Publications

2023

Schroeder, J.W., Hurto, R., Randall, J.R., Wozniak, K.J., Timko, T.A., Nye, T.M. Wang, J.D. Freddolino, P.L‡. and L.A. Simmons‡ (2023) RNA-DNA hybrids cause genome-wide instability through base deamination, genomic rearrangements, and induction of the DNA damage response. Science Advances Jul 28;9(30):eadi5945. doi: 10.1126/sciadv.adi5945. (‡co-corresponding authors) https://pubmed.ncbi.nlm.nih.gov/37494439/

Lowder, F.C. and L.A. Simmons (2023) Bacillus subtilis encodes a discrete flap endonuclease that cleaves RNA-DNA hybrids. PLOS Genetics doi:10.1371/journal.pgen.1010585. Link

Blaine H.C., Simmons L.A., and C.L Stallings (2023) Diverse mechanisms of helicase Loading during DNA replication initiation in bacteria. Journal of Bacteriology. Mar 6:e0048722. doi: 10.1128/jb.00487-22.

Fernandez* NL, Chen*, Z., Fuller, D.E.H, van Gijtenbeek, L.A Nye, T.M. Biteen J.S. and L.A. Simmons (2023) Single-molecule dynamics of DNA methyltransferase DnmA are regulated by DNA methylation and RNA-DNA hybrids. mBio Jan 16:e0318522. doi: 10.1128/mbio.03185-22. *Equally contributed Link

2022

McLean, E.K., Nye, T.M., Lowder, F.C., and L.A. Simmons (2022) Impact of RNA-DNA hybrids on genome integrity in bacteria. Annual Review of Microbiology. Jun 2. doi: 10.1146/annurev-micro-102521-014450.

Wozniak, K.J. and L.A. Simmons (2022) Genome editing methods for Bacillus subtilis. Methods in Molecular Biology. 2479:159-174. doi: 10.1007/978-1-0716-2233-9_11 PubMed

Wozniak K.J., Burby P.E., Nandakumar J., and L.A. Simmons (2022). “Structure and kinase activity of bacterial cell cycle regulator CcrZ.” PLOS Genetics May 16;18(5):e1010196. doi: 10.1371/journal.pgen.1010196. Link

Wozniak, K.J. and L.A. Simmons (2022) Bacterial DNA excision repair pathways. Nature Reviews Microbiology https://doi.org/10.1038/s41579-022-00694-0. PubMed

Matthews, L.A. and L.A. Simmons (2022) The Bacillus subtilis PriA winged helix domain is critical for surviving DNA damage. Journal of Bacteriology Jan 10:JB0053921. doi: 10.1128/JB.00539-21. PubMed

Amemiya, H.M., Goss, T.A., Nye, T.M., Hurto, R., Simmons, L.A. and P.L. Freddolino (2022) Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria. EMBO Journal. Dec 28; e108708.doi:10.15252/embj.2021108708. Link

2021

McLean, E.K., Lenhart, JS., and L.A. Simmons (2021) RecA is required for the assembly of RecN into DNA repair complexes on the nucleoid. Journal of Bacteriology Sep 23;203(20):e0024021. doi: 10.1128/JB.00240-21. PubMed

Masser, E.A., Burby P.E., Hawkins, W.D., Gustafson, B.R., Lenhart, J.S. and L.A. Simmons (2021) DNA damage checkpoint activation affects peptidoglycan synthesis and late divisome components. Molecular Microbiology Aug;116(2):707-722. doi: 10.1111/mmi.14765. PubMed

Wozniak, K.J. and L.A. Simmons (2021) Hydroxyurea induces a stress response that alters DNA replication and nucleotide metabolism in Bacillus subtilis Journal of Bacteriology JB.00171-21. doi: 10.1128/JB.00171-21. PubMed

Nye, T.M., McLean E.K., Burrage, A.M, Dennison, D.D., Kearns, D.B., L.A. Simmons (2021). RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in Bacillus subtilis ancestral strain NCIB 3610. Molecular Microbiology Jan;115(1):99-115. doi: 10.1111/mmi.14601. PubMed

2020

Nye, T.M. Fernandez, N. L. and L.A. Simmons (2020) 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.55: (6) 575-591. Oct 15:1-16. doi: 10.1080/10409238.2020.1828257. PubMed

Matthews, L.A. and L.A. Simmons (2020) Regulation of DNA Binding and High Order Oligomerization of the DnaB Helicase Loader. Journal of Bacteriology JB.00286-20. doi: 10.1128/JB.00286-20. PubMed

Schroeder J.W., Sankar, S.T., Wang, J.D. and L.A. Simmons (2020) The roles of replication-transcription conflict in mutagenesis and evolution of genome organization. PLoS Genetics 16(8):e1008987. Link

Nye, T.M., van Gijtenbeek, L.A., Stevens, A.G.,  Schroeder, J.W., Matthews, L.A. Randall, J.R., and L.A. Simmons (2020) Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis. Nucleic Acids Research  48(10):5332-5348 doi: 10.1093/nar/gkaa266. Link

Burby, P.E. and L.A. Simmons (2020) Regulating cell division by monitoring genome integrity and DNA replication status. Journal of Bacteriology 202(2). pii: e00408-19. doi: 10.1128/JB.00408-19. PubMed

2019

Nye, T. M., K. M. Jacob, S. R. Dawid, L. A. Simmons, and M. E. Watson, Jr. (2019) DNA methylation from a type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PLoS Pathogens 17;15(6):e1007841. doi: 10.1371/journal.ppat.1007841.

Almawi,A.A., Scotland, M.K.  Randall,J.R., Pillon, M.C., Liu, L., Martin, H.K., Simmons, L.A.,Sutton, M.D., and A. Guarné (2019) Binding of MutL to the sliding b-clamp is species dependent. Nucleic Acids Research 47(9):4831-4842

Randall, J.R., Nye, T.M., Wozniak, K.J. and L.A. Simmons‡ (2019) RNase HIII is important for Okazaki fragment maturation in Bacillus subtilis. Journal of Bacteriology. 201(7). pii: e00686-18. doi: 10.1128/JB.00686-18.

Li,Y., Chen, Z., Matthews, L.A., Simmons, L.A. ‡and J.S. Biteen‡ (2019) Dynamic exchange of two  essential DNA polymerases during  replication and after fork arrest. (‡co-corresponding authors)  Biophysical Journal

Burby, P.E. and L.A. Simmons‡ (2019) A bacterial DNA repair pathway specific to a natural antibiotic Molecular Microbiology 111(2):338-353

Burby, P.E., Simmons, Z.W., and L.A. Simmons‡ (2019) DdcA antagonizes a bacterial DNA damage checkpoint. Molecular Microbiology111(1):237-253.

Matthews, L.A., and L.A Simmons‡ (2019) Cryptic protein interactions regulate DNA replication initiation. Molecular Microbiology 111(1):118-130.

2018

Burby, P.E. Simmons, Z.W., Schroeder J.W., and L.A. Simmons‡ (2018) Discovery of a dual protease mechanism that promotes DNA damage checkpoint recovery PLoS Genetics. 14(7):e1007512.

Clark, D.L., Simmons, L.A. and R.G. Bowker (2018) Aspects of courtship risks and mating success in the dimorphic jumping spider, Maevia inclemens(Araneae:Salticidae) Journal of Arachnology 46(1):1-6. (Undergraduate thesis research-published at last!!)

Li, Y., Schroeder,J.W., Simmons, L.A.and J.S. Biteen (2018) Visualizing bacterial DNA replication and repair with molecular resolution. Current Opinion in Microbiology Nov 30; 43:38-45. doi: 10.1016/j.mib.2017.11.009. Review

Schroeder,J.W., Yeesin, P., Simmons, L.A.and J. D. Wang (2018) Sources of spontaneous mutagenesis in bacteria. Critical Reviews in Biochemistry and Molecular Biology. 53(1):29-48 Review

Randall, J.R., Hirst, W.G., and L.A. Simmons‡ (2018) Substrate specificity for bacterial RNase HII and HIII is influenced by metal availability. Journal of Bacteriology JB.00401-17. doi: 10.1128/JB.00401-17 (‡Corresponding)

  • Awarded a Spotlight in the Journal of Bacteriology

2017

Schroeder,J.W., Randall, J.R., Hirst, W.G., O’Donnell, M.E‡. and L.A. Simmons‡ (2017) Mutagenic cost of ribonucleotides in bacterial DNA. Proc. Natl. Acad. Sci. USA. Oct 31;114(44):11733-11738. doi: 10.1073/pnas.1710995114(‡Co-corresponding)

Waack, U., Johnson, T.L., Chedid, K., Xi, C., Simmons, L.A., Mobley, H and M. Sandkvist (2017) Targeting the Type II Secretion System: Development, Optimization, and Validation of a High-Throughput Screen for the identification of Small Molecule Inhibitors Frontiers in Cellular and Infection Microbiology7:380 (1-12).

Burby, P.E. and L.A. Simmons‡ (2017) CRISPR/Cas9 editing of the Bacillus subtilis genome.Bio-protocols. (‡corresponding author) 7(8): e2272. DOI: 10.21769/BioProtoc.2272.

Nye, T.M. Schroeder, J.W. Kearns, D.B. and L.A. Simmons‡ (2017) Complete genome sequence of undomesticated Bacillus subtilis strain NCIB 3610. Genome Announcements May 18;5(20). pii: e00364-17.

Burby, P.E. and L.A. Simmons‡ (2017) MutS2 promotes homologous recombination in Bacillus subtilis. Journal of Bacteriology 199:e00703-16.

  • Awarded a Spotlight in the Journal of Bacteriology

Burby, P.E., Nye, T.M., Schroeder, J.W., and L.A. Simmons‡ (2017) Implementation and data analysis of Tn-seq, whole genome resequencing, and single-molecule real time sequencing for bacterial genetics Journal of Bacteriology. 199:e00560-16 (‡corresponding author) Review

2016

Liao, Y., Li, Y., Schroeder, J.W., Simmons, L.A.,‡ and J.S. Biteen‡ (2016) Single-molecule DNA polymerase dynamics at a bacterial replisome in live cells. Biophysical Journal 111:2562-256.

  • Awarded “Best of 2016 highlight’ Biophysical Journal.
  • Editor’s Choice Physics Week January 24th 2017

Saputo, S., Norman, K., Murante, T., Horton, B.N. DiDone, L., Colquhoun, J., Schroeder, J.W., Simmons, L.A., Kumar, A., Krysan, D. (2016) Complex haploinsufficiency-based genetic analysis of the NDR/Lats kinase Cbk1 provides insight into its multiple functions in C. albicans. Genetics 203(3):1217-33

Tuson, H.H., Aliaj, A., Brandes, E.R., Simmons L.A., and J.S. Biteen (2016) Addressing the requirements of high sensitivity single-molecule imaging of low-copy number proteins in bacteria. ChemPhysChem 18;17(10):1435-40.

Schroeder J.W., Hirst W.G., Szewczyk G.A. and L.A. Simmons‡ (2016) The effect of local sequence context on mutational bias of genes encoded on the leading and lagging strands. Current Biology 26:692-697. PMID: 26923786.

2015

Liao, Y., Schroeder, J.W., Gao, B., Simmons, L.A*., and J.S. Biteen*  (2015) Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair. Proc. Natl. Acad. Sci. USA. 2015 Nov 2. pii: 201507386.* Co-Corresponding

  • Highlighted article in PNAS Early Edition: “High-resolution Imaging Illuminates DNA Repair”
  • News highlight in Biotechniques: “How a cell identifies DNA errors” by Robin Donovan
  • Commentary in PNAS: “How MutS finds a needle in a haystack” by Mark Sutton
  • Selected by F1000 Microbiology

Pillon, M.C., Babu V.M., Randall, J.R., Cai, J., Simmons, L.A., Sutton, M.D., and A, Guarné. (2015) The Sliding clamp tethers the endonuclease domain of MutL to DNA. Nucleic Acids Res pii: gkv918.

Lenhart, J.S., Pillon M.C., Guarné A.,* Biteen J.S.,*and L.A. Simmons*. (2015) Mismatch repair in Gram-positive bacteria. Research Microbiology. doi: 10.1016/j.resmic.2015.08.006. *Co-corresponding

Schroeder, J.W., Randall, J. R., Matthews, L.A. and L.A. Simmons. (2015) Ribonucleotides in Bacterial DNA. Critical Reviews in Biochemistry and Molecular Biology. 50(3):181-93.

2014

Matthews, L.A. and L.A. Simmons. (2014) Bacterial non homologous end joining requires teamwork. Journal of Bacteriology. Oct;196(19):3363-5.

Lenhart, J.S., Brandes, E.R.,  Schroeder, J.W.,Sorenson, R. J., Showalter, H.D. and L.A. Simmons. (2014) RecO and RecR provide distinct roles that couple RecA to DNA replication forks in Bacillus subtilis. Journal of Bacteriology. Aug;196(15):2851-60.

Walsh*,B.W., Bolz*, S.A.,Wessell, S.R., Schroeder, J.W., Keck, J.L. and L.A. Simmons. (2014) RecD2 helicase limits replication fork stress in Bacillus subtilis. (*equally contributed) Journal of Bacteriology.196:1359-1368.

2013

Schroeder, J.W. and L.A. Simmons (2013) Complete genome sequence of Bacillus subtilis strain PY79.  Genome Announcements. pii: e01085-13. doi: 10.1128

Lenhart, J.S., Pillon, M.C., Guarné, A., and L.A. Simmons (2013).  Trapping and visualizing intermediate steps in the mismatch repair pathway in vivo. Molecular Microbiology . Nov;90(4):680-98. PubMed

Chodavarapu, S., Felczak, M.M., Simmons, L.A., Murillo, A., and Kagun,i J.M. (2013).  Mutant DnaAs of Escherichia coli that are refractory to negative control.Nucleic Acids Research. 41(22):10254-67. PubMed

Yao, N., Schroeder, J.W., Yurieva, O., Simmons, L.A. and M.E. O’Donnell. (2013).   The cost of rNTP/dNTP pool imbalance at the replication fork.  Proc. Natl. Acad. Sci. USA. 110(32):12942-7. PubMed

Marceau, A.H.*, Bernstein, D.A.*, Walsh, B.W., Shapiro, W., Simmons, L.A., and J. L. Keck. (2013).  Protein interactions in genome maintenance as novel antibacterial targets. PLoS One . 8(3):e58765. *these authors contributed equally . PubMed

Lenhart, J.S., Anushi, A., Hingorani, M.M. and L.A. Simmons. (2013).   DnaN provides a platform for spatiotemporal coupling of mismatch detection to DNA replication. Molecular Microbiology. 87(3):553-68. PubMed

2012

Bolz, N.J., Lenhart, J.S., Weindorf, S.C., Simmons, L.A. (2012).  Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis. Journal of Bacteriology. 194(19)5361-5367. PubMed

Walsh, B.W., Lenhart, J.S., Schroeder, J.W. and L.A. Simmons. (2012).  Far Western blotting as a rapid and efficient method for detecting interactions between DNA replication and DNA repair proteins. Methods in Molecular Biology. 922:161-8. PubMed

Lenhart, J.S., Schroeder, J.W., Walsh, B.W. and L.A. Simmons. (2012).  DNA repair and genome maintenance in Bacillus subtilis. Microbiology and Molecular Biology Reviews . Sep;76(3):530-64. PubMed

Coope,r L.A., Simmons, L.A., Mobley, H.L. (2012).  Involvement of Mismatch Repair in the Reciprocal Control of Motility and Adherence of Uropathogenic Escherichia coli. Infection and Immunity . Jun;80(6):1969-79. PubMed

2011

Klocko, A.D., Schroeder, J.S. Walsh, B.W., Lenhart, J.S., Evans, M.L. and L.A. Simmons. (2011). Mismatch repair causes the dynamic release of an essential DNA polymerase from the replication fork. Molecular Microbiology. Nov;82(3):648-63. PubMed

Davies, B.W. Bogard, R.W, Dupes N.M., Gerstenfeld T.A., Simmons, L.A. and J. J. Mekalanos . (2011).   DNA damage and reactive nitrogen species are barriers to Vibrio cholerae colonization of the infant mouse intestine . PLoS Pathogens. 7 e1001295. PubMed

Davies, B.W., Köhrer, C., Jacob, A.I.*, Simmons, L.A.*, Zhu, J., Aleman, L.M., Rajbhandary, U.L., Walker, G.C. (2010).  Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Molecular Microbiology. Oct;78(2):506-18. * Equally contributed. PubMed

2010

Pillon, M.C., Lorenowicz, J.J., Uckelmann, M., Klocko, A.D., Mitchell, R.R., Chung, Y.S., Modrich, P., Walker, G.C., Simmons, L.A., Friedhoff, P., Guarné, A. (2010). Structure of the endonuclease domain of MutL:Unlicensed to cut. Molecular Cell. 39(1):145-151. PubMed

Dupes, N.M. *, Walsh, B.W. *, Klocko, A.D.,Lenhart, J. S., Peterson, H.L., Gessert, D.A., Pavlick, C.E and L.A. Simmons. (2010).   Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. Journal of Bacteriology. 192(13):3452-63. * These authors contributed equally. PubMed

Klocko, A.D., Crafton, K.M., Walsh, B.W., Lenhart, J.S. and L.A. Simmons. (2010).  Imaging mismatch repair and cellular responses to DNA damage in Bacillus subtilis. Journal of Visualized Experiments. Feb 8;(36): 1-4. PubMed

2009

Davies, B.W., Kohanski, M.A., Simmons, L.A.*, J. A. Winkler*, Collins, J.J., and G.C. Walker . (2009).   Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Molecular Cell. 36:845-860. *These authors contributed equally.  PubMed

  • Previewed  in Molecular Cell

Foti J.J., Simmons, L.A., Beuning, P.J. and G.C. Walker. (2009).   Signal transduction in the Escherichia coli SOS response. Handbook of Cell Signaling. Volume 3 second addition Chapter 258, pp. 2127-2136. Elsevier Science.

Kobayashi, H., De Nisco, N.J., Chien P, Simmons, L.A. and G. C. Walker. (2009).   Sinorhizobium meliloti CpdR1 is critical for coordinating cell-cycle progression and the symbiotic chronic infection. Molecular Microbiology. 73:586-600. Cover illustration. PubMed

Simmons, L.A.‡, Goranov, A. I., Kobayashi, H., Davies, B.D., Yuan, D.S., Grossman, A. D., and G.C. Walker.. (2009). Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. Journal of Bacteriology. 191:1152-1161. ‡Corresponding author. . PubMed

Articles below were published prior to my arrival at the University of Michigan on Sept 1st 2008.

Simmons, L.A. Grossman, A.D., and G.C. Walker. (2008). Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis. Journal of Bacteriology. 190(20):6758-68. PubMed

Simmons, L. A*., J. J. Foti*, S. E. Cohen, and G. C. Walker. (2008). T. Nyström, J. M. Slauch, and C. L. Squires (ed.),  EcoSal-Escherichia coli and Salmonella: cellular and molecular biology. In A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, Chapter 5.4.3, The SOS Regulatory Network, in press. http://www.ecosal.org. ASM Press, Washington, D.C. *These authors contributed equally.

Simmons, L.A., Davies, B.W., Grossman, A.D. and G.C. Walker. (2008). Beta clamp directs localization of mismatch repair in Bacillus subtilis. Molecular Cell. 29:291-301.

  • Selected by F1000

Kobayashi, H., Simmons, L.A., Yuan, S. D., Broughton W.J. and G.C. Walker. (2008). Multiple Ku orthologs mediate non-homologous end joining in the free-living and during chronic infection of Sinorhizobium meliloti 1021. Molecular Microbiology. 67: 350–363. PubMed

Simmons, L.A. Grossman, A.D. and G.C. Walker. (2007). Replication is required for the RecA localization response to DNA damage in Bacillus subtilis. Proc. Natl. Acad. Sci. USA. 104: 1360-1365. PubMed

Godoy, V.G., Jarosz, D.F., Walker, F.L., Simmons, L.A. and G.C. Walker. (2006). Escherichia coli Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression. EMBO Journal. 25: 868-879. PubMed

Felczak, M.M., Simmons, L.A. and J.M. Kaguni. (2005). An essential tryptophan of Escherichia coli DnaA protein functions in oligomerization at the E. coli replication origin. Journal of Biological Chemistry. 280: 24627-24633. PubMed

Simmons, L.A., Breier, A.M., Cozzarelli, N.R. and J.M. Kaguni. (2004). Hyperinitiation of DNA replication in Escherichia coli leads to replication fork collapse and inviability. Molecular Microbiology. 51: 349-358. PubMed

Simmons, L.A., Felczak, M.F. and J.M. Kaguni. (2003). 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: 849-858. PubMed

Simmons, L.A. and J.M. Kaguni. (2003). The dnaAcos allele of E. coli: hyperactive initiation is caused by substitution of A184V and Y271H, resulting in defective ATP binding and aberrant DNA replication control. Molecular Microbiology. 47: 755-765. PubMed