Waksman Institute of Microbiology

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2020

'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses

Boon, M., De Zitter, E., De Smet, J., Wagemans, J., Voet, M., Pennemann, F. L., Schalck, T., Kuznedelov, K., Severinov, K., Van Meervelt, L., De Maeyer, M. & Lavigne, R., Jan 10 2020, In : Nucleic acids research. 48, 1, p. 445-459 15 p.

Research output: Contribution to journalArticle

Open Access

Highly efficient and durable III-V semiconductor-catalyst photocathodes: Via a transparent protection layer

Hwang, S., Young, J. L., Mow, R., Laursen, A. B., Li, M., Yang, H., Batson, P. E., Greenblatt, M., Steiner, M. A., Friedman, D., Deutsch, T. G., Garfunkel, E. & Dismukes, G. C., Mar 2020, In : Sustainable Energy and Fuels. 4, 3, p. 1437-1442 6 p.

Research output: Contribution to journalArticle

In vitro and in vivo growth inhibition of human cervical cancer cells via human papillomavirus E6/E7 mRNAs’ cleavage by CRISPR/Cas13a system

Chen, Y., Jiang, H., Wang, T., He, D., Tian, R., Cui, Z., Tian, X., Gao, Q., Ma, X., Yang, J., Wu, J., Tan, S., Xu, H., Tang, X., Wang, Y., Yu, Z., Han, H., Das, B. C., Severinov, K., Hitzeroth, I. I. & 10 others, Debata, P. R., Xu, W., Fan, W., Jin, Z., Cao, C., Yu, M., Xie, W., Huang, Z., Hu, Z. & You, Z., Jun 2020, In : Antiviral Research. 178, 104794.

Research output: Contribution to journalArticle

Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize

Li, C., Xiang, X., Huang, Y., Zhou, Y., An, D., Dong, J., Zhao, C., Liu, H., Li, Y., Wang, Q., Du, C., Messing, J., Larkins, B. A., Wu, Y. & Wang, W., Dec 1 2020, In : Nature communications. 11, 1, 17.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence

Isaev, A., Drobiazko, A., Sierro, N., Gordeeva, J., Yosef, I., Qimron, U., Ivanov, N. V. & Severinov, K., Jun 4 2020, In : Nucleic acids research. 48, 10, p. 5397-5406 10 p.

Research output: Contribution to journalArticle

Open Access

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Li, L., Molodtsov, V., Lin, W., Ebright, R. H. & Zhang, Y., Mar 17 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 11, p. 5801-5809 9 p.

Research output: Contribution to journalArticle

SLC17a6/7/8 vesicular glutamate transporter homologs in nematodes

Serrano-Saiz, E., Vogt, M. C., Levy, S., Wang, Y., Kaczmarczyk, K. K., Mei, X., Bai, G., Singson, A., Grant, B. D. & Hobert, O., Jan 1 2020, In : Genetics. 214, 1, p. 163-178 16 p.

Research output: Contribution to journalArticle

Symbiosis extended: exchange of photosynthetic O2 and fungal-respired CO2 mutually power metabolism of lichen symbionts

ten Veldhuis, M. C., Ananyev, G. & Dismukes, G. C., Mar 1 2020, In : Photosynthesis research. 143, 3, p. 287-299 13 p.

Research output: Contribution to journalArticle

Open Access

The MAPK substrate MASS proteins regulate stomatal development in Arabidopsis

Xue, X., Bian, C., Guo, X., Di, R. & Dong, J., Apr 2020, In : PLoS genetics. 16, 4, e1008706.

Research output: Contribution to journalArticle

Open Access

Towards coeliac-safe bread

Zhang, Z., Deng, Y., Zhang, W., Wu, Y. & Messing, J., Apr 1 2020, In : Plant biotechnology journal. 18, 4, p. 1056-1065 10 p.

Research output: Contribution to journalArticle

Open Access

Water and vapor transport in algal-fungal lichen: Modeling constrained by laboratory experiments, an application for Flavoparmelia caperata

Potkay, A., ten Veldhuis, M. C., Fan, Y., Mattos, C. R. C., Ananyev, G. & Dismukes, G. C., Apr 1 2020, In : Plant Cell and Environment. 43, 4, p. 945-964 20 p.

Research output: Contribution to journalArticle

2019

A conserved but plant-specific CDK-mediated regulation of DNA replication protein A2 in the precise control of stomatal terminal division

Yang, K., Zhu, L., Wang, H., Jiang, M., Xiao, C., Hu, X., Vanneste, S., Dong, J. & Le, J., Sep 3 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 36, p. 18126-18131 6 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison

Ghilarov, D., Stevenson, C. E. M., Travin, D. Y., Piskunova, J., Serebryakova, M., Maxwell, A., Lawson, D. M. & Severinov, K., Feb 21 2019, In : Molecular cell. 73, 4, p. 749-762.e5

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Bioactive cell-like hybrids from dendrimersomes with a human cell membrane and its components

Yadavalli, S. S., Xiao, Q., Sherman, S. E., Hasley, W. D., Klein, M. L., Goulian, M. & Percec, V., Jan 15 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 3, p. 744-752 9 p.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor

Dong, S. H., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K. & Nair, S. K., Jan 1 2019, In : Chemical Science. 10, 8, p. 2391-2395 5 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site

Gordeeva, J., Morozova, N., Sierro, N., Isaev, A., Sinkunas, T., Tsvetkova, K., Matlashov, M., Truncaite, L., Morgan, R. D., Ivanov, N. V., Siksnys, V., Zeng, L. & Severinov, K., Jan 10 2019, In : Nucleic acids research. 47, 1, p. 253-265 13 p.

Research output: Contribution to journalArticle

5 Scopus citations

Candidate gene identification of existing or induced mutations with pipelines applicable to large genomes

Dong, J., Tu, M., Feng, Y., Zdepski, A., Ge, F., Kumar, D., Slovin, J. P. & Messing, J., Feb 1 2019, In : Plant Journal. 97, 4, p. 673-682 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

Common metabolic networks contribute to carbon sink strength of sorghum internodes: Implications for bioenergy improvement

Li, Y., Tu, M., Feng, Y., Wang, W. & Messing, J., Nov 20 2019, In : Biotechnology for Biofuels. 12, 1, 274.

Research output: Contribution to journalArticle

Open Access

Creating stable interfaces between reactive materials: titanium nitride protects photoabsorber-catalyst interface in water-splitting photocathodes

Hwang, S., Porter, S. H., Laursen, A. B., Yang, H., Li, M., Manichev, V., Calvinho, K. U. D., Amarasinghe, V., Greenblatt, M., Garfunkel, E. & Dismukes, G. C., Jan 1 2019, In : Journal of Materials Chemistry A. 7, 5, p. 2400-2411 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

Crossing the Thauer limit: Rewiring cyanobacterial metabolism to maximize fermentative H2 production

Kumaraswamy, K. G., Krishnan, A., Ananyev, G., Zhang, S., Bryant, D. A. & Dismukes, G. C., Mar 2019, In : Energy and Environmental Science. 12, 3, p. 1035-1045 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

Bayfield, O. W., Klimuk, E., Winkler, D. C., Hesketh, E. L., Chechik, M., Cheng, N., Dykeman, E. C., Minakhin, L., Ranson, N. A., Severinov, K., Steven, A. C. & Antson, A. A., Feb 26 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 9, p. 3556-3561 6 p.

Research output: Contribution to journalArticle

11 Scopus citations

Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis

Zhong, S., Liu, M., Wang, Z., Huang, Q., Hou, S., Xu, Y. C., Ge, Z., Song, Z., Huang, J., Qiu, X., Shi, Y., Xiao, J., Liu, P., Guo, Y. L., Dong, J., Dresselhaus, T., Gu, H. & Qu, L. J., Jan 1 2019, In : Science. 364, 6443, eaau9564.

Research output: Contribution to journalArticle

16 Scopus citations

Dchs1-fat4 regulation of osteogenic differentiation in mouse

Crespo-Enriquez, I., Hodgson, T., Zakaria, S., Cadoni, E., Shah, M., Allen, S., Al-Khishali, A., Mao, Y., Yiu, A., Petzold, J., Villagomez-Olea, G., Pitsillides, A. A., Irvine, K. D. & Francis-West, P., Jul 2019, In : Development (Cambridge). 146, 14, dev176776.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Defining the seed sequence of the Cas12b CRISPR-Cas effector complex

Jain, I., Minakhin, L., Mekler, V., Sitnik, V., Rubanova, N., Severinov, K. & Semenova, E., Apr 3 2019, In : RNA Biology. 16, 4, p. 413-422 10 p.

Research output: Contribution to journalArticle

5 Scopus citations

Detection of spacer precursors formed in vivo during primed CRISPR adaptation

Shiriaeva, A. A., Savitskaya, E., Datsenko, K. A., Vvedenskaya, I. O., Fedorova, I., Morozova, N., Metlitskaya, A., Sabantsev, A., Nickels, B. E., Severinov, K. & Semenova, E., Dec 1 2019, In : Nature communications. 10, 1, 4603.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Early girl is a novel component of the Fat signaling pathway

Misra, J. R. & Irvine, K. D., Jan 1 2019, In : PLoS genetics. 15, 1, e1007955.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Effects of population dynamics on establishment of a restriction-modification system in a bacterial host

Graovac, S., Rodic, A., Djordjevic, M., Severinov, K. & Djordjevic, M., Jan 7 2019, In : Molecules. 24, 1, 198.

Research output: Contribution to journalArticle

Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes

Rojas, M., Yu, Q., Williams-Carrier, R., Maliga, P. & Barkan, A., May 1 2019, In : Nature Plants. 5, 5, p. 505-511 7 p.

Research output: Contribution to journalArticle

8 Scopus citations

Functionalised bicyclic tetramates derived from cysteine as antibacterial agents

Panduwawala, T. D., Iqbal, S., Thompson, A. L., Genov, M., Pretsch, A., Pretsch, D., Liu, S., Ebright, R. H., Howells, A., Maxwell, A. & Moloney, M. G., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 22, p. 5615-5632 18 p.

Research output: Contribution to journalArticle

4 Scopus citations

Genetic interactions between the DBL-1/BMP-like pathway and dpy body size–associated genes in Caenorhabditis elegans

Lakdawala, M. F., Madhu, B., Faure, L., Vora, M., Padgett, R. W. & Gumienny, T. L., Jan 1 2019, In : Molecular biology of the cell. 30, 26, p. 3151-3160 10 p.

Research output: Contribution to journalArticle

Human marfan and marfan-like syndrome associated mutations lead to altered trafficking of the type II TGFβ receptor in Caenorhabditis elegans

Lin, J., Vora, M., Kane, N. S., Gleason, R. J. & Padgett, R. W., May 2019, In : PloS one. 14, 5, e0216628.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

LLG2/3 Are Co-receptors in BUPS/ANX-RALF Signaling to Regulate Arabidopsis Pollen Tube Integrity

Ge, Z., Zhao, Y., Liu, M. C., Zhou, L. Z., Wang, L., Zhong, S., Hou, S., Jiang, J., Liu, T., Huang, Q., Xiao, J., Gu, H., Wu, H. M., Dong, J., Dresselhaus, T., Cheung, A. Y. & Qu, L. J., Oct 7 2019, In : Current Biology. 29, 19, p. 3256-3265.e5

Research output: Contribution to journalArticle

8 Scopus citations

NAC-type transcription factors regulate accumulation of starch and protein in maize seeds

Zhang, Z., Dong, J., Ji, C., Wu, Y. & Messing, J., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 166, 23, p. 11223-11228 6 p.

Research output: Contribution to journalArticle

9 Scopus citations

Narya, a RING finger domain-containing protein, is required for meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster

Lake, C. M., Nielsen, R. J., Bonner, A. M., Eche, S., White-Brown, S., McKim, K. S. & Hawley, R. S., Jan 1 2019, In : PLoS genetics. 15, 1, e1007886.

Research output: Contribution to journalArticle

2 Scopus citations

Natural diversity of CRISPR spacers of Thermus: Evidence of local spacer acquisition and global spacer exchange

Lopatina, A., Medvedeva, S., Artamonova, D., Kolesnik, M., Sitnik, V., Ispolatov, Y. & Severinov, K., May 13 2019, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 374, 1772, 20180092.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

NEEDLE1 encodes a mitochondria localized ATP-dependent metalloprotease required for thermotolerant maize growth

Liu, Q., Galli, M., Liu, X., Federici, S., Buck, A., Cody, J., Labra, M. & Gallavotti, A., Sep 24 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 39, p. 19736-19742 7 p.

Research output: Contribution to journalArticle

Open Access

Organization and function of tension-dependent complexes at adherens junctions

Rauskolb, C., Cervantes, E., Madere, F. & Irvine, K. D., Apr 1 2019, In : Journal of cell science. 132, 7, jcs224063.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Oriented Cell Divisions Are Not Required for Drosophila Wing Shape

Zhou, Z., Alégot, H. & Irvine, K. D., Mar 4 2019, In : Current Biology. 29, 5, p. 856-864.e3

Research output: Contribution to journalArticle

6 Scopus citations

Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela

An, D., Zhou, Y., Li, C., Xiao, Q., Wang, T., Zhang, Y., Wu, Y., Li, Y., Chao, D. Y., Messing, J. & Wang, W., Sep 17 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 38, p. 18893-18899 7 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

RAMOSA1 ENHANCER LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture 1[open]

Liu, X., Galli, M., Camehl, I. & Gallavotti, A., Jan 1 2019, In : Plant physiology. 179, 1, p. 348-363 16 p.

Research output: Contribution to journalArticle

3 Scopus citations

Recruitment of Jub by α-catenin promotes Yki activity and Drosophila wing growth

Alégot, H., Markosian, C., Rauskolb, C., Yang, J., Kirichenko, E., Wang, Y. C. & Irvine, K. D., Mar 1 2019, In : Journal of cell science. 132, 5, jcs222018.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Reiterative synthesis by the ribosome and recognition of the N-terminal formyl group by biosynthetic machinery contribute to evolutionary conservation of the length of antibiotic microcin c peptide precursor

Zukher, I., Pavlov, M., Tsibulskaya, D., Kulikovsky, A., Zyubko, T., Bikmetov, D., Serebryakova, M., Nair, S. K., Ehrenberg, M., Dubiley, S. & Severinova, K., Mar 1 2019, In : mBio. 10, 2, e00768-19.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome

Sutormin, D., Rubanova, N., Logacheva, M., Ghilarov, D. & Severinov, K., Feb 2019, In : Nucleic acids research. 47, 3

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Sister centromere fusion during meiosis I depends on maintaining cohesins and destabilizing microtubule attachments

Wang, L. I., Das, A. & McKim, K. S., May 2019, In : PLoS genetics. 15, 5, e1008072.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Structural basis of ECF-σ-factor-dependent transcription initiation

Lin, W., Mandal, S., Degen, D., Cho, M. S., Feng, Y., Das, K. & Ebright, R. H., Dec 1 2019, In : Nature communications. 10, 1, 710.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Structural basis of Q-dependent antitermination

Yin, Z., Kaelber, J. T. & Ebright, R. H., Sep 10 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 37, p. 18384-18390 7 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference

You, L., Ma, J., Wang, J., Artamonova, D., Wang, M., Liu, L., Xiang, H., Severinov, K., Zhang, X. & Wang, Y., Jan 10 2019, In : Cell. 176, 1-2, p. 239-253.e16

Research output: Contribution to journalArticle

15 Scopus citations

Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation

Musharova, O., Sitnik, V., Vlot, M., Savitskaya, E., Datsenko, K. A., Krivoy, A., Fedorov, I., Semenova, E., Brouns, S. J. J. & Severinov, K., Jun 2019, In : Molecular microbiology. 111, 6, p. 1558-1570 13 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Targeting bone morphogenetic protein receptor 2 sensitizes lung cancer cells to TRAIL by increasing cytosolic Smac/DIABLO and the downregulation of X-linked inhibitor of apoptosis protein

Nemoyer, R., Mondal, A., Vora, M., Langenfeld, E., Glover, D., Scott, M., Lairson, L., Rongo, C., Augeri, D. J., Peng, Y., Jabbour, S. K. & Langenfeld, J., Nov 19 2019, In : Cell Communication and Signaling. 17, 1, 150.

Research output: Contribution to journalArticle

Open Access