other:Article Title: Identification of a proteolysis regulator for an essential enzyme in Mycobacterium tuberculosis
Article Snippet: For growth curves in minimal media Mtb were grown to mid log, washed 3x in 1x DPBS (Corning) with 0.05% Tween-80 (“PBS-T”), and resuspended at OD 0.05 in Sauton’s (3.7 mM potassium phosphate, monobasic; 2.4 mM magnesium sulfate heptahydrate; 30 mM L-(+)-asparagine monohydrate; 3.5 mM zinc sulfate; 9.5 mM citric acid trisodium salt dihyrate (Acros Organics); 6.0% glycerol; 0.005% ferric ammonium citrate (MP Biochemicals); 0.05% Tween-80) or Proscauer-Beck (0.5% potassium phosphate monobasic, 0.06% magnesium sulfate heptahydrate, 1.5% glycerol, 0.25% magnesium citrate, dibasic anhydrous (Chem-Impex International), 0.05% Tween 80, and 10 mM L-(+)-asparagine monohydrate) media.
Virus:Article Title: The hidden bacterial microproteome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025
Article Title: CLCC1 promotes membrane fusion during herpesvirus nuclear egress
Article Snippet: .. Next, virus was pelleted by centrifugation at 41,000 g for 40 min at 4 °C, resuspended in the Opti-MEM medium (Gibco, cat #31985088) containing 10% glycerol (Chem- Impex, cat #30144), and stored at -80 °C for future use. ..
Recombinant:Article Title: The hidden bacterial microproteome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025
Saline:Article Title: The hidden bacterial microproteome.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025
Lysis:
Sonication:
Transformation Assay:Article Title: Identification of gut bacteria reductases that biotransform steroid hormones
Article Snippet: Liquid chromatography separation was performed on a Phenomenex Kinetex C18 100 Å LC Column (100 × 3 mm, 2.6 μm particle size) with mobile phase A (water with 0.1% formic acid) and mobile phase B (acetonitrile with 0.1% formic acid). .. Transformed E. coli strains were cultured by inoculating glycerol stocks derived from agar colony plates into 250 mL of LB medium (Sigma-Aldrich, 0000324647) supplemented with either 50 μg/mL kanamycin or 100 μg/mL carbenicillin (Chem-Impex, 001453-230228 & Bio Basic, Q3030310). ..
Cell Culture:Article Title: Identification of gut bacteria reductases that biotransform steroid hormones
Article Snippet: Liquid chromatography separation was performed on a Phenomenex Kinetex C18 100 Å LC Column (100 × 3 mm, 2.6 μm particle size) with mobile phase A (water with 0.1% formic acid) and mobile phase B (acetonitrile with 0.1% formic acid). .. Transformed E. coli strains were cultured by inoculating glycerol stocks derived from agar colony plates into 250 mL of LB medium (Sigma-Aldrich, 0000324647) supplemented with either 50 μg/mL kanamycin or 100 μg/mL carbenicillin (Chem-Impex, 001453-230228 & Bio Basic, Q3030310). ..
Derivative Assay:Article Title: Identification of gut bacteria reductases that biotransform steroid hormones
Article Snippet: Liquid chromatography separation was performed on a Phenomenex Kinetex C18 100 Å LC Column (100 × 3 mm, 2.6 μm particle size) with mobile phase A (water with 0.1% formic acid) and mobile phase B (acetonitrile with 0.1% formic acid). .. Transformed E. coli strains were cultured by inoculating glycerol stocks derived from agar colony plates into 250 mL of LB medium (Sigma-Aldrich, 0000324647) supplemented with either 50 μg/mL kanamycin or 100 μg/mL carbenicillin (Chem-Impex, 001453-230228 & Bio Basic, Q3030310). ..
Centrifugation:Article Title: CLCC1 promotes membrane fusion during herpesvirus nuclear egress
Article Snippet: .. Next, virus was pelleted by centrifugation at 41,000 g for 40 min at 4 °C, resuspended in the Opti-MEM medium (Gibco, cat #31985088) containing 10% glycerol (Chem- Impex, cat #30144), and stored at -80 °C for future use. ..
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