Waksman Institute of Microbiology

Research Output 1972 2019

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
Replication Protein A
DNA Replication
varespladib methyl
Phosphorylation
DNA Repair
4 Citations (Scopus)

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
DNA Gyrase
Poisons
Ligases
Peptides
Topoisomerase Inhibitors
2 Citations (Scopus)

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

Indoleacetic Acids
Arabidopsis
Zea mays
auxins
biosynthesis
3 Citations (Scopus)

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
Biosynthesis
Nucleotides
Anti-Bacterial Agents
Peptides
Ubiquitin-Activating Enzymes
3 Citations (Scopus)

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

Bacteriophages
Methylation
Escherichia coli
DNA
CRISPR-Cas Systems
1 Citation (Scopus)

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

Genetic Association Studies
mutagenesis
Genome
Zea mays
mutation

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., Apr 1 2019, In : Biology of the Cell. 111, 4, p. 95-107 13 p.

Research output: Contribution to journalArticle

Cilia
Microtubules
Head
Caenorhabditis elegans
Sensory Receptor Cells
3 Citations (Scopus)

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., Jan 1 2019, In : Journal of Materials Chemistry A. 7, 5, p. 2400-2411 12 p.

Research output: Contribution to journalArticle

Photocathodes
Titanium nitride
Photocurrents
Catalysts
Water

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

Clustered Regularly Interspaced Short Palindromic Repeats
DNA
Nucleic acid sequences
RNA
Prokaryotic Cells

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., Mar 1 2019, In : Energy and Environmental Science. 12, 3, p. 1035-1045 11 p.

Research output: Contribution to journalArticle

Metabolism
Glucose
glucose
Pentoses
metabolism
6 Citations (Scopus)

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

DNA Packaging
Capsid
Viruses
DNA
Product Packaging
5 Citations (Scopus)

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

Pollen Tube
Reproductive Isolation
Arabidopsis
Cysteine
Peptides

Cytological Immunostaining of HMGA2, LRP1B, and TP63 as Potential Biomarkers for Triaging Human Papillomavirus-Positive Women

Jiang, Y., Zhu, C., He, D., Gao, Q., Tian, X., Ma, X., Wu, J., Das, B. C., Severinov, K., Hitzeroth, I. I., Debata, P. R., Liu, R., Zou, L., Shi, L., Xu, H., Wang, K., Bao, Y., Ka-Kit, L. R., You, Z., Cui, Z. & 1 others, Hu, Z., Jul 1 2019, In : Translational Oncology. 12, 7, p. 959-967 9 p.

Research output: Contribution to journalArticle

Open Access
Biomarkers
Triage
Area Under Curve
ROC Curve
Sensitivity and Specificity

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. & Francis-West, P., Jul 1 2019, In : Development (Cambridge). 146, 14, dev176776.

Research output: Contribution to journalArticle

Open Access
Osteoblasts
Craniofacial Abnormalities
Phenotype
Mutation
3 Citations (Scopus)

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

Clustered Regularly Interspaced Short Palindromic Repeats
Seeds
Guide RNA
Alicyclobacillus
Amino Acid Motifs

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
Clustered Regularly Interspaced Short Palindromic Repeats
spacers
deoxyribonucleic acid
DNA
immunity

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

Maffioli, S. I., Sosio, M., Ebright, R. & 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

Bacterial RNA
Biosynthesis
DNA-Directed RNA Polymerases
RNA
Nucleosides

Early girl is a novel component of the Fat signaling pathway

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

Research output: Contribution to journalArticle

Open Access
fat
Fats
membrane
lipids
Membranes

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

DNA Restriction-Modification Enzymes
Population dynamics
Population Dynamics
constrictions
Gene expression regulation
3 Citations (Scopus)

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

transgenes
chloroplasts
proteins
plastids
high-value products
2 Citations (Scopus)

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

RNA-binding proteins
transgenes
plastids
green fluorescent protein
tubers

Erratum: Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome (Nucleic acids research (2018))

Sutormin, D., Rubanova, N., Logacheva, M., Ghilarov, D. & Severinov, K., Feb 20 2019, In : Nucleic acids research. 47, 3, 1 p.

Research output: Contribution to journalComment/debate

Open Access
Nucleotide Mapping
DNA Gyrase
DNA Cleavage
Nucleic Acids
Genome
2 Citations (Scopus)

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., 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

cysteine
DNA-Directed RNA Polymerases
Skeleton
Cysteine
Bacteria
1 Citation (Scopus)

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., May 1 2019, In : PloS one. 14, 5, e0216628.

Research output: Contribution to journalArticle

Open Access
transforming growth factors
Marfan Syndrome
Growth Factor Receptors
Caenorhabditis elegans
Transforming Growth Factors

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

Pollen Tube
pollen tubes
Arabidopsis
receptors
Glycosylphosphatidylinositols
2 Citations (Scopus)

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

Drosophila
Fluorescent Antibody Technique
Fluorescence
Antibodies
Proteins

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

Savage-Dunn, C., Gleason, R. J., Liu, J. & Padgett, R., 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

Mutagenesis
Signal Transduction
1 Citation (Scopus)

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

Zein
Starch
Endosperm
Zea mays
Seeds
1 Citation (Scopus)

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. & Hawley, R. S., Jan 1 2019, In : PLoS genetics. 15, 1, e1007886.

Research output: Contribution to journalArticle

RING Finger Domains
Double-Stranded DNA Breaks
Drosophila melanogaster
maturation
DNA
1 Citation (Scopus)

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
Clustered Regularly Interspaced Short Palindromic Repeats
Thermus
bacteriophages
Bacteriophages
CRISPR-Cas Systems

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
Meristem
Metalloproteases
Zea mays
Indoleacetic Acids
Mitochondria

New Tools for Engineering the Arabidopsis Plastid Genome

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

Research output: Contribution to journalLetter

Open Access
Plastid Genomes
Arabidopsis
engineering
plastid genome
1 Citation (Scopus)

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
Adherens Junctions
Myosins
Cytoskeleton
Embryonic Structures
Epithelium
3 Citations (Scopus)

Oriented Cell Divisions Are Not Required for Drosophila Wing Shape

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

Research output: Contribution to journalArticle

Spindle Apparatus
Cell Division
Drosophila
cell division
Cells

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
Embryophyta
Genome
Genes
Environmental Biodegradation
Terminal Repeat Sequences
1 Citation (Scopus)

Post-transcriptional adaptation of the aquatic plant Spirodela polyrhiza under stress and hormonal stimuli

Fourounjian, P., Tang, J., Tanyolac, B., Feng, Y., Gelfand, B., Kakrana, A., Tu, M., Wakim, C., Meyers, B. C., Ma, J. & Messing, J., Jun 1 2019, In : Plant Journal. 98, 6, p. 1120-1133 14 p.

Research output: Contribution to journalReview article

Spirodela polyrhiza
aquatic plants
MicroRNAs
microRNA
Araceae
1 Citation (Scopus)

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

Zea mays
corn
transcription factors
phenotype
Transcription Factors
3 Citations (Scopus)

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
Catenins
Drosophila
Adherens Junctions
Growth
Proteins
1 Citation (Scopus)

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. & Severinov, K., Mar 1 2019, In : mBio. 10, 2, e00768-19.

Research output: Contribution to journalArticle

Open Access
Ribosomes
Anti-Bacterial Agents
Peptides
Amino Acids
Operon

Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles

Tian, R., Cui, Z., He, D., Tian, X., Gao, Q., Ma, X., Yang, J. R., Wu, J., Das, B. C., Severinov, K., Hitzeroth, I. I., Debata, P. R., Xu, W., Zhong, H., Fan, W., Chen, Y., Jin, Z., Cao, C., Yu, M., Xie, W. & 5 others, Huang, Z., Bao, Y., Xie, H., Yao, S. & Hu, Z., Oct 16 2019, In : Carcinogenesis. 40, 10, p. 1220-1228 9 p.

Research output: Contribution to journalArticle

Uterine Cervical Neoplasms
Papillomavirus Infections
Triage
Machine Learning
Biomarkers

RNA Polymerase Reaches 60: Transcription Initiation, Elongation, Termination, and Regulation in Prokaryotes

Ebright, R., Werner, F. & Zhang, X., Jan 1 2019, (Accepted/In press) In : Journal of molecular biology.

Research output: Contribution to journalEditorial

DNA-Directed RNA Polymerases
3 Citations (Scopus)

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 1 2019, In : Nucleic acids research. 47, 3

Research output: Contribution to journalArticle

Open Access
Nucleotide Mapping
DNA Gyrase
DNA Cleavage
Genome
Escherichia coli
1 Citation (Scopus)

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
Centromere
Meiosis
centromeres
Microtubules
meiosis
2 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

Open Access
DNA-Directed RNA Polymerases
Transcription
Transcription Factors
Mycobacterium tuberculosis
DNA
2 Citations (Scopus)

Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway

Sumida, T., Dubiley, S., Wilcox, B., Severinov, K. & Tagami, S., Jun 12 2019, In : ACS chemical biology. 14, 7, p. 1619-1627 9 p.

Research output: Contribution to journalArticle

Peptide Biosynthesis
Biosynthesis
Protein Sorting Signals
Peptides
Proteins

Structural basis of Q-dependent antitermination

Yin, Z., Kaelber, J. T. & Ebright, R., 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
DNA-Directed RNA Polymerases
Bacteriophages
RNA
Sigma Factor
Gene Expression

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition

Travin, D. Y., Watson, Z. L., Metelev, M., Ward, F. R., Osterman, I. A., Khven, I. M., Khabibullina, N. F., Serebryakova, M., Mergaert, P., Polikanov, Y. S., Cate, J. H. D. & Severinov, K., Dec 1 2019, In : Nature communications. 10, 1, 4563.

Research output: Contribution to journalArticle

Open Access
azoles
ribosomes
Azoles
Ribosomes
peptides
11 Citations (Scopus)

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

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Parturition
1 Citation (Scopus)

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 1 2019, In : Molecular microbiology. 111, 6, p. 1558-1570 13 p.

Research output: Contribution to journalArticle

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Cas Systems
Escherichia coli
RNA