Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters

MSystems
Jessica M VeraRobert Landick

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 σA -35 and -10 promoter elements closely resemble canonical Es...Continue Reading

References

Mar 1, 1991·Journal of Bacteriology·H MoyleM M Susskind
Mar 1, 1987·Journal of Bacteriology·T ConwayL O Ingram
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Dec 14, 2004·Nature Biotechnology·Jeong-Sun SeoHyen Sam Kang
Jun 28, 2005·Nucleic Acids Research·Nicholas R Markham, Michael Zuker
Dec 26, 2006·Nucleic Acids Research·Ryan K ShultzabergerThomas D Schneider
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Oct 10, 2009·Nature Biotechnology·Shihui YangSteven D Brown
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jun 18, 2010·Journal of Bioinformatics and Computational Biology·Ivan Antonov, Mark Borodovsky
May 24, 2011·Methods in Enzymology·Virgil A Rhodius, Carol A Gross
May 24, 2012·Molecular Systems Biology·Omri WurtzelRotem Sorek
Dec 29, 2012·PLoS Computational Biology·Robert C BrewsterRob Phillips
Jun 29, 2013·Nature Methods·Rachel Anne Mooney, Robert Landick
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 6, 2014·Applied and Environmental Microbiology·Seung Hee ChoLydia M Contreras
Jun 14, 2014·Proceedings of the National Academy of Sciences of the United States of America·Rembrandt J F HaftRobert Landick
Jul 30, 2014·Nature Reviews. Microbiology·Joseph T Wade, David C Grainger
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jan 1, 2014·BioTechniques·Haythem LatifBernhard O Palsson
Mar 30, 2016·Annual Review of Biochemistry·Ananya Ray-SoniRobert Landick
Jun 28, 2016·Nucleic Acids Research·Tatiana TatusovaJames Ostell
Oct 21, 2016·Microbial Biotechnology·Shihui YangMin Zhang
Nov 4, 2016·Nature Protocols·Stefka TyanovaJuergen Cox
Jan 13, 2017·PloS One·Christian LangeJörg Soppa
Jan 18, 2018·Nature Communications·Fidel RamírezThomas Manke

❮ Previous
Next ❯

Citations

Sep 27, 2020·Applied and Environmental Microbiology·Amy B BantaJason M Peters
Nov 11, 2020·Proceedings of the National Academy of Sciences of the United States of America·Kemardo K HenryRichard L Gourse
May 3, 2021·Biotechnology for Biofuels·Magdalena M FelczakMichaela A TerAvest
Jun 22, 2021·Journal of Bacteriology·Kemardo K HenryRichard L Gourse
Aug 5, 2021·Annual Review of Microbiology·Robert Landick

❮ Previous
Next ❯

Datasets Mentioned

BETA
CP023715.1
CP023716.1
CP023717.1
CP023718.1
CP023719.1
and
IPR007627
GSE139939
PXD016962

Methods Mentioned

BETA
RNA-seq
ribo-seq
dRNA-seq
term-seq
X-ray
light scattering
in
PCR
electrophoresis

Software Mentioned

RSEM
DESeq
R
genomeCoverageBed
BEDTools
TTGNNN
multiscan
DESeq2 differential gene expression analysis
Perl
fastx

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.