Waksman Institute of Microbiology

Research Output 1972 2019

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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
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

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

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)

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
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
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)

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
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., May 1 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
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

Systematic prediction of functionally linked genes in bacterial and archaeal genomes

Shmakov, S. A., Faure, G., Makarova, K. S., Wolf, Y. I., Severinov, K. V. & Koonin, E. V., Oct 1 2019, In : Nature Protocols. 14, 10, p. 3013-3031 19 p.

Research output: Contribution to journalArticle

Archaeal Genome
Bacterial Genomes
Genes
Operon
Network protocols

The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates

Ananyev, G., Roy-Chowdhury, S., Gates, C., Fromme, P. & Dismukes, G., Feb 1 2019, In : ACS Catalysis. 9, 2, p. 1396-1407 12 p.

Research output: Contribution to journalArticle

Photosystem II Protein Complex
Oxidation
Crystals
Electrons
Water

Transcriptome and metabolome reveal distinct carbon allocation patterns during internode sugar accumulation in different sorghum genotypes

Li, Y., Wang, W., Feng, Y., Tu, M., Wittich, P. E., Bate, N. J. & Messing, J., Feb 1 2019, In : Plant biotechnology journal. 17, 2, p. 472-487 16 p.

Research output: Contribution to journalArticle

metabolome
Sorghum
Metabolome
Transcriptome
transcriptome

Using an endogenous CRISPR-Cas system for genome editing in the human pathogen Clostridium difficile

Maikova, A., Kreis, V., Boutserin, A., Severinov, K. & Soutourina, O., Jan 1 2019, In : Applied and environmental microbiology. 85, 20, e01416-19.

Research output: Contribution to journalArticle

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium difficile
genome
pathogen
1 Citation (Scopus)

‘Birth defects’ of photosystem II make it highly susceptible to photodamage during chloroplast biogenesis

Shevela, D., Ananyev, G., Vatland, A. K., Arnold, J., Mamedov, F., Eichacker, L. A., Dismukes, G. & Messinger, J., May 1 2019, In : Physiologia Plantarum. 166, 1, p. 165-180 16 p.

Research output: Contribution to journalArticle

Photosystem II Protein Complex
Chloroplasts
photosystem II
chloroplasts
Thylakoids
2018
4 Citations (Scopus)

Analysis of the Pseudouridimycin Biosynthetic Pathway Provides Insights into the Formation of C-nucleoside Antibiotics

Sosio, M., Gaspari, E., Iorio, M., Pessina, S., Medema, M. H., Bernasconi, A., Simone, M., Maffioli, S. I., Ebright, R. & Donadio, S., May 17 2018, In : Cell Chemical Biology. 25, 5, p. 540-549.e4

Research output: Contribution to journalArticle

Biosynthetic Pathways
Nucleosides
Genes
Anti-Bacterial Agents
Multigene Family
1 Citation (Scopus)

A new high-throughput assay for determining soluble sugar in sorghum internode-extracted juice

Li, Y., Mehta, R. & Messing, J., Oct 1 2018, In : Planta. 248, 4, p. 785-793 9 p.

Research output: Contribution to journalArticle

Sorghum
internodes
juices
sugars
assays
2 Citations (Scopus)

A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation

Ooi, W. Y., Murayama, Y., Mekler, V., Minakhin, L., Severinov, K., Yokoyama, S. & Sekine, S. I., Jan 1 2018, In : Nucleic acids research. 46, 1, p. 431-441 11 p.

Research output: Contribution to journalArticle

Thermus
DNA-Directed RNA Polymerases
Bacteriophages
Thermus thermophilus
DNA
3 Citations (Scopus)

Avoidance of trinucleotide corresponding to consensus protospacer adjacent motif controls the efficiency of prespacer selection during primed adaptation

Musharova, O., Vyhovskyi, D., Medvedeva, S., Guzina, J., Zhitnyuk, Y., Djordjevic, M., Severinov, K. & Savitskaya, E., Nov 1 2018, In : mBio. 9, 6, e02169-18.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
DNA
CRISPR-Cas Systems
Escherichia coli
Consensus Sequence

bantam microRNA is a negative regulator of the Drosophila decapentaplegic pathway

Kane, N. S., Vora, M., Padgett, R. & Li, Y., Apr 3 2018, In : Fly. 12, 2, p. 105-117 13 p.

Research output: Contribution to journalArticle

Bantam
microRNA
Drosophila
imaginal discs
bone morphogenetic proteins
6 Citations (Scopus)

Biosynthesis of Translation Inhibitor Klebsazolicin Proceeds through Heterocyclization and N-Terminal Amidine Formation Catalyzed by a Single YcaO Enzyme

Travin, D. Y., Metelev, M., Serebryakova, M., Komarova, E. S., Osterman, I. A., Ghilarov, D. & Severinov, K., Apr 25 2018, In : Journal of the American Chemical Society. 140, 16, p. 5625-5633 9 p.

Research output: Contribution to journalArticle

Amidines
Biosynthesis
Peptides
Azoles
Enzymes
3 Citations (Scopus)

Caenorhabditis elegans sperm membrane protein interactome

Marcello, M. R., Druzhinina, M. & Singson, A., Jan 1 2018, In : Biology of reproduction. 98, 6, p. 776-783 8 p.

Research output: Contribution to journalArticle

Caenorhabditis elegans
Spermatozoa
Membrane Proteins
Spermatogenesis
Fertilization