Vera et al. 2020 (PRJNA587699)

General Details

Title Genome-scale transcription–translation mapping reveals novel features of Zymomonas mobilis promoters and transcription units 
Organism
Number of Samples 78
Release Date 2019/11/05 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP228586
ENA SRP228586
GEO GSE139939
BioProject PRJNA587699

Publication

Title
Authors Vera JM,Ghosh IN,Zhang Y,Hebert AS,Coon JJ,Landick R
Journal mSystems
Publication Date 2020 Jul 21
Abstract Zymomonas mobilis is an ethanologenic alphaproteobacterium with promise for the industrial conversion of renewable plant biomass into fuels and chemical bioproducts. Limited functional annotation of the Z. mobilis genome is a current barrier to both fundamental studies of Z. mobilis and its development as a synthetic biology chassis. To gain insight, we collected sample-matched multiomics data, including RNA sequencing (RNA-seq), transcription start site (TSS) sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry, across different growth conditions and used these data to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins. We developed statistical methods for annotating transcript 5' and 3' ends, enabling the identification of 3,940 TSSs and their corresponding promoters and 2,091 transcription termination sites, which were distinguished from RNA processing sites by the lack of an adjacent RNA 5' end. Our results revealed that Z. mobilis σ A -35 and -10 promoter elements closely resemble canonical Escherichia coli -35 and -10 elements, with one notable exception: the Z. mobilis -10 element lacks the highly conserved -7 thymine observed in E. coli and other previously characterized σ A promoters. The σ A promoters of another alphaproteobacterium, Caulobacter crescentus , similarly lack the conservation of -7 thymine in their -10 elements. Our results anchor the development of Z. mobilis as a platform for synthetic biology and establish strategies for empirical genome annotation that can complement purely computational methods. IMPORTANCE Efforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the Z. mobilis genome presented in this work, we provide crucial knowledge for the development of synthetic genetic parts tailored to Z. mobilis This information is vital as researchers continue to develop Z. mobilis for synthetic biology applications. Our methods and statistical analyses also provide ways to rapidly advance the understanding of poorly characterized bacteria via empirical data that enable the experimental validation of sequence-based prediction for genome characterization and annotation. Copyright © 2020 Vera et al.
PMC PMC7566282
PMID 32694125
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR10400965 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400966 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400967 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400968 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400969 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400970 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400971 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400972 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400973 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400974 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400975 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400976 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400977 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400978 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400979 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400980 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400981 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400982 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400989 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400990 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400991 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400992 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400993 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400994 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400995 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400996 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400997 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400998 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10400999 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401000 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401001 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401002 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401003 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401004 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401005 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401006 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401007 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401008 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401009 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401010 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401011 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401012 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401013 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401014 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401015 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401016 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401017 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401018 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401019 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401020 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401021 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401022 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401023 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401024 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401025 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401026 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401027 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401028 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401029 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401030 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401031 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401032 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401033 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401034 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401035 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401036 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401037 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401038 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401039 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401040 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401041 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401042 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401043 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401044 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401045 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401046 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401047 PRJNA587699 Zymomonas mobilis Ribo-Seq
SRR10401048 PRJNA587699 Zymomonas mobilis Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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