Academy of Sciences 113, no. 31 (July 19, 2016): 8693–98. http://dx.doi.org/10.1073/pnas.1601056113.

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The coliphage HK022 protein Nun transcription elongation arrest factor inhibits RNA polymerase translocation. In vivo, Nun acts specifically to block transcription of the coliphage λ chromosome. Using in vitro assays, we demonstrate that Nun cross-links RNA in an RNA:DNA hybrid within a ternary elongation complex (TEC). Both the 5′ and the 3′ ends of the RNA cross-link Nun, implying that Nun contacts RNA polymerase both at the upstream edge of the RNA:DNA hybrid and in the vicinity of the catalytic center. This finding suggests that Nun may inhibit translocation by more than one mechanism. Transcription elongation factor GreA efficiently blocked Nun cross-linking to the 3′ end of the transcript, whereas the highly homologous GreB factor did not. Surprisingly, both factors strongly suppressed Nun cross-linking to the 5′ end of the RNA, suggesting that GreA and GreB can enter the RNA exit channel as well as the secondary channel, where they are known to bind. These findings extend the known action mechanism for these ubiquitous cellular factors.

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8

Li, Kun, Tianyi Jiang, Bo Yu, Limin Wang, Chao Gao, Cuiqing Ma, Ping Xu, and Yanhe Ma. "Transcription Elongation Factor GreA Has Functional Chaperone Activity." PLoS ONE 7, no. 12 (December 12, 2012): e47521. http://dx.doi.org/10.1371/journal.pone.0047521.

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9

Toulme, F. "GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming." EMBO Journal 19, no. 24 (December 15, 2000): 6853–59. http://dx.doi.org/10.1093/emboj/19.24.6853.

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10

Laptenko, O. "Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase." EMBO Journal 22, no. 23 (December 1, 2003): 6322–34. http://dx.doi.org/10.1093/emboj/cdg610.

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11

Doherty, Geoff P., Donna H. Meredith, and Peter J. Lewis. "Subcellular Partitioning of Transcription Factors in Bacillus subtilis." Journal of Bacteriology 188, no. 11 (June 1, 2006): 4101–10. http://dx.doi.org/10.1128/jb.01934-05.

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ABSTRACT RNA polymerase (RNAP) requires the interaction of various transcription elongation factors to efficiently transcribe RNA. During transcription of rRNA operons, RNAP forms highly processive antitermination complexes by interacting with NusA, NusB, NusG, NusE, and possibly several unidentified factors to increase elongation rates to around twice those observed for mRNA. In previous work we used cytological assays with Bacillus subtilis to identify the major sites of rRNA synthesis within the cell, which are called transcription foci. Using this cytological assay, in conjunction with both quantitative native polyacrylamide gel electrophoresis and Western blotting, we investigated the total protein levels and the ratios of NusB and NusG to RNAP in both antitermination and mRNA transcription complexes. We determined that the ratio of RNAP to NusG was 1:1 in both antitermination and mRNA transcription complexes, suggesting that NusG plays important regulatory roles in both complexes. A ratio of NusB to RNAP of 1:1 was calculated for antitermination complexes with just a 0.3:1 ratio in mRNA complexes, suggesting that NusB is restricted to antitermination complexes. We also investigated the cellular abundance and subcellular localization of transcription restart factor GreA. We found no evidence which suggests that GreA is involved in antitermination complex formation and that it has a cellular abundance which is around twice that of RNAP. Surprisingly, we found that the vast majority of GreA is associated with RNAP, suggesting that there is more than one binding site for GreA on RNAP. These results indicate that transcription elongation complexes are highly dynamic and are differentially segregated within the nucleoid according to their functions.

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12

Maddalena, Lea L. de, Henrike Niederholtmeyer, Matti Turtola, Zoe N. Swank, Georgiy A. Belogurov, and Sebastian J. Maerkl. "GreA and GreB Enhance Expression ofEscherichia coliRNA Polymerase Promoters in a Reconstituted Transcription–Translation System." ACS Synthetic Biology 5, no. 9 (May 19, 2016): 929–35. http://dx.doi.org/10.1021/acssynbio.6b00017.

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13

Świątek, Łukasz, Inga Wasilewska, Anastazja Boguszewska, Agnieszka Grzegorczyk, Jakub Rezmer, Barbara Rajtar, Małgorzata Polz-Dacewicz, and Elwira Sieniawska. "Herb Robert’s Gift against Human Diseases: Anticancer and Antimicrobial Activity of Geranium robertianum L." Pharmaceutics 15, no. 5 (May 22, 2023): 1561. http://dx.doi.org/10.3390/pharmaceutics15051561.

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Geranium robertianum L. is a widely distributed plant used as a traditional herbal medicine, but the knowledge of its biological properties still needs to be improved. Thus, the purpose of this presented research was to assess the phytochemical profile of extracts from aerial parts of G. robertianum, commercially available in Poland and to study their anticancer potential and antimicrobial properties, including the antiviral, antibacterial, and antifungal effects. Additionally, the bioactivity of fractions obtained from the hexane and ethyl acetate extract was analyzed. The phytochemical analysis revealed the presence of organic and phenolic acids, hydrolysable tannins (gallo- and ellagitannins), and flavonoids. Significant anticancer activity was found for G. robertianum hexane extract (GrH) and ethyl acetate extract (GrEA) with an SI (selectivity index) between 2.02 and 4.39. GrH and GrEA inhibited the development of HHV-1-induced cytopathic effect (CPE) in virus-infected cells and decreased the viral load by 0.52 log and 1.42 log, respectively. Among the analyzed fractions, only those obtained from GrEA showed the ability to decrease the CPE and reduce the viral load. The extracts and fractions from G. robertianum showed a versatile effect on the panel of bacteria and fungi. The highest activity was observed for fraction GrEA4 against Gram-positive bacteria, including Micrococcus luteus ATCC 10240 (MIC 8 μg/mL), Staphylococcus epidermidis ATCC 12228 (MIC 16 μg/mL), Staphylococcus aureus ATCC 43300 (MIC 125 μg/mL), Enterococcus faecalis ATCC 29212 (MIC 125 μg/mL), and Bacillus subtilis ATCC 6633 (MIC 125 μg/mL). The observed antibacterial effect may justify the traditional use of G. robertianum to treat hard-to-heal wounds.

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14

Laranjeira, Ronaldo. "Artigo do GREA-USP não declara conflito de interesse." Revista Brasileira de Psiquiatria 28, no. 1 (March 2006): 83. http://dx.doi.org/10.1590/s1516-44462006000100019.

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15

Sivaramakrishnan, Priya, Leonardo A. Sepúlveda, Jennifer A. Halliday, Jingjing Liu, María Angélica Bravo Núñez, Ido Golding, Susan M. Rosenberg, and Christophe Herman. "The transcription fidelity factor GreA impedes DNA break repair." Nature 550, no. 7675 (October 2017): 214–18. http://dx.doi.org/10.1038/nature23907.

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16

Borukhov, S., A. Polyakov, V. Nikiforov, and A. Goldfarb. "GreA protein: a transcription elongation factor from Escherichia coli." Proceedings of the National Academy of Sciences 89, no. 19 (October 1, 1992): 8899–902. http://dx.doi.org/10.1073/pnas.89.19.8899.

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17

Qian, Jin, Wenxuan Xu, Yan Yan, Irina Artsimovitch, David Dunlap, and Laura Finzi. "Force and GreA Modulate Transcriptional Pauses at Elongational Obstacles." Biophysical Journal 118, no. 3 (February 2020): 542a. http://dx.doi.org/10.1016/j.bpj.2019.11.2970.

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18

Lu, C. D., D. H. Kwon, and A. T. Abdelal. "Identification of greA encoding a transcriptional elongation factor as a member of the carA-orf-carB-greA operon in Pseudomonas aeruginosa PAO1." Journal of bacteriology 179, no. 9 (1997): 3043–46. http://dx.doi.org/10.1128/jb.179.9.3043-3046.1997.

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19

Grudniak, A. M., B. Nowicka-Sans, M. Maciag, and K. I. Wolska. "Influence ofEscherichia coli DnaK and DnaJ molecular chaperones on tryptophanase (TnaA) amount and GreA, GreB stability." Folia Microbiologica 49, no. 5 (September 2004): 507–12. http://dx.doi.org/10.1007/bf02931525.

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20

Kulish, Dmitry, Jookyung Lee, Ivan Lomakin, Beata Nowicka, Asis Das, Seth Darst, Kristjan Normet, and Sergei Borukhov. "The Functional Role of Basic Patch, a Structural Element ofEscherichia coliTranscript Cleavage Factors GreA and GreB." Journal of Biological Chemistry 275, no. 17 (April 21, 2000): 12789–98. http://dx.doi.org/10.1074/jbc.275.17.12789.

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21

Darst, Seth A., Charles E. Stebbins, Sergei Borukhov, Marianna Orlova, Guoha Feng, Robert Landick, and Alex Goldfarb. "Crystallization of GreA, a Transcript Cleavage Factor from Escherichia coli." Journal of Molecular Biology 242, no. 4 (September 1994): 582–85. http://dx.doi.org/10.1006/jmbi.1994.1603.

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22

Sparkowski, J., and A. Das. "Location of a new gene, greA, on the Escherichia coli chromosome." Journal of Bacteriology 173, no. 17 (1991): 5256–57. http://dx.doi.org/10.1128/jb.173.17.5256-5257.1991.

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23

Potrykus, Katarzyna, Daniel Vinella, Helen Murphy, Agnieszka Szalewska-Palasz, Richard D'Ari, and Michael Cashel. "Antagonistic Regulation ofEscherichia coliRibosomal RNArrnBP1 Promoter Activity by GreA and DksA." Journal of Biological Chemistry 281, no. 22 (April 5, 2006): 15238–48. http://dx.doi.org/10.1074/jbc.m601531200.

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24

Stebbins, Charles E., Sergei Borukhov, Marianna Orlova, Andrey Polyakov, Alex Goldfarb, and Seth A. Darst. "Crystal structure of the GreA transcript cleavage factor from Escherichia coli." Nature 373, no. 6515 (February 1995): 636–40. http://dx.doi.org/10.1038/373636a0.

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25

Sen, Ranjan, Hiroki Nagai, and Nobuo Shimamoto. "Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factor GreA and GreB." Genes to Cells 6, no. 5 (May 2001): 389–401. http://dx.doi.org/10.1046/j.1365-2443.2001.00436.x.

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26

Ștefan, Cristian Valentin. "Recidivă postexecutorie. Pedepse anterioare succesive. Calculul duratei termenului de reabilitare judecătorească." Criminal Law Writings (Caiete de Drept Penal), no. 3 (February 1, 2021): 132–36. http://dx.doi.org/10.24193/cdp.2020.3.8.

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În vederea stabilirii stării de recidivă postexecutorie, în ipoteza unor pedepse anterioare succesive, durata termenului de reabilitare judecătorească nu se calculează în mod necesar în funcţie de pedeapsa cea mai grea, ci în funcţie de pedeapsa cea din urmă, aplicată pentru infracţiunea care constituie primul termen al pluralităţii.

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27

Erie, D., O. Hajiseyedjavadi, M. Young, and P. von Hippel. "Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription." Science 262, no. 5135 (November 5, 1993): 867–73. http://dx.doi.org/10.1126/science.8235608.

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28

Derbyshire, M. E. "Statistical Rationale for Grant-Related Expenditure Assessment (GREA) Concerning Personal Social Services." Journal of the Royal Statistical Society. Series A (General) 150, no. 4 (1987): 309. http://dx.doi.org/10.2307/2982041.

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29

Lagares, Antonio, Daniela F. Hozbor, Karsten Niehaus, Augusto J. L. Pich Otero, Jens Lorenzen, Walter Arnold, and Alfred Pühler. "Genetic Characterization of a Sinorhizobium meliloti Chromosomal Region Involved in Lipopolysaccharide Biosynthesis." Journal of Bacteriology 183, no. 4 (February 15, 2001): 1248–58. http://dx.doi.org/10.1128/jb.183.4.1248-1258.2001.

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ABSTRACT The genetic characterization of a 5.5-kb chromosomal region ofSinorhizobium meliloti 2011 that contains lpsB, a gene required for the normal development of symbiosis withMedicago spp., is presented. The nucleotide sequence of this DNA fragment revealed the presence of six genes: greAand lpsB, transcribed in the forward direction; andlpsE, lpsD, lpsC, and lrp, transcribed in the reverse direction. Except for lpsB, none of thelps genes were relevant for nodulation and nitrogen fixation. Analysis of the transcriptional organization oflpsB showed that greA and lpsB are part of separate transcriptional units, which is in agreement with the finding of a DNA stretch homologous to a “nonnitrogen” promoter consensus sequence between greA and lpsB. The opposite orientation of lpsB with respect to its first downstream coding sequence, lpsE, indicated that the altered LPS and the defective symbiosis of lpsB mutants are both consequences of a primary nonpolar defect in a single gene. Global sequence comparisons revealed that the greA-lpsB andlrp genes of S. meliloti have a genetic organization similar to that of their homologous loci in R. leguminosarum bv. viciae. In particular, high sequence similarity was found between the translation product of lpsB and a core-related biosynthetic mannosyltransferase of R. leguminosarum bv. viciae encoded by the lpcC gene. The functional relationship between these two genes was demonstrated in genetic complementation experiments in which the S. meliloti lpsB gene restored the wild-type LPS phenotype when introduced into lpcC mutants of R. leguminosarum. These results support the view that S. meliloti lpsB also encodes a mannosyltransferase that participates in the biosynthesis of the LPS core. Evidence is provided for the presence of otherlpsB-homologous sequences in several members of the familyRhizobiaceae.

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30

Hsu, L. M., N. V. Vo, and M. J. Chamberlin. "Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro." Proceedings of the National Academy of Sciences 92, no. 25 (December 5, 1995): 11588–92. http://dx.doi.org/10.1073/pnas.92.25.11588.

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31

Esyunina, Daria, Aleksei Agapov, and Andrey Kulbachinskiy. "Regulation of transcriptional pausing through the secondary channel of RNA polymerase." Proceedings of the National Academy of Sciences 113, no. 31 (July 18, 2016): 8699–704. http://dx.doi.org/10.1073/pnas.1603531113.

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Transcriptional pausing has emerged as an essential mechanism of genetic regulation in both bacteria and eukaryotes, where it serves to coordinate transcription with other cellular processes and to activate or halt gene expression rapidly in response to external stimuli. Deinococcus radiodurans, a highly radioresistant and stress-resistant bacterium, encodes three members of the Gre family of transcription factors: GreA and two Gre factor homologs, Gfh1 and Gfh2. Whereas GreA is a universal bacterial factor that stimulates RNA cleavage by RNA polymerase (RNAP), the functions of lineage-specific Gfh proteins remain unknown. Here, we demonstrate that these proteins, which bind within the RNAP secondary channel, strongly enhance site-specific transcriptional pausing and intrinsic termination. Uniquely, the pause-stimulatory activity of Gfh proteins depends on the nature of divalent ions (Mg2+ or Mn2+) present in the reaction and is also modulated by the nascent RNA structure and the trigger loop in the RNAP active site. Our data reveal remarkable plasticity of the RNAP active site in response to various regulatory stimuli and highlight functional diversity of transcription factors that bind inside the secondary channel of RNAP.

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32

Jing, Bo Peng, Qiu Dong-Yan Kong Juan, Peng Yan Liu Gui-Ying, Guo Xiao-Yu Sun Xiang-Jin Xu Yan-Fang, Sun Rui-hua Pang Wei Zhou, and Jin-Hui Zhao Quan-Xiu Wang. "Screening and Validation of Rice OsAAP6 Interaction Protein." Journal of Biotechnology Research, no. 91 (June 28, 2023): 21–32. http://dx.doi.org/10.32861/jbr.91.21.32.

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The protein content of rice seeds is an extremely important quality trait, but its genetic basis and molecular regulatory mechanism are still unclear. This study focuses on a positive regulatory gene OsAAP6 of grain protein content in rice. Proteins that interact with OsAAP6 were screened using yeast two hybrid experiments, and validated using in vivo point-to-point experiments and bimolecular fluorescence complementarity tests (BiFC). The main results are as follows: 98 positive colonies that may interact with OsAAP6 were screened from a rice cDNA library using yeast two hybrid technology. After sequencing and analysis, 40 proteins that may interact with OsAAP6 were ultimately obtained. Through comparative analysis, three proteins (Pyruvate phosphate dikinase (PPDR), WRKY, and GreA) were selected from these 40 proteins that may interact with each other. In vivo point-to-point experiments in yeast and bimolecular fluorescence complementarity (BiFC) experiments in rice were used to further verify that PPDK, WRKY, and GreA can interact with OsAAP6 protein, respectively. Therefore, the results of this study will provide important clues for further revealing the molecular mechanism by which the OsAAP6 gene regulates grain protein content.

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33

Andrade, Arthur Guerra de. "Resposta ao Prof. Laranjeira: "Artigo do GREA-USP não declara conflito de interesse"." Revista Brasileira de Psiquiatria 28, no. 1 (March 2006): 83–84. http://dx.doi.org/10.1590/s1516-44462006000100020.

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34

Lin, Yin, Zheng Yichun, and Li Zhen. "Study of the occurrence of Fe in sericites of Grea Mica Mine, China." Geochimica et Cosmochimica Acta 70, no. 18 (August 2006): A359. http://dx.doi.org/10.1016/j.gca.2006.06.726.

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35

Yuzenkova, Yulia, Pamela Gamba, Martijn Herber, Laetitia Attaiech, Sulman Shafeeq, Oscar P. Kuipers, Stefan Klumpp, Nikolay Zenkin, and Jan-Willem Veening. "Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae." Nucleic Acids Research 42, no. 17 (September 4, 2014): 10987–99. http://dx.doi.org/10.1093/nar/gku790.

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36

Vinella, D., K. Potrykus, H. Murphy, and M. Cashel. "Effects on Growth by Changes of the Balance between GreA, GreB, and DksA Suggest Mutual Competition and Functional Redundancy in Escherichia coli." Journal of Bacteriology 194, no. 2 (November 4, 2011): 261–73. http://dx.doi.org/10.1128/jb.06238-11.

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37

Gaviria-Cantin, Tania, Andrés Felipe Vargas, Youssef El Mouali, Carlos Jonay Jiménez, Annika Cimdins-Ahne, Cristina Madrid, Ute Römling, and Carlos Balsalobre. "Gre Factors Are Required for Biofilm Formation in Salmonella enterica Serovar Typhimurium by Targeting Transcription of the csgD Gene." Microorganisms 10, no. 10 (September 27, 2022): 1921. http://dx.doi.org/10.3390/microorganisms10101921.

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Rdar biofilm formation of Salmonella typhimurium and Escherichia coli is a common ancient multicellular behavior relevant in cell–cell and inter-organism interactions equally, as in interaction with biotic and abiotic surfaces. With the expression of the characteristic extracellular matrix components amyloid curli fimbriae and the exopolysaccharide cellulose, the central hub for the delicate regulation of rdar morphotype expression is the orphan transcriptional regulator CsgD. Gre factors are ubiquitously interacting with RNA polymerase to selectively overcome transcriptional pausing. In this work, we found that GreA/GreB are required for expression of the csgD operon and consequently the rdar morphotype. The ability of the Gre factors to suppress transcriptional pausing and the 147 bp 5′-UTR of csgD are required for the stimulatory effect of the Gre factors on csgD expression. These novel mechanism(s) of regulation for the csgD operon might be relevant under specific stress conditions.

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38

Traverse, Charles C., and Howard Ochman. "A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli." G3: Genes|Genomes|Genetics 8, no. 7 (May 16, 2018): 2257–64. http://dx.doi.org/10.1534/g3.118.200209.

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39

Lee, D. N., G. Feng, and R. Landick. "GreA-induced transcript cleavage is accompanied by reverse translocation to a different transcription complex conformation." Journal of Biological Chemistry 269, no. 35 (September 1994): 22295–303. http://dx.doi.org/10.1016/s0021-9258(17)31789-1.

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40

Bubunenko, Mikhail G., Carolyn B. Court, Alison J. Rattray, Deanna R. Gotte, Maria L. Kireeva, Jorge A. Irizarry-Caro, Xintian Li, et al. "A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli." Genetics 206, no. 1 (March 24, 2017): 179–87. http://dx.doi.org/10.1534/genetics.116.198960.

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41

Kusuya, Y., K. Kurokawa, S. Ishikawa, N. Ogasawara, and T. Oshima. "Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells." Journal of Bacteriology 193, no. 12 (April 22, 2011): 3090–99. http://dx.doi.org/10.1128/jb.00086-11.

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42

Rutherford, Steven T., Justin J. Lemke, Catherine E. Vrentas, Tamas Gaal, Wilma Ross, and Richard L. Gourse. "Effects of DksA, GreA, and GreB on Transcription Initiation: Insights into the Mechanisms of Factors that Bind in the Secondary Channel of RNA Polymerase." Journal of Molecular Biology 366, no. 4 (March 2007): 1243–57. http://dx.doi.org/10.1016/j.jmb.2006.12.013.

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43

Potrykus, Katarzyna, Helen Murphy, Xiongfong Chen, Jonathan A. Epstein, and Michael Cashel. "Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL." Nucleic Acids Research 38, no. 5 (December 14, 2009): 1636–51. http://dx.doi.org/10.1093/nar/gkp1150.

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44

Wackler, Barbara, Gerald Lackner, Yit Heng Chooi, and Dirk Hoffmeister. "Characterization of the Suillus grevillei Quinone Synthetase GreA Supports a Nonribosomal Code for Aromatic α-Keto Acids." ChemBioChem 13, no. 12 (June 22, 2012): 1798–804. http://dx.doi.org/10.1002/cbic.201200187.

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45

Petushkov, Ivan, Daria Esyunina, Vladimir Mekler, Konstantin Severinov, Danil Pupov, and Andrey Kulbachinskiy. "Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase." Biochemical Journal 474, no. 24 (December 1, 2017): 4053–64. http://dx.doi.org/10.1042/bcj20170436.

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In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5′-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ70 subunit of Escherichia coli RNAP. We show that substitutions and deletions in σ region 3.2 decrease the rate of promoter escape and lead to accumulation of inactive complexes during transcription initiation. Secondary channel factors differentially regulate this process depending on the promoter and mutations in σ region 3.2. GreA generally increase the rate of promoter escape; DksA also stimulates promoter escape on certain templates, while GreB either stimulates or inhibits this process depending on the template. When observed, the stimulation of promoter escape correlates with the accumulation of stressed transcription complexes with scrunched DNA, while changes in the RNA 5′-end structure modulate promoter clearance. Thus, the initiation-to-elongation transition is controlled by a complex interplay between RNAP-binding protein factors and the growing RNA chain.

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Nag, Jeetendra Kumar, Nidhi Shrivastava, Dhanvantri Chahar, Chhedi Lal Gupta, Preeti Bajpai, and Shailja Misra-Bhattacharya. "Wolbachia Transcription Elongation Factor “Wol GreA” Interacts with α2ββ′σ Subunits of RNA Polymerase through Its Dimeric C-Terminal Domain." PLoS Neglected Tropical Diseases 8, no. 6 (June 19, 2014): e2930. http://dx.doi.org/10.1371/journal.pntd.0002930.

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47

Artsimovitch, Irina, Vladimir Svetlov, Larry Anthony, Richard R. Burgess, and Robert Landick. "RNA Polymerases from Bacillus subtilisand Escherichia coli Differ in Recognition of Regulatory Signals In Vitro." Journal of Bacteriology 182, no. 21 (November 1, 2000): 6027–35. http://dx.doi.org/10.1128/jb.182.21.6027-6035.2000.

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ABSTRACT Adaptation of bacterial cells to diverse habitats relies on the ability of RNA polymerase to respond to various regulatory signals. Some of these signals are conserved throughout evolution, whereas others are species specific. In this study we present a comprehensive comparative analysis of RNA polymerases from two distantly related bacterial species, Escherichia coli and Bacillus subtilis, using a panel of in vitro transcription assays. We found substantial species-specific differences in the ability of these enzymes to escape from the promoter and to recognize certain types of elongation signals. Both enzymes responded similarly to other pause and termination signals and to the general E. coli elongation factors NusA and GreA. We also demonstrate that, although promoter recognition depends largely on the ς subunit, promoter discrimination exhibited in species-specific fashion by both RNA polymerases resides in the core enzyme. We hypothesize that differences in signal recognition are due to the changes in contacts made between the β and β′ subunits and the downstream DNA duplex.

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Connolly, Leo A. "Verba Pura Problems: Proto-Germanic Forms with j, Unexpected ē1." Journal of Germanic Linguistics 22, no. 3 (September 2010): 221–53. http://dx.doi.org/10.1017/s1470542710000012.

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The standard view that thematic verba pura contained Proto-Germanic j is examined in detail and rejected: we must reconstruct PG +sē1e/a- +rōe/a-, not +sē1je/a- +rōje/a-. The Gmc. verba pura typically have stems ending in ē1 (Go. saian, OE sāwan, ON sā, OHG sāen ‘sow’) or ō (OE rōwan, ON rōa ‘row’). While ō in these verbs seems always to reflect PIE o + a non-coloring laryngeal E, ē1 occurs in verbs with laryngeals of any color: saian <+seE-, OHG krāen ‘crow’ <+greA- (a-coloring), OE cnāwan ‘know’< +ǵneO- (o-coloring). A solution is offered according to which in Germanic, E was lost relatively early, e and o in hiatus were then lengthened to ē1ō, after which remaining o > a. Later, when A and O were lost, a in hiatus was lengthened to ā and reanalyzed as /ē1/. However, +knē1- might instead reflect a Narten present in +ǵnēO-.*

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Koulich, Dmitry, Vadim Nikiforov, and Sergei Borukhov. "Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor 1 1Edited by G. R. Smith." Journal of Molecular Biology 276, no. 2 (February 1998): 379–89. http://dx.doi.org/10.1006/jmbi.1997.1545.

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Feng, G. H., D. N. Lee, D. Wang, C. L. Chan, and R. Landick. "GreA-induced transcript cleavage in transcription complexes containing Escherichia coli RNA polymerase is controlled by multiple factors, including nascent transcript location and structure." Journal of Biological Chemistry 269, no. 35 (September 1994): 22282–94. http://dx.doi.org/10.1016/s0021-9258(17)31788-x.

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