MOESM6 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Functional genomics of pH homeostasis in <it>Corynebacterium glutamicum </it>revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Persicke Marcus
Hüser Andrea
Rückert Christian
Poetsch Ansgar
Trötschel Christian
Krämer Reinhard
Ochrombel Ines
Follmann Martin
Seiferling Dominic
Kalinowski Jörn
Marin Kay

December 2009

Abstract Background The maintenance of internal pH in bacterial cells is challenged by natural stres...

Table_1_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

Table_3_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

MOESM7 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 7. Extracellular amino acid concentrations in media from C. thermocellum LL1210 chem...

MOESM2 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 2. Raw and processed read counts, alignment statistics, log2-fold changes in the gen...

MOESM1 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 1. Data logs, substrate and product concentrations, internal and external pH reading...

MOESM5 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 5: Figure S3. Differential expression of genes found in Clostridia sporulation casca...

MOESM3 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 3: Figure S1. Average optical density at wave-length 600nm (A and C) and average ter...

MOESM4 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 4: Figure S2. Average growth (A), terminal pH (B), and remaining substrates and prod...

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason M. Whitham
Ji-Won Moon
Miguel Rodriguez
Nancy L. Engle
Dawn M. Klingeman
Thomas Rydzak
Malaney M. Abel
Timothy J. Tschaplinski
Adam M. Guss
Steven D. Brown

April 2018

Abstract Background Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic t...

MOESM5 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

Suresh Poudel (3627245)
Richard Giannone (3455150)
Miguel Rodriguez (1594399)
Babu Raman (264806)
Madhavi Martin (3627248)
Nancy Engle (3436811)
Jonathan Mielenz (3627242)
Intawat Nookaew (163890)
Steven Brown (637397)
Timothy Tschaplinski (3436805)
David Ussery (81242)
Robert Hettich (3455141)

January 2017

Additional file 5: Table S4. Expression level of transcripts for C. thermocellum grown on switchgras...

MOESM1 of Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism

Ranjita Biswas (586794)
Charlotte Wilson (3466343)
Richard Giannone (3455150)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Manesh Shah (117747)
Robert Hettich (3455141)
Steven Brown (637397)
Adam Guss (3455138)

January 2017

Additional file 1:Â Supplemental Tables. Table S1. Primers used in this study. Table S2. Calculation...

MOESM2 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

Satyakam Dash (3995477)
Ali Khodayari (3995480)
Jilai Zhou (612821)
Evert Holwerda (3455144)
Daniel Olson (2916260)
Lee Lynd (3453692)
Costas Maranas (1310631)

May 2017

Additional file 2. The genome-scale model iCth446 with GPRs and metabolite information, list of TICs

MOESM1 of Integrated intracellular metabolic profiling and pathway analysis approaches reveal complex metabolic regulation by Clostridium acetobutylicum

Huanhuan Liu (169314)
Di Huang (360305)
Jianping Wen (403000)

February 2016

Additional file 1. All the metabolites detected in our study and the results of pathway analysis

MOESM8 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

Suresh Poudel (3627245)
Richard Giannone (3455150)
Miguel Rodriguez (1594399)
Babu Raman (264806)
Madhavi Martin (3627248)
Nancy Engle (3436811)
Jonathan Mielenz (3627242)
Intawat Nookaew (163890)
Steven Brown (637397)
Timothy Tschaplinski (3436805)
David Ussery (81242)
Robert Hettich (3455141)

January 2017

Additional file 8: Fig. S1. Temporal expression based clustering of proteins differentially expresse...

Functional genomics of pH homeostasis in <it>Corynebacterium glutamicum </it>revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Persicke Marcus
Hüser Andrea
Rückert Christian
Poetsch Ansgar
Trötschel Christian
Krämer Reinhard
Ochrombel Ines
Follmann Martin
Seiferling Dominic
Kalinowski Jörn
Marin Kay

December 2009

Abstract Background The maintenance of internal pH in bacterial cells is challenged by natural stres...

Table_1_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

Table_3_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

MOESM7 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 7. Extracellular amino acid concentrations in media from C. thermocellum LL1210 chem...

MOESM2 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 2. Raw and processed read counts, alignment statistics, log2-fold changes in the gen...

MOESM1 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 1. Data logs, substrate and product concentrations, internal and external pH reading...

MOESM5 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 5: Figure S3. Differential expression of genes found in Clostridia sporulation casca...

MOESM3 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 3: Figure S1. Average optical density at wave-length 600nm (A and C) and average ter...

MOESM4 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason Whitham (5069207)
Ji-Won Moon (1719163)
Miguel Rodriguez (1594399)
Nancy Engle (3436811)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Malaney Abel (5069210)
Timothy Tschaplinski (3436805)
Adam Guss (3455138)
Steven Brown (637397)

April 2018

Additional file 4: Figure S2. Average growth (A), terminal pH (B), and remaining substrates and prod...

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Jason M. Whitham
Ji-Won Moon
Miguel Rodriguez
Nancy L. Engle
Dawn M. Klingeman
Thomas Rydzak
Malaney M. Abel
Timothy J. Tschaplinski
Adam M. Guss
Steven D. Brown

April 2018

Abstract Background Clostridium (Ruminiclostridium) thermocellum is a model fermentative anaerobic t...

MOESM5 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

Suresh Poudel (3627245)
Richard Giannone (3455150)
Miguel Rodriguez (1594399)
Babu Raman (264806)
Madhavi Martin (3627248)
Nancy Engle (3436811)
Jonathan Mielenz (3627242)
Intawat Nookaew (163890)
Steven Brown (637397)
Timothy Tschaplinski (3436805)
David Ussery (81242)
Robert Hettich (3455141)

January 2017

Additional file 5: Table S4. Expression level of transcripts for C. thermocellum grown on switchgras...

MOESM1 of Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism

Ranjita Biswas (586794)
Charlotte Wilson (3466343)
Richard Giannone (3455150)
Dawn Klingeman (3469250)
Thomas Rydzak (394477)
Manesh Shah (117747)
Robert Hettich (3455141)
Steven Brown (637397)
Adam Guss (3455138)

January 2017

Additional file 1:Â Supplemental Tables. Table S1. Primers used in this study. Table S2. Calculation...

MOESM2 of Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

Satyakam Dash (3995477)
Ali Khodayari (3995480)
Jilai Zhou (612821)
Evert Holwerda (3455144)
Daniel Olson (2916260)
Lee Lynd (3453692)
Costas Maranas (1310631)

May 2017

Additional file 2. The genome-scale model iCth446 with GPRs and metabolite information, list of TICs

MOESM1 of Integrated intracellular metabolic profiling and pathway analysis approaches reveal complex metabolic regulation by Clostridium acetobutylicum

Huanhuan Liu (169314)
Di Huang (360305)
Jianping Wen (403000)

February 2016

Additional file 1. All the metabolites detected in our study and the results of pathway analysis

MOESM8 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

Suresh Poudel (3627245)
Richard Giannone (3455150)
Miguel Rodriguez (1594399)
Babu Raman (264806)
Madhavi Martin (3627248)
Nancy Engle (3436811)
Jonathan Mielenz (3627242)
Intawat Nookaew (163890)
Steven Brown (637397)
Timothy Tschaplinski (3436805)
David Ussery (81242)
Robert Hettich (3455141)

January 2017

Additional file 8: Fig. S1. Temporal expression based clustering of proteins differentially expresse...

Functional genomics of pH homeostasis in <it>Corynebacterium glutamicum </it>revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Persicke Marcus
Hüser Andrea
Rückert Christian
Poetsch Ansgar
Trötschel Christian
Krämer Reinhard
Ochrombel Ines
Follmann Martin
Seiferling Dominic
Kalinowski Jörn
Marin Kay

December 2009

Abstract Background The maintenance of internal pH in bacterial cells is challenged by natural stres...

Table_1_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

Table_3_Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production.XLSX

Julia D. Hofmann (5182013)
Andreas Otto (204448)
Mareike Berges (5648108)
Rebekka Biedendieck (282150)
Annika-Marisa Michel (5648111)
Dörte Becher (90765)
Dieter Jahn (9897)
Meina Neumann-Schaal (3399446)

August 2018

The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium diffic...

MOESM6 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Abstract

Extracted data

MOESM6 of Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

Abstract

Extracted data

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