Genome-scale transcription–translation mapping reveals features of Zymomonas mobilis transcription units and promoters

Jessica M. Vera, Indro Neil Ghosh, Yaoping Zhang, Alex S. Hebert, Joshua J. Coon, Robert Landick

mSystems 5:e00250-20

https://doi.org/10.1128/mSystems.00250-20

System Details

All of the scripts provided here were run on CentOS Linux 7 using Python 2.7.16 and Perl 5.26.2

Content

DataFiles/

NC_000913.2.fa: Escherichia coli str. K-12 substr. MG1655, complete genome
NC_011916.fa: Caulobacter crescentus NA1000, complete genome
ZM4.fa: compilation of Z. mobilis ZM4 chromosome and plasmid sequences [1]
Thomason_2015.EcoTSS.bed: E. coli TSS annotations [2]
Zhou_2015.CcrTSS.bed: C. crescentus TSS annotations [3]
Zymo.up100.promoters.fa: 3080 Z. mobilis TSS annotations from this study

Scripts/

bedsfetch.pl: convert a BED annotation to a fasta sequence
cherrypick35.pl: filter and malign preliminary -35 elements
defined_functions.py: library of user defined functions for get-10Consensus.py
get-10Consensus.py: perform malign on inputted promoter sequences, return preliminary -10 element results
filterBed.pl: manipulate BED files
multiscan.pl: produce final Sigma A/70 model results
parse-10align.pl: parse preliminary -10 element results from get-10Consensus.py, return discriminator lengths, generate preliminary set of -35 sequences
parseTSS15bp.pl: remove TSS within 15bp of an upstream TSS in the same orientation
get_sig70_from_fasta.sh: wrapper script for pipeline starting with 100bp promoter sequences
get_sig70_from_TSS.sh: warpper script for pipeline starting with TSS annotations (used for E. coli and C. crescentus analysis)

Citations

[1] Biotechnol Biofuels. 2018 May 2;11:125. doi: 10.1186/s13068-018-1116-x
[2] J Bacteriol. 2015 Jan 1;197(1):18-28. doi: 10.1128/JB.02096-14
[3] PLoS Genet. 2015 Jan 8;11(1):e1004831. doi: 10.1371/journal.pgen.1004831