Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Enzymes | ||
| HaeIII | New England Biolabs (NEB) (Ipswich, MA, USA) | Cat# R0108S |
| NgoIV | NEB | Cat# R0564S |
| NlaIV | NEB | Cat# R0126S |
| AsiSI | NEB | Cat# R0630S |
| BamHI | NEB | Cat# R0136S |
| NotI | NEB | Cat# R1089S |
| SphI | NEB | Cat# R1082S |
| PstI | NEB | Cat# R0140S |
| BstUI | NEB | Cat# R0518S |
| HaeII | NEB | Cat# R0107S |
| SacI | NEB | Cat# R0156S |
| NdeI | NEB | Cat# R0111S |
| ClaI | NEB | Cat# R0197S |
| SalI | NEB | Cat# R0138S |
| PmeI | NEB | Cat# R0560S |
| AseI | NEB | Cat# R0526S |
| M.CviPI | NEB | Cat# M0227L |
| M.SssI | NEB | Cat# M0226L |
| DNAse I | Invitrogen (Carlsbad, CA, USA) | Cat# 18047019 |
| Proteinase K | Sigma (St. Louis, MO,USA) | Cat# P2308 |
| RNAse A | Qiagen (Hilden, Germany) | Cat# 19101 |
| RNAse A, DNAse and protease-free | Thermo Fisher (Waltham, MA, USA) | Cat# EN0531 |
| T4 ligase | Promega (Madison, WI, USA) | Cat# M0226L |
| Phusion Polymerase | Thermo Fisher | Cat# F531L |
| DNA Polymerase I Klenow Fragment | Promega | Cat# M2201 |
| Bacterial strains (Table S1) | ||
| E. coli (DH5α) | Lab collection | N/A |
| E. coli Turbo Electrocompetent 5alpha | NEB | Cat# 2984H |
| N. gonorrhoeae (MS11) | (Segal et al., 1985) | N/A |
| ΔpilT | (Dietrich et al., 2009) | N/A |
| ΔpilT/ipilT | This study | N/A |
| ΔcomP | This study | N/A |
| ΔcomP/comPWT | This study | N/A |
| TD3 | This study | N/A |
| N400 | (Tonjum et al., 1995) | N/A |
| i35A | This study | N/A |
| N. elongata | ATCC | N/A |
| N. lactamica | ATCC | N/A |
| N. cinerea | ATCC | N/A |
| N. mucosa | ATCC | N/A |
| N. sicca | ATCC | N/A |
| N. polysaccharea | ATCC | N/A |
| N. meningitidis | Lab collection | N/A |
| Oligonucleotides | ||
| Primers used for cloning and sequencing (Table S1) | This study | N/A |
| DNA fragments (Table S1) | This study | N/A |
| Plasmids | ||
| pCR-Blunt | Thermo Fisher | Cat# K270020 |
| pUC19 | AddGene (Watertown, MA, USA) | Cat# 50005 |
| pBeloBAC11 | NEB | Cat# E4154 |
| pKH37 | (Kohler et al., 2007) | N/A |
| pNBNeiKan | (Weyand et al., 2016) | N/A |
| pMR68 | (Ramsey et al., 2012) | N/A |
| Growth Media | ||
| GC medium base | Difco Laboratories Inc (Detroit, MI, USA) | Cat# 228920 |
| GCB containing Kellogg’s Supplements I and II | (Kellogg et al., 1963) | N/A |
| GCB containing vancomycin, colistin, nystatin | (Jacobs and Kraus, 1975) | N/A |
| Glutaraldehyde | Electron Microscopy Sciences (EMS) (Hatfield, PA, USA) | Cat# 16000 |
| Osmium tetroxide | EMS | Cat# 19100 |
| Uranyl acetate | EMS | Cat# 22400 |
| Chemicals | ||
| IPTG | GoldBio (Olivette, MO, USA) | Cat# I2481C50 |
| X-gal | Research Products International (RPI) (Mount Prospect, IL, USA) | Cat# B71800 |
| S-adenosylmethionine (SAM) | NEB | Cat# B9003S |
| BSA | Sigma | Cat# A2153 |
| Ampicilin | GoldBio | Cat# 69523 |
| Kanamycin | GoldBio | Cat# K120SL25 |
| Erythromycin | Sigma | Cat# E5389 |
| Chloramphenicol | Sigma | Cat# C0378 |
| Vancomycin | RPI | Cat# V065500 |
| Colistin | RPI | Cat# C70700 |
| Nystatin | RPI | Cat# N82020 |
| Ethanol | Sigma | Cat# 459836 |
| Isopropanol | Sigma | Cat# I9516 |
| Phenol | Sigma | Cat# 108952 |
| Isoamyl alcohol | Sigma | Cat# 123513 |
| Tissue Culture Plates | ||
| Microplate dish (6-well) | Corning (Corning, NY, USA) | Cat# 0720083 |
| Microplate dish (12-well) | Corning | Cat# 087721B |
| Microplate dish (24-well) | Corning | Cat# 353847 |
| Animal Model: Mice | ||
| Female BALB/c (6-8 weeks old) | National Cancer Institute and Charles River (Jerse et al., 2011) | Cat# Strain_028 |
| Other lab reagents | ||
| 0.22 μM PES Steriflip filter | Millipore (Burlington, MA, USA) | Cat# SE1M179M6 |
| 0.22 μM filter | Millipore | Cat# SLGV033RS |
| Nucleobond Midi Columns | Macherey-Nagel (Düren, Germany) | Cat# 740410 |
| Agarose | Sigma | Cat# A2576 |
| Megabase Agarose | Bio-Rad (Hercules, CA, USA) | Cat# 1613108 |
| Phase Lock Gels | VWR (Radnor, PA, USA) | Cat# 2302820 |
| Gel Extraction Kit | Qiagen | Cat# 28706 |
| Gel Extraction Kit | Thermo Fisher | Cat# K0691 |
| Wizard Genomic DNA Purification Kit | Promega | Cat# A1120 |
| Dacron Swabs | Thermo Fisher | Cat# 164KS01 |
| CHEF Electrophoresis System | Bio-Rad | Cat# 1703670 |
| Model 422 Electro-Eluter | Bio-Rad | Cat# 1652976 |
| NanoDrop spectrophotometer | Thermo Fisher | RR_ID:SCR_015804 |
| Software and algorithms | ||
| Blastn | NCBI | RR_ID:SCR_007190 https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| GraphPad Prism 5.0 | GraphPad (San Diego,CA, USA) | RR_ID: SCR_002798 https://www.graphpad.com |
| SMRT-Analysis | PacBio (Menlo Park, CA, USA) | RR_ID: SCR_002942 https://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ |
| Quiver | (Chin et al., 2013) | N/A https://github.com/PacificBiosciences/GenomicConsensus |
| Vim Text Editor | Vim | N/A https://www.vim.org/ |