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Lyle A. Simmons, Ph.D. - Publications

Affiliations: 
2003 Michigan State University, East Lansing, MI 
Area:
Biochemistry, Molecular Biology, Genetics
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68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Reed TT, Kendal AH, Wozniak KJ, Simmons LA. DNA replication initiation timing is important for maintaining genome integrity. Biorxiv : the Preprint Server For Biology. PMID 38948856 DOI: 10.1101/2024.06.18.599555  0.463
2024 Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Research. PMID 38661211 DOI: 10.1093/nar/gkae308  0.396
2024 Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Biorxiv : the Preprint Server For Biology. PMID 38405983 DOI: 10.1101/2024.02.15.580553  0.394
2023 Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide. Science Advances. 9: eadi5945. PMID 37494439 DOI: 10.1126/sciadv.adi5945  0.328
2023 Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide. Biorxiv : the Preprint Server For Biology. PMID 37214986 DOI: 10.1101/2023.05.08.539860  0.346
2023 Lowder FC, Simmons LA. Bacillus subtilis encodes a discrete flap endonuclease that cleaves RNA-DNA hybrids. Plos Genetics. 19: e1010585. PMID 37146086 DOI: 10.1371/journal.pgen.1010585  0.389
2023 Blaine HC, Simmons LA, Stallings CL. Diverse Mechanisms of Helicase Loading during DNA Replication Initiation in Bacteria. Journal of Bacteriology. e0048722. PMID 36877032 DOI: 10.1128/jb.00487-22  0.446
2023 Fernandez NL, Chen Z, Fuller DEH, van Gijtenbeek LA, Nye TM, Biteen JS, Simmons LA. DNA Methylation and RNA-DNA Hybrids Regulate the Single-Molecule Localization of a DNA Methyltransferase on the Bacterial Nucleoid. Mbio. e0318522. PMID 36645292 DOI: 10.1128/mbio.03185-22  0.415
2022 McLean EK, Nye TM, Lowder FC, Simmons LA. The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria. Annual Review of Microbiology. PMID 35655343 DOI: 10.1146/annurev-micro-102521-014450  0.318
2022 Wozniak KJ, Burby PE, Nandakumar J, Simmons LA. Structure and kinase activity of bacterial cell cycle regulator CcrZ. Plos Genetics. 18: e1010196. PMID 35576203 DOI: 10.1371/journal.pgen.1010196  0.396
2022 Wozniak KJ, Simmons LA. Bacterial DNA excision repair pathways. Nature Reviews. Microbiology. PMID 35210609 DOI: 10.1038/s41579-022-00694-0  0.356
2022 Matthews LA, Simmons LA. The Bacillus subtilis PriA Winged Helix Domain Is Critical for Surviving DNA Damage. Journal of Bacteriology. 204: e0053921. PMID 35007156 DOI: 10.1128/JB.00539-21  0.456
2021 Amemiya HM, Goss TJ, Nye TM, Hurto RL, Simmons LA, Freddolino PL. Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria. The Embo Journal. e108708. PMID 34961960 DOI: 10.15252/embj.2021108708  0.324
2021 McLean EK, Lenhart JS, Simmons LA. RecA is required for the assembly of RecN into DNA repair complexes on the nucleoid. Journal of Bacteriology. JB0024021. PMID 34339298 DOI: 10.1128/JB.00240-21  0.453
2021 Masser EA, Burby PE, Hawkins WD, Gustafson BR, Lenhart JS, Simmons LA. DNA damage checkpoint activation affects peptidoglycan synthesis and late divisome components in Bacillus subtilis. Molecular Microbiology. PMID 34097787 DOI: 10.1111/mmi.14765  0.436
2021 Wozniak KJ, Simmons LA. Hydroxyurea induces a stress response that alters DNA replication and nucleotide metabolism in . Journal of Bacteriology. PMID 34031038 DOI: 10.1128/JB.00171-21  0.346
2020 Nye TM, Fernandez NL, Simmons LA. A positive perspective on DNA methylation: regulatory functions of DNA methylation outside of host defense in Gram-positive bacteria. Critical Reviews in Biochemistry and Molecular Biology. 1-16. PMID 33059472 DOI: 10.1080/10409238.2020.1828257  0.348
2020 Nye TM, McLean EK, Burrage AM, Dennison DD, Kearns DB, Simmons LA. RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610. Molecular Microbiology. PMID 32896031 DOI: 10.1111/Mmi.14601  0.402
2020 Matthews LA, Simmons LA. Regulation of DNA Binding and High Order Oligomerization of the DnaB Helicase Loader. Journal of Bacteriology. PMID 32817095 DOI: 10.1128/JB.00286-20  0.462
2019 Burby PE, Simmons LA. Regulation of cell division in bacteria by monitoring genome integrity and DNA replication status. Journal of Bacteriology. PMID 31548275 DOI: 10.1128/JB.00408-19  0.411
2019 Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A. Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic Acids Research. PMID 30916336 DOI: 10.1093/nar/gkz115  0.553
2019 Li Y, Chen Z, Matthews LA, Simmons LA, Biteen JS. Dynamic Exchange of Two Essential DNA Polymerases during Replication and after Fork Arrest. Biophysical Journal. PMID 30686488 DOI: 10.1016/J.Bpj.2019.01.008  0.465
2019 Randall JR, Nye TM, Wozniak KJ, Simmons LA. RNase HIII is important for Okazaki fragment processing in . Journal of Bacteriology. PMID 30670546 DOI: 10.1128/JB.00686-18  0.348
2018 Burby PE, Simmons LA. A bacterial DNA repair pathway specific to a natural antibiotic. Molecular Microbiology. PMID 30379365 DOI: 10.1111/mmi.14158  0.397
2018 Burby PE, Simmons ZW, Simmons LA. DdcA antagonizes a bacterial DNA damage checkpoint. Molecular Microbiology. PMID 30315724 DOI: 10.1111/mmi.14151  0.431
2018 Matthews LA, Simmons LA. Cryptic protein interactions regulate DNA replication initiation. Molecular Microbiology. PMID 30285297 DOI: 10.1111/mmi.14142  0.447
2018 Burby PE, Simmons ZW, Schroeder JW, Simmons LA. Discovery of a dual protease mechanism that promotes DNA damage checkpoint recovery. Plos Genetics. 14: e1007512. PMID 29979679 DOI: 10.1371/journal.pgen.1007512  0.416
2017 Li Y, Schroeder JW, Simmons LA, Biteen JS. Visualizing bacterial DNA replication and repair with molecular resolution. Current Opinion in Microbiology. 43: 38-45. PMID 29197672 DOI: 10.1016/J.Mib.2017.11.009  0.389
2017 Schroeder JW, Randall JR, Hirst WG, O'Donnell ME, Simmons LA. Mutagenic cost of ribonucleotides in bacterial DNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078353 DOI: 10.1073/pnas.1710995114  0.41
2016 Liao Y, Li Y, Schroeder JW, Simmons LA, Biteen JS. Single-Molecule DNA Polymerase Dynamics at a Bacterial Replisome in Live Cells. Biophysical Journal. 111: 2562-2569. PMID 28002733 DOI: 10.1016/J.Bpj.2016.11.006  0.365
2016 Burby PE, Simmons LA. MutS2 promotes homologous recombination in Bacillus subtilis. Journal of Bacteriology. PMID 27799325 DOI: 10.1128/JB.00682-16  0.433
2016 Lenhart JS, Pillon MC, Guarné A, Biteen JS, Simmons LA. Mismatch repair in Gram-positive bacteria. Research in Microbiology. 167: 4-12. PMID 26343983 DOI: 10.1016/J.Resmic.2015.08.006  0.466
2016 Li Y, Schroeder JW, Liao Y, Simmons LA, Biteen JS. Super-Resolution Imaging of DNA Replisome Dynamics in Live Bacillus Subtilis Biophysical Journal. 110: 646a-647a. DOI: 10.1016/J.Bpj.2015.11.3461  0.345
2015 Pillon MC, Babu VM, Randall JR, Cai J, Simmons LA, Sutton MD, Guarné A. The sliding clamp tethers the endonuclease domain of MutL to DNA. Nucleic Acids Research. PMID 26384423 DOI: 10.1093/Nar/Gkv918  0.618
2014 Schroeder JW, Randall JR, Matthews LA, Simmons LA. Ribonucleotides in bacterial DNA. Critical Reviews in Biochemistry and Molecular Biology. 1-13. PMID 25387798 DOI: 10.3109/10409238.2014.981647  0.36
2014 Matthews LA, Simmons LA. Bacterial nonhomologous end joining requires teamwork. Journal of Bacteriology. 196: 3363-5. PMID 25049091 DOI: 10.1128/JB.02042-14  0.363
2014 Lenhart JS, Brandes ER, Schroeder JW, Sorenson RJ, Showalter HD, Simmons LA. RecO and RecR are necessary for RecA loading in response to DNA damage and replication fork stress. Journal of Bacteriology. 196: 2851-60. PMID 24891441 DOI: 10.1128/Jb.01494-14  0.443
2014 Walsh BW, Bolz SA, Wessel SR, Schroeder JW, Keck JL, Simmons LA. RecD2 helicase limits replication fork stress in Bacillus subtilis. Journal of Bacteriology. 196: 1359-68. PMID 24443534 DOI: 10.1128/Jb.01475-13  0.498
2014 Liao Y, Schroeder JW, Simmons LA, Biteen JS. Single-Molecule Fluorescence Imaging Reveals Mismatch Repair Dynamics in Live Bacillus Subtilis Biophysical Journal. 106: 435a. DOI: 10.1016/J.Bpj.2013.11.2450  0.404
2014 Tuson HH, Liao Y, Simmons LA, Biteen JS. Single-Molecule Fluorescence Imaging of Reco Localization and Dynamics in Bacillus Subtilis Biophysical Journal. 106: 397a. DOI: 10.1016/J.Bpj.2013.11.2243  0.442
2013 Lenhart JS, Pillon MC, Guarné A, Simmons LA. Trapping and visualizing intermediate steps in the mismatch repair pathway in vivo. Molecular Microbiology. 90: 680-98. PMID 23998896 DOI: 10.1111/mmi.12389  0.482
2013 Chodavarapu S, Felczak MM, Simmons LA, Murillo A, Kaguni JM. Mutant DnaAs of Escherichia coli that are refractory to negative control. Nucleic Acids Research. 41: 10254-67. PMID 23990329 DOI: 10.1093/Nar/Gkt774  0.665
2013 Yao NY, Schroeder JW, Yurieva O, Simmons LA, O'Donnell ME. Cost of rNTP/dNTP pool imbalance at the replication fork. Proceedings of the National Academy of Sciences of the United States of America. 110: 12942-7. PMID 23882084 DOI: 10.1073/pnas.1309506110  0.453
2013 Marceau AH, Bernstein DA, Walsh BW, Shapiro W, Simmons LA, Keck JL. Protein interactions in genome maintenance as novel antibacterial targets. Plos One. 8: e58765. PMID 23536821 DOI: 10.1371/Journal.Pone.0058765  0.347
2013 Lenhart JS, Sharma A, Hingorani MM, Simmons LA. DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication. Molecular Microbiology. 87: 553-68. PMID 23228104 DOI: 10.1111/Mmi.12115  0.387
2013 Liao Y, Schroeder J, Simmons L, Biteen J. In Vivo Visualization of Mismatch Repair in Bacillus Subtilis using Single-Molecule Fluorescence Microscopy Biophysical Journal. 104: 77a. DOI: 10.1016/J.Bpj.2012.11.465  0.415
2012 Walsh BW, Lenhart JS, Schroeder JW, Simmons LA. Far Western blotting as a rapid and efficient method for detecting interactions between DNA replication and DNA repair proteins. Methods in Molecular Biology (Clifton, N.J.). 922: 161-8. PMID 22976184 DOI: 10.1007/978-1-62703-032-8_11  0.348
2012 Lenhart JS, Schroeder JW, Walsh BW, Simmons LA. DNA repair and genome maintenance in Bacillus subtilis. Microbiology and Molecular Biology Reviews : Mmbr. 76: 530-64. PMID 22933559 DOI: 10.1128/MMBR.05020-11  0.396
2012 Bolz NJ, Lenhart JS, Weindorf SC, Simmons LA. Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis. Journal of Bacteriology. 194: 5361-7. PMID 22843852 DOI: 10.1128/JB.01142-12  0.461
2012 Cooper LA, Simmons LA, Mobley HL. Involvement of mismatch repair in the reciprocal control of motility and adherence of uropathogenic Escherichia coli. Infection and Immunity. 80: 1969-79. PMID 22473602 DOI: 10.1128/Iai.00043-12  0.315
2011 Klocko AD, Schroeder JW, Walsh BW, Lenhart JS, Evans ML, Simmons LA. Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Molecular Microbiology. 82: 648-63. PMID 21958350 DOI: 10.1111/J.1365-2958.2011.07841.X  0.467
2011 Kasili R, Huang CC, Walker JD, Simmons LA, Zhou J, Faulk C, Hülskamp M, Larkin JC. BRANCHLESS TRICHOMES links cell shape and cell cycle control in Arabidopsis trichomes. Development (Cambridge, England). 138: 2379-88. PMID 21558384 DOI: 10.1242/Dev.058982  0.418
2011 Davies BW, Bogard RW, Dupes NM, Gerstenfeld TA, Simmons LA, Mekalanos JJ. DNA damage and reactive nitrogen species are barriers to Vibrio cholerae colonization of the infant mouse intestine. Plos Pathogens. 7: e1001295. PMID 21379340 DOI: 10.1371/Journal.Ppat.1001295  0.315
2010 Davies BW, Köhrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Molecular Microbiology. 78: 506-18. PMID 20807199 DOI: 10.1111/J.1365-2958.2010.07351.X  0.331
2010 Pillon MC, Lorenowicz JJ, Uckelmann M, Klocko AD, Mitchell RR, Chung YS, Modrich P, Walker GC, Simmons LA, Friedhoff P, Guarné A. Structure of the endonuclease domain of MutL: unlicensed to cut. Molecular Cell. 39: 145-51. PMID 20603082 DOI: 10.1016/J.Molcel.2010.06.027  0.412
2010 Dupes NM, Walsh BW, Klocko AD, Lenhart JS, Peterson HL, Gessert DA, Pavlick CE, Simmons LA. Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. Journal of Bacteriology. 192: 3452-63. PMID 20453097 DOI: 10.1128/JB.01435-09  0.364
2010 Kasili R, Walker JD, Simmons LA, Zhou J, De Veylder L, Larkin JC. SIAMESE cooperates with the CDH1-like protein CCS52A1 to establish endoreplication in Arabidopsis thaliana trichomes. Genetics. 185: 257-68. PMID 20194967 DOI: 10.1534/genetics.109.113274  0.385
2010 Klocko AD, Crafton KM, Walsh BW, Lenhart JS, Simmons LA. Imaging mismatch repair and cellular responses to DNA damage in Bacillus subtilis. Journal of Visualized Experiments : Jove. PMID 20142799 DOI: 10.3791/1736  0.412
2009 Simmons LA, Goranov AI, Kobayashi H, Davies BW, Yuan DS, Grossman AD, Walker GC. Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. Journal of Bacteriology. 191: 1152-61. PMID 19060143 DOI: 10.1128/Jb.01292-08  0.346
2008 Simmons LA, Foti JJ, Cohen SE, Walker GC. The SOS Regulatory Network. Ecosal Plus. 2008. PMID 25325076 DOI: 10.1128/ecosalplus.5.4.3  0.328
2008 Kobayashi H, Simmons LA, Yuan DS, Broughton WJ, Walker GC. Multiple Ku orthologues mediate DNA non-homologous end-joining in the free-living form and during chronic infection of Sinorhizobium meliloti. Molecular Microbiology. 67: 350-63. PMID 18067541 DOI: 10.1111/J.1365-2958.2007.06036.X  0.334
2007 Simmons LA, Grossman AD, Walker GC. Replication is required for the RecA localization response to DNA damage in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 104: 1360-5. PMID 17229847 DOI: 10.1073/Pnas.0607123104  0.446
2006 Godoy VG, Jarosz DF, Walker FL, Simmons LA, Walker GC. Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression. The Embo Journal. 25: 868-79. PMID 16482223 DOI: 10.1038/Sj.Emboj.7600986  0.442
2005 Felczak MM, Simmons LA, Kaguni JM. An essential tryptophan of Escherichia coli DnaA protein functions in oligomerization at the E. coli replication origin. The Journal of Biological Chemistry. 280: 24627-33. PMID 15878847 DOI: 10.1074/Jbc.M503684200  0.66
2005 Kamau E, Tsihlis ND, Simmons LA, Grove A. Surface salt bridges modulate the DNA site size of bacterial histone-like HU proteins. The Biochemical Journal. 390: 49-55. PMID 15845027 DOI: 10.1042/Bj20050274  0.444
2004 Simmons LA, Breier AM, Cozzarelli NR, Kaguni JM. Hyperinitiation of DNA replication in Escherichia coli leads to replication fork collapse and inviability. Molecular Microbiology. 51: 349-58. PMID 14756777 DOI: 10.1046/J.1365-2958.2003.03842.X  0.647
2003 Simmons LA, Felczak M, Kaguni JM. DnaA Protein of Escherichia coli: oligomerization at the E. coli chromosomal origin is required for initiation and involves specific N-terminal amino acids. Molecular Microbiology. 49: 849-58. PMID 12864864 DOI: 10.1046/J.1365-2958.2003.03603.X  0.675
2003 Simmons LA, Kaguni JM. The DnaAcos allele of Escherichia coli: hyperactive initiation is caused by substitution of A184V and Y271H, resulting in defective ATP binding and aberrant DNA replication control. Molecular Microbiology. 47: 755-65. PMID 12535074 DOI: 10.1046/J.1365-2958.2003.03333.X  0.679
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