Waksman Institute of Microbiology

Research Output

2020

Cell polarity: Regulators and mechanisms in plants

Yang, K., Wang, L., Le, J. & Dong, J., Jan 1 2020, In : Journal of Integrative Plant Biology. 62, 1, p. 132-147 16 p.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

Ciliary rab28 and the BBSome negatively regulate extracellular vesicle shedding

Akella, J. S., Carter, S. P., Nguyen, K., Tsiropoulou, S., Moran, A. L., Silva, M., Rizvi, F., Kennedy, B. N., Hall, D. H., Barr, M. M. & Blacque, O. E., Feb 2020, In : eLife. 9, e50580.

Research output: Contribution to journalArticle

Open Access

Detection of CRISPR adaptation

Shiriaeva, A., Fedorov, I., Vyhovskyi, D. & Severinov, K., Jan 1 2020, In : Biochemical Society transactions. 48, 1, p. 257-269 13 p.

Research output: Contribution to journalReview article

Open Access
1 Scopus citations

DNA targeting by Clostridium cellulolyticum CRISPR-Cas9 Type II-C system

Fedorova, I., Arseniev, A., Selkova, P., Pobegalov, G., Goryanin, I., Vasileva, A., Musharova, O., Abramova, M., Kazalov, M., Zyubko, T., Artamonova, T., Artamonova, D., Shmakov, S., Khodorkovskii, M. & Severinov, K., Feb 28 2020, In : Nucleic acids research. 48, 4, p. 2026-2034 9 p.

Research output: Contribution to journalArticle

Open Access

'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

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

VanBuren, R., Man Wai, C., Wang, X., Pardo, J., Yocca, A. E., Wang, H., Chaluvadi, S. R., Han, G., Bryant, D., Edger, P. P., Messing, J., Sorrells, M. E., Mockler, T. C., Bennetzen, J. L. & Michael, T. P., Dec 1 2020, In : Nature communications. 11, 1, 884.

Research output: Contribution to journalArticle

Open Access

Hyperbranched poly(β-amino ester) based polyplex nanopaticles for delivery of CRISPR/Cas9 system and treatment of HPV infection associated cervical cancer

Gao, X., Jin, Z., Tan, X., Zhang, C., Zou, C., Zhang, W., Ding, J., Das, B. C., Severinov, K., Hitzeroth, I. I., Debata, P. R., He, D., Ma, X., Tian, X., Gao, Q., Wu, J., Tian, R., Cui, Z., Fan, W., Huang, Z. & 4 others, Cao, C., Bao, Y., Tan, S. & Hu, Z., May 10 2020, In : Journal of Controlled Release. 321, p. 654-668 15 p.

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

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

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
6 Scopus citations

Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling

Matthes, M. S., Best, N. B., Robil, J. M., Malcomber, S., Gallavotti, A. & McSteen, P., Mar 4 2019, In : Molecular Plant. 12, 3, p. 298-320 23 p.

Research output: Contribution to journalReview article

10 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
8 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
4 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

Cell type-specific structural plasticity of the ciliary transition zone in C. elegans

Akella, J. S., Silva, M., Morsci, N. S., Nguyen, K. C., Rice, W. J., Hall, D. H. & Barr, M. M., Apr 2019, In : Biology of the Cell. 111, 4, p. 95-107 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

Chinese scientists and US leadership in the life sciences

Signatories to the Statement, Nov 1 2019, In : Nature biotechnology. 37, 11, p. 1261-1263 3 p.

Research output: Contribution to journalLetter

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
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

CRISPR–Cas molecular beacons as tool for studies of assembly of CRISPR–Cas effector complexes and their interactions with DNA

Mekler, V., Kuznedelov, K., Minakhin, L., Murugan, K., Sashital, D. G. & Severinov, K., Jan 1 2019, Methods in Enzymology. Bailey, S. (ed.). Academic Press Inc., p. 337-363 27 p. (Methods in Enzymology; vol. 616).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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

8 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

13 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

Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase

Maffioli, S. I., Sosio, M., Ebright, R. H. & Donadio, S., Mar 29 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 3-4, p. 335-343 9 p.

Research output: Contribution to journalReview article

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

Efficient: In vivo synthesis of lasso peptide pseudomycoidin proceeds in the absence of both the leader and the leader peptidase

Zyubko, T., Serebryakova, M., Andreeva, J., Metelev, M., Lippens, G., Dubiley, S. & Severinov, K., Jan 1 2019, In : Chemical Science. 10, 42, p. 9699-9707 9 p.

Research output: Contribution to journalArticle

Open Access

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

5 Scopus citations

Engineered RNA-binding protein for transgene activation in non-green plastids

Yu, Q., Barkan, A. & Maliga, P., May 1 2019, In : Nature Plants. 5, 5, p. 486-490 5 p.

Research output: Contribution to journalLetter

4 Scopus citations

Erratum: tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance (Cell Systems (2019)8(4)(302–314.e8), (S240547121930078X), (10.1016/j.cels.2019.03.008))

Masuda, I., Matsubara, R., Christian, T., Rojas, E. R., Yadavalli, S. S., Zhang, L., Goulian, M., Foster, L. J., Huang, K. C. & Hou, Y. M., May 22 2019, In : Cell Systems. 8, 5, 1 p.

Research output: Contribution to journalComment/debate

Open Access

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

2 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

5 Scopus citations

Localization of Hippo Signaling Components in Drosophila by Fluorescence and Immunofluorescence

Rauskolb, C. & Irvine, K., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 61-73 13 p. (Methods in Molecular Biology; vol. 1893).

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Mutagenesis and imaging studies of BMP signaling mechanisms in C. elegans

Savage-Dunn, C., Gleason, R. J., Liu, J. & Padgett, R. W., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 51-73 23 p. (Methods in Molecular Biology; vol. 1891).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 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

7 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

New tools for engineering the Arabidopsis PLASTID GENome

Yu, Q., LaManna, L. M., Kelly, M. E., Lutz, K. A. & Maliga, P., Jan 1 2019, In : Plant physiology. 181, 2, p. 394-398 5 p.

Research output: Contribution to journalLetter

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