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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Bioeng. Biotechnol.</journal-id>
<journal-title>Frontiers in Bioengineering and Biotechnology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Bioeng. Biotechnol.</abbrev-journal-title>
<issn pub-type="epub">2296-4185</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">766674</article-id>
<article-id pub-id-type="doi">10.3389/fbioe.2021.766674</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Bioengineering and Biotechnology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Genomics Characterization of an Engineered <italic>Corynebacterium glutamicum</italic> in Bioreactor Cultivation Under Ionic Liquid Stress</article-title>
<alt-title alt-title-type="left-running-head">Banerjee et&#x20;al.</alt-title>
<alt-title alt-title-type="right-running-head">Genomics of Engineered <italic>Corynebacterium glutamicum</italic>
</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Banerjee</surname>
<given-names>Deepanwita</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="fn" rid="fn1">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1263339/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Eng</surname>
<given-names>Thomas</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="fn" rid="fn1">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/912595/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sasaki</surname>
<given-names>Yusuke</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1462644/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Srinivasan</surname>
<given-names>Aparajitha</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1459663/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Oka</surname>
<given-names>Asun</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Herbert</surname>
<given-names>Robin A.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/912609/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Trinh</surname>
<given-names>Jessica</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Singan</surname>
<given-names>Vasanth R.</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/334840/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Sun</surname>
<given-names>Ning</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/608619/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Putnam</surname>
<given-names>Dan</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Scown</surname>
<given-names>Corinne D.</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff6">
<sup>6</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/199437/overview"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Simmons</surname>
<given-names>Blake</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/75460/overview"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Mukhopadhyay</surname>
<given-names>Aindrila</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="corresp" rid="c001">&#x2a;</xref>
<uri xlink:href="https://loop.frontiersin.org/people/34841/overview"/>
</contrib>
</contrib-group>
<aff id="aff1">
<label>
<sup>1</sup>
</label>Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, <addr-line>Emeryville</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<aff id="aff2">
<label>
<sup>2</sup>
</label>Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, <addr-line>Berkeley</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<aff id="aff3">
<label>
<sup>3</sup>
</label>Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, <addr-line>Emeryville</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<aff id="aff4">
<label>
<sup>4</sup>
</label>Joint Genome Institute, Lawrence Berkeley National Laboratory, <addr-line>Berkeley</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<aff id="aff5">
<label>
<sup>5</sup>
</label>Department of Plant Sciences, University of California, Davis, <addr-line>Davis</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<aff id="aff6">
<label>
<sup>6</sup>
</label>Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, <addr-line>Berkeley</addr-line>, <addr-line>CA</addr-line>, <country>United&#x20;States</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>
<bold>Edited by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/631730/overview">Yu Wang</ext-link>, Tianjin Institute of Industrial Biotechnology (CAS), China</p>
</fn>
<fn fn-type="edited-by">
<p>
<bold>Reviewed by:</bold> <ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/401355/overview">Xinqing Zhao</ext-link>, Shanghai Jiao Tong University, China</p>
<p>
<ext-link ext-link-type="uri" xlink:href="https://loop.frontiersin.org/people/466468/overview">Julio Augusto Freyre-Gonzalez</ext-link>, National Autonomous University of Mexico, Mexico</p>
</fn>
<corresp id="c001">&#x2a;Correspondence: Aindrila Mukhopadhyay, <email>amukhopadhyay@lbl.gov</email>
</corresp>
<fn fn-type="equal" id="fn1">
<label>
<sup>&#x2020;</sup>
</label>
<p>These authors have contributed equally to this work and share first authorship</p>
</fn>
<fn fn-type="other">
<p>This article was submitted to Synthetic Biology, a section of the journal Frontiers in Bioengineering and Biotechnology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>18</day>
<month>11</month>
<year>2021</year>
</pub-date>
<pub-date pub-type="collection">
<year>2021</year>
</pub-date>
<volume>9</volume>
<elocation-id>766674</elocation-id>
<history>
<date date-type="received">
<day>29</day>
<month>08</month>
<year>2021</year>
</date>
<date date-type="accepted">
<day>27</day>
<month>10</month>
<year>2021</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2021 Banerjee, Eng, Sasaki, Srinivasan, Oka, Herbert, Trinh, Singan, Sun, Putnam, Scown, Simmons and Mukhopadhyay.</copyright-statement>
<copyright-year>2021</copyright-year>
<copyright-holder>Banerjee, Eng, Sasaki, Srinivasan, Oka, Herbert, Trinh, Singan, Sun, Putnam, Scown, Simmons and Mukhopadhyay</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these&#x20;terms.</p>
</license>
</permissions>
<abstract>
<p>
<italic>Corynebacterium glutamicum</italic> is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence <italic>vs</italic> absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50&#xa0;mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an <italic>C. glutamicum</italic> strain engineered to produce&#x20;IP.</p>
</abstract>
<kwd-group>
<kwd>
<italic>Corynebacterium glutamicum</italic>
</kwd>
<kwd>RNAseq</kwd>
<kwd>fed-batch</kwd>
<kwd>bioreactor</kwd>
<kwd>ionic Liquid</kwd>
<kwd>isopentenol</kwd>
<kwd>acetoin</kwd>
<kwd>lignin hydrolysate</kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="s1">
<title>Introduction</title>
<p>Due to process advantages, biological methods for the production of amino acids over chemical synthesis methods fostered the identification of natural glutamine overproducing microbes (<xref ref-type="bibr" rid="B35">Kinoshita et&#x20;al., 1958</xref>). Since then, <italic>Corynebacterium glutamicum</italic> has been used successfully to produce specialty glutamine and specialty amino acids to meet global demand. The advent of accessible whole-genome sequencing and mutagenesis methods have enabled a clearer understanding of how specific isolates can overproduce these desired molecules, as well as how they maintain productivity across volumetrically-larger scales (<xref ref-type="bibr" rid="B7">Becker et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B54">P&#xe9;rez-Garc&#xed;a and Wendisch, 2018</xref>; <xref ref-type="bibr" rid="B77">Wolf et&#x20;al., 2021</xref>). Using <italic>C. glutamicum</italic> to produce non-native metabolites as next-generation biofuels is an attractive large-volume market with the potential to reduce global carbon emissions. Potential biofuels can be produced from terpenes, which use different metabolic precursors (reviewed in (<xref ref-type="bibr" rid="B54">P&#xe9;rez-Garc&#xed;a and Wendisch, 2018</xref>)). We have previously described the heterologous expression of the terpenoid isopentenol (IP; also known as 3-methyl-3-buten-1-ol or isoprenol) pathway in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>). IP can be used directly as a drop-in biogasoline (<xref ref-type="bibr" rid="B59">Reninger and McPhee, 2008</xref>; <xref ref-type="bibr" rid="B12">Chou and Keasling, 2012</xref>) or as a precursor to a jet fuel, DMCO (<xref ref-type="bibr" rid="B4">Baral et&#x20;al., 2021</xref>). Producing IP was improved using optimal pathway homologs, specific media formulation and aeration conditions and an empirically determined carbon/nitrogen ratio (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>).</p>
<p>In this study we build upon this established system to analyze the behavior of <italic>C. glutamicum</italic> strains engineered to produce IP in a bioreactor. The bioreactor cultivation and process conditions can provide key diagnostic information essential to build robust production platform strains (<xref ref-type="bibr" rid="B76">Wehrs et&#x20;al., 2019</xref>). In addition, it is also valuable to understand microbial response to the carbon feedstock that is anticipated for actual production. Here, we explore the use of plant-based lignocellulosic hydrolysate generated using ionic liquid (IL) as a pretreatment reagent. Toxicity from residual pretreatment reagents such as ILs is a known source of growth impediment (<xref ref-type="bibr" rid="B23">Hou et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B64">Santos et&#x20;al., 2014</xref>). <italic>C. glutamicum</italic> is tolerant to many ILs, another attribute that makes it an ideal host for biomass conversion (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>). In this study, we characterize an IP-producing engineered <italic>C. glutamicum</italic> strain with long-read Pacific Biosciences (PacBio) whole-genome sequencing. This high-quality assembly allowed accurate mapping for differential RNA expression analysis from a diagnostic fed-batch <italic>C. glutamicum</italic> IP production run. These side-by-side experiments characterize the cellular response to the IL, cholinium lysinate ([Ch][Lys]), when grown in a fed-batch stirred tank bioreactor.</p>
</sec>
<sec sec-type="results" id="s2">
<title>Results</title>
<sec id="s2-1">
<title>Characterization of Isopentenol Production and Ionic Liquid Tolerance in <italic>C. glutamicum</italic> Strains</title>
<p>We established that the strain reported in <xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>, <italic>C. glutamicum</italic> (previously referred to as ATCC 13032 NHRI 1.1.2) outperformed another isolate, ATCC 13032&#x20;&#x2206;<italic>cglIM</italic> &#x2206;<italic>cgLIR</italic> &#x2206;<italic>cgLIIR</italic> (referred to as <italic>&#x201c;&#x2206;mrr&#x201d;</italic>) (<xref ref-type="fig" rid="F1">Figure&#x20;1A</xref>). <italic>C. glutamicum</italic> &#x2206;<italic>mrr</italic> was first described in <xref ref-type="bibr" rid="B6">Baumgart et&#x20;al., 2013</xref> and is a methylation-deficient strain widely used due to its improved plasmid transformation and genomic integration rate (<xref ref-type="bibr" rid="B66">Sch&#xe4;fer et&#x20;al., 1997</xref>; <xref ref-type="bibr" rid="B6">Baumgart et&#x20;al., 2013</xref>). When <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 is used in conjunction with an IP production pathway, it can produce 300&#xa0;mg/L IP from pure glucose, but the product titers are near the lower detection limit by GC-FID in the <italic>C. glutamicum</italic> ATCC 13032&#x20;&#x2206;<italic>mrr</italic> strain. While only <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 produced IP, both the type strain and this specific isolate tolerate high concentrations of exogenous ILs (<xref ref-type="fig" rid="F1">Figure&#x20;1B</xref>), suggesting that IL tolerance was a shared feature between these two isolates despite differences in IP production.</p>
<fig id="F1" position="float">
<label>FIGURE 1</label>
<caption>
<p>Growth and isopentenol production characterization of two genetically distinct engineered <italic>C. glutamicum</italic> strains, <bold>(A)</bold> Isopentenol (IP) production in <italic>C. glutamicum</italic> strains of the genotypes indicated harboring an IP production plasmid. Cells were cultivated in 24-well deep well plates. IP titers reported at 48-h time points are corrected for evaporation in this plate format (Materials and Methods), <bold>(B)</bold> Growth curves for <italic>C. glutamicum</italic> strains of the indicated strain backgrounds cultivated in CGXII media in the presence or absence of the IL, cholinium lysinate ([Ch][Lys]), [Ch][Lys] was exogenously added to the culture media at the start of the time course, <bold>(C)</bold> Production of IP from <italic>C. glutamium</italic> grown in CGXII minimal media with pure glucose (4% w/v) or ensiled [Ch][Lys] pretreated sorghum hydrolysate. An optimized IP production plasmid carrying a <italic>hmgR</italic> variant from <italic>Silicibacter pomeroyi</italic> was used. The optical density of cultures as a proxy for cell density is noted on the right-hand panel.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g001.tif"/>
</fig>
<p>We also confirmed the ability of <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 to handle renewable carbon streams from sorghum biomass using an improved carbon extraction protocol enhanced by the use of ensiled biomass (<xref ref-type="bibr" rid="B45">Magurudeniya et&#x20;al., 2021</xref>). The ensiling process enables naturally occurring lactic-acid secreting bacteria to partially decompose the hemicellulose in sorghum while stored in a silo before downstream processing. After ensiling, the biomass was pretreated with [Ch][Lys] followed by enzymatic saccharification (Materials and Methods). This hydrolysate contained 48.7&#xa0;g/L glucose, 17.9&#xa0;g/L xylose, and trace concentrations of aromatic compounds. Our optimized <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 with an optimized IP production system had no detected growth defects when grown with 58% (v/v) hydrolysate supplemented media and produced 1&#xa0;g/L IP from pure glucose or &#x223c;600&#xa0;mg/L IP from sorghum hydrolysate (<xref ref-type="fig" rid="F1">Figure&#x20;1C</xref>). These results showcase its versatility with handling actual plant biomass derived carbon streams. For the remainder of this study, we focus on characterizing the genetic differences present in <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 relative to other closely related <italic>C. glutamicum</italic> strains that might explain the IP production values between these two strains.</p>
</sec>
<sec id="s2-2">
<title>Genomic Characterization of <italic>C. glutamicum</italic> BRC-JBEI 1.1.2</title>
<p>While 16S rRNA sequencing suggested that <italic>C. glutamicum</italic> &#x2206;<italic>mrr</italic> strain as in the <italic>C. glutamicum</italic> ATCC 13032 strain background, this same method indicated that <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 is related to <italic>C. glutamicum</italic> CICC10112 or SCgG1/SCgG2. To overcome the limitation inherent to 16S rRNA-based identification, we turned to using whole genome sequencing. Only SCgG1 and SCgG2 have been characterized with whole-genome sequencing, and to our knowledge there was no additional information about <italic>C. glutamicum</italic> CICC10112 beyond the partial 16S ribosomal sequence. As 16S rRNA is inconclusive for isolate-level identification (<xref ref-type="bibr" rid="B62">Sabat et&#x20;al., 2017</xref>; <xref ref-type="bibr" rid="B21">Hahne et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B28">Johnson et&#x20;al., 2019</xref>), we reasoned that the whole-genome sequencing in this IP producing strain would ensure an accurate reference genome in downstream RNAseq analysis if the improved performance observed in this strain was due to variations in the strain background. One of the major limitations in short-read sequencing is the difficulty in assembling overlapping contigs to generate a high-quality <italic>de novo</italic> assembly of a single contiguous read. Therefore, we chose PacBio long-read sequencing (<xref ref-type="bibr" rid="B36">Koren and Phillippy, 2015</xref>) for optimal coverage over short read sequencing as a potential solution. However, routine methods for lysing and isolating <italic>C. glutamicum</italic> genomic DNA were insufficient for building high-quality genome assemblies since the physical lysis method we employed (<xref ref-type="bibr" rid="B14">Eng et&#x20;al., 2018</xref>) shears DNA to fragments ranging from 2 to 8&#xa0;kb in size. Detergent-based lysis methods failed to extract genomic DNA, even with prolonged incubation times. We developed a method to isolate larger DNA fragments approximately 20&#xa0;kb in size for the PacBio Sequel (Pacific Biosciences) assembly pipeline using a zymolyase protease treatment for cell lysis (see Materials and Methods). This modified DNA extraction protocol enabled us to use PacBio long read sequencing to generate a high-quality <italic>de novo</italic> genome assembly.</p>
<p>We now report a new genome assembly of a single contiguous scaffold of 3,352,276 bases with 53.83% GC content (<xref ref-type="fig" rid="F2">Figure&#x20;2</xref>). Genome-wide average nucleotide identity (ANI) confirmed this isolate was 99.9987% identical to <italic>C. glutamicum</italic> SCgG1 and SCgG2 as well as another sequenced <italic>C. glutamicum</italic> isolate, Z188. The average nucleotide identity alignment for the 28 sequenced <italic>C. glutamicum</italic> isolates has been deposited at the database of the Joint Genome Institute (<ext-link ext-link-type="uri" xlink:href="https://genome.jgi.doe.gov/portal/">https://genome.jgi.doe.gov/portal/</ext-link>), Project ID 1203597 and is also included in <xref ref-type="sec" rid="s10">Supplementary Table S1</xref>. <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 differs from SCgG1 only by a few single nucleotide polymorphisms (&#x223c;10) and two additional genes that are absent from SCgG1, a putative transposase and a hypothetical protein coding sequence that is 414&#xa0;bp in length. When <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 was compared with more commonly used reference strains, <italic>C. glutamicum</italic> R and 13032 (Bielefeld), we identified genomic islands encoding genes unique to BRC-JBEI 1.1.2. Genome topology analysis also identified a 140&#xa0;kb inversion in the genome of BRC-JBEI 1.1.2 isolate (<xref ref-type="fig" rid="F2">Figure&#x20;2A</xref>). Out of 3,097 genes, homology mapping indicated that 85% (2,641 genes) were at least 80% identical to known genes in <italic>C. glutamicum</italic> ATCC 13032. With a less restrictive % identity threshold of 50%, the identical ratio could account for 89% (2,777 genes). Nonetheless, 320 genes did not meet the minimum % identity threshold and could not be annotated with this reference genome (<xref ref-type="sec" rid="s10">Supplementary Figure&#x20;S1</xref>).</p>
<fig id="F2" position="float">
<label>FIGURE 2</label>
<caption>
<p>Comparison of the <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 strain with closely related <italic>C. glutamicum</italic> strains, <bold>(A)</bold> A meta-analysis of gene function using clusters of orthologous genes (COGs) analysis. The total number of genes in each category for each strain is represented with colored bars as indicated, <bold>(B)</bold> Mauve genome alignment of <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 with <italic>C. glutamicum</italic> R and 13032 (Bielefeld). Similar genomic regions share the same color across the three different genomes compared. A 140&#xa0;kb chromosomal inversion is highlighted in light blue, and the relative direction of the inversion in each strain is indicated with a black arrow. Individual genes are indicated with open rectangles underneath the colored&#x20;area.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g002.tif"/>
</fig>
<p>Some of these unknown genes that were unique to BRC-JBEI 1.1.2 might be related to the catabolism of IL. Intriguingly, a putative choline dehydrogenase, <italic>Ga0373873_2846</italic>, showed only 40% identity to other known choline dehydrogenases primarily found in Gram-negative microbes such as <ext-link ext-link-type="uri" xlink:href="https://fitprivate.genomics.lbl.gov/cgi-bin/org.cgi?orgId=BFirm">
<italic>Burkholderia phytofirmans</italic> PsJN</ext-link> and <ext-link ext-link-type="uri" xlink:href="https://fitprivate.genomics.lbl.gov/cgi-bin/org.cgi?orgId=Cup4G11">
<italic>Cupriavidus basilensis</italic> FW507-4G11</ext-link>. Meta-COG analysis of these four <italic>C. glutamicum</italic> genomes revealed that <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 contains over 100 additional genes related to the transport or metabolism of inorganic ions, carbohydrates, and amino acids, suggesting a broader metabolic capacity to utilize a more significant number of substrates than the type strain (<xref ref-type="fig" rid="F2">Figure&#x20;2</xref>). In summary, this genome sequencing analysis was valuable for characterizing differences between <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 and the more routinely studied type strain ATCC 13032. Due to its similarity with SCgG1 and SCgG2, <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 is likely an industrial glutamate overproducing isolate but has more annotations in the inorganic ion and amino acid transport and metabolism COG categories than its nearest neighbors, SCgG1, SCgG2, and Z188 that need further characterization.</p>
</sec>
<sec id="s2-3">
<title>Transcriptome Analysis Identifies Changes in <italic>C. glutamicum</italic> Beyond Metabolism During Scale-Up</title>
<p>Next, we sought to build a systems-level understanding of <italic>C. glutamicum</italic> gene expression changes in bioreactors upon exogenous IL treatment. This data could be useful for subsequent Design-Build-Test-Learn (DBTL) cycles in providing the diagnostic information for future strain optimization strategies (<xref ref-type="bibr" rid="B52">Opgenorth et&#x20;al., 2019</xref>). We prepared samples from sequential time points during a scaleup campaign to analyze shifts in gene expression as a proxy for changes in metabolic and regulatory behavior in both [Ch][Lys] treated and untreated runs. First, we determined if the failure to produce IP was due to loss of the production pathway, possibly due to loss of the plasmid-borne IP pathway genes. The IP production pathway is composed of 5 genes in 2 adjacent operons under the <italic>trc</italic> and <italic>lacUV5</italic> promoters, namely <italic>mk, pmd</italic> and <italic>atoB, hmgS, hmgR</italic> respectively. Using the transcripts per million (TPM) metrics, we examined absolute gene expression levels as well as changes over the course of the production campaign. The IP pathway started off high for both <italic>hmgR</italic> and <italic>hmgS</italic> in the shake flask (200,000 TPM), but expression of these two genes decreased between 10-16x over the duration of the 65-h fed batch. Expression amounts of <italic>atoB</italic> in the shake flask were comparatively lower (1,500 TPM) but decreased 4x at the shake flask to bioreactor transition. <italic>atoB</italic> TPM counts remained low for the duration of the subsequent time points. Since the pathway genes were still expressed during this run, we then focused on analyzing gene expression changes in the native <italic>C. glutamicum</italic> genome.</p>
<p>To interpret the differential gene expression results with genes identified in the new assembly for <italic>C. glutamicum</italic> BRC-JBEI 1.1.2, we mapped gene names and identifiers from <italic>C. glutamicum</italic> ATCC 13032 back onto the open reading frames (ORFs) in <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 as genes in the type strain genome have been broadly characterized. We used a medium confidence cutoff of 70% identity to capture most homologs when analyzing this dataset. First, we characterised gene expression upon inoculating cells from the seed culture in a shake flask to the bioreactor. This differential gene expression (DEG) was calculated as the ratio of an early time point in the bioreactor (6.5&#xa0;h post inoculation in the stirred tank) divided by values from the seed culture immediately before transfer. This time point was chosen to give cells approximately three doublings to ensure the cells were rapidly growing under these new conditions. The result showed differential expression of 258 genes after 6.5&#xa0;h (<xref ref-type="fig" rid="F3">Figure&#x20;3</xref>, and <xref ref-type="sec" rid="s10">Supplementary Dataset&#x20;S1</xref>).</p>
<fig id="F3" position="float">
<label>FIGURE 3</label>
<caption>
<p>Genome wide expression differences in diverse cellular processes upon shifting to a stirred tank bioreactor, <bold>(A)</bold> <italic>Left side.</italic> Schematic showing scale transition from 25&#xa0;ml seed culture of IP producing <italic>C. glutamicum</italic> in CGXII media to a stirred tank bioreactor. <italic>Right side.</italic> Volcano plot comparing differential gene expression (6.5&#xa0;h post inoculation /shake flask) via RNAseq analysis to absolute confidence (<italic>p</italic> value) of the same time points. Fold changes greater than 4 (log<sub>2</sub> &#x3d; 2) and absolute confidence values &#x3e; 2 (<italic>p</italic>&#x20;&#x3c; 0.001) are considered significant. The threshold for significance is demarcated with dotted lines and the corresponding genes are colored blue. Genes with insignificant differential expression are indicated in grey. Genes with confidence values &#x3e; 40 are placed above the break on the <italic>y</italic> axis, <bold>(B)</bold> Analysis of gene classes enriched in the scale transition. Differentially expressed genes from a) were binned into functional categories based on COG annotations and putative function by BLAST alignment. Upregulated genes are indicated in dark blue; downregulated genes are indicated in light&#x20;red.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g003.tif"/>
</fig>
<sec id="s2-3-1">
<title>Overexpressed Metabolic Genes</title>
<p>Many genes encoding metabolic functions were differentially expressed in the transition from shake flask to stirred tank format. We used a fold change cutoff of 4 (log<sub>2</sub> &#x3e; 2) and a <italic>p</italic> value &#x3c; 0.001 to identify both large and statistically significant changes (<xref ref-type="fig" rid="F3">Figure&#x20;3A</xref>). Gene ontology (GO) (<xref ref-type="bibr" rid="B2">Ashburner et&#x20;al., 2000</xref>) enrichment annotations identified the highest number of DEGs belonging to metabolism and transport processes (<xref ref-type="fig" rid="F3">Figure&#x20;3B</xref>). The strongest fold changes (16-fold increase or higher) were in metabolism; Cgl2807 (<italic>adhA</italic>, zinc dependent alcohol dehydrogenase), Cgl1396 (acetylglutamate kinase), Cgl2886 and Cgl2887 (two FAD-dependent oxidoreductases) and Cgl3007 (<italic>mez,</italic> malic enzyme). Of these genes, Cgl2807/<italic>adhA</italic> encodes for a Zn-dependent alcohol dehydrogenase that together with Cgl2796 has been reported to maintain redox balance (<xref ref-type="bibr" rid="B80">Zhang et&#x20;al., 2018</xref>). While the cells had been previously adapted in CGXII medium for the seed culture, we observed differentially increased gene expression of several amino acid biosynthesis pathways. Increased gene expression for nearly complete pathways needed for methionine, leucine, and arginine biosynthesis were detected, as well as the gene responsible for glutamate synthesis, <italic>gdh</italic>. Three genes responsible for the conversion of propionate to succinate and pyruvate through the methylcitrate cycle were also upregulated. Upregulated DEGs encoding for myo-inositol metabolism directing flux towards acetyl-CoA and DHAP included Cgl0163/<italic>iolE,</italic> Cgl0161/<italic>iolB,</italic> Cgl0158/<italic>iolC</italic>, Cgl0160/<italic>iolA/msmA</italic>, and Cgl0157/<italic>iolR.</italic> Of the myo-inositol pathway genes, <italic>iolR</italic> was reported to regulate PTS-independent glucose uptake by repressing the expression of glucokinases in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B81">Zhou et&#x20;al., 2015</xref>). The upregulation of myo-inositol catabolic pathways could be attributed to supplemental yeast extract amended to the CGXII medium in the bioreactor. Yeast extract was added to the bioreactors as it was found to improve IP production in <italic>Escherichia coli</italic> (<xref ref-type="bibr" rid="B30">Kang et&#x20;al., 2019</xref>). Inositol is found in the yeast extract (&#x3e;160&#xa0;mg/g range) for many commercial preparations.</p>
</sec>
<sec id="s2-3-2">
<title>Overexpressed Regulatory and Stress Responsive Genes</title>
<p>A wide range of regulatory factors and stress responsive genes were also upregulated at the shake flask to bioreactor transition time point. Cgl2988/<italic>malR</italic>, which encodes for a MarR type transcriptional regulator and Cgl3007/<italic>mez</italic> were both highly upregulated. MalR represses expression of the malic enzyme gene, <italic>mez</italic> (<xref ref-type="bibr" rid="B38">Krause et&#x20;al., 2012</xref>) and is a global regulator of stress-responsive cell envelope remodeling in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B25">H&#xfc;nnefeld et&#x20;al., 2019</xref>). Cgl2996/<italic>ino-1</italic> (myo-inositol-1-phosphate synthase) is the first enzyme in mycothiol biosynthesis and plays a major role in the detoxification of stress-inducing factors, maintaining the redox balance and protection against oxidative stress (<xref ref-type="bibr" rid="B82">Chen et&#x20;al., 2019</xref>). The universal stress response protein Cgl1407/<italic>uspA2</italic> and HSP 60 family chaperonin, Cgl2716/<italic>groEL</italic> were also upregulated.</p>
</sec>
<sec id="s2-3-3">
<title>Underexpressed Metabolic, Transporter and Regulatory Genes</title>
<p>A similar number of genes were downregulated during the transition from shake flask to bioreactor (<xref ref-type="fig" rid="F3">Figure&#x20;3B</xref>). Of the genes uniquely downregulated at 6.5&#xa0;h, included Cgl1427/<italic>cmk,</italic> cytidyl kinase, Cgl2605/<italic>bioD,</italic> thioredoxin reductase. Cgl1427 has been reported to be crucial for maintaining triphosphate pools (ATP, CTP) under oxygen-limiting environments (<xref ref-type="bibr" rid="B70">Takeno et&#x20;al., 2013</xref>) but it&#x2019;s downregulation implies these early time points are not oxygen-limited. Several genes involved in transport were also significantly downregulated with a cutoff threshold log<sub>2</sub> ratio less than &#x2212;4. These included ABC transporter ATPase proteins Cgl1351, Cgl1546/<italic>pacL</italic> (cation specific) and Cgl1567 along with Cgl2222, a major facilitator superfamily (MFS) transporter. Downregulated genes Cgl0026-Cgl0029 have been reported to be Zur-binding sites that are involved in zinc homeostasis in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B67">Schr&#xf6;der et&#x20;al., 2010</xref>). Other downregulated transporters included the lysine exporter Cgl1262/<italic>lysE,</italic> exporter systems for branched chain amino acid and methionine (<italic>brnE/brnF</italic>) along with several MFS transporters (Cgl1065, Cgl1076/<italic>pcaK</italic>, Cgl0380, Cgl0381, Cgl2685/<italic>lmrB</italic>) and the ABC type phosphate uptake system (<italic>pstSCAB</italic>). Several other ABC transporter subunits (permease or substrate-binding domain or the ATPase) responsible for transport of iron, calcium, cobalt, cadmium, copper, sn-glycerol-3-phosphate were also downregulated. Downregulated transcriptional regulators during this scale transition phase belong to the GntR family (Cgl2316), ArsR family (Cgl2279), PadR family (Cgl2979) and CopY family (Cgl0385). A complete list of DEGs can be found in <xref ref-type="sec" rid="s10">Supplementary Dataset S1 through S6</xref> and at the JGI Genome Portal (<ext-link ext-link-type="uri" xlink:href="https://genome.jgi.doe.gov/portal/">https://genome.jgi.doe.gov/portal/</ext-link>) under Project ID 1203597.</p>
</sec>
</sec>
<sec id="s2-4">
<title>Metabolic Pathway Alterations During Fed-Batch Cultivation Indicated by Differentially Expressed Genes</title>
<p>After inoculation into the bioreactors, we benchmarked the bioreactor run with online and offline measurements including growth, glucose consumption, and organic acid secretion, with and without [Ch][Lys]. We noted several differences between cells grown in the control reactor and the [Ch][Lys] treated reactor. While cells were pulse-fed the same feed solution to restore glucose levels back to 60&#xa0;g/L, the [Ch][Lys] treated engineered strain produced much less acetate and succinate than the control (<xref ref-type="fig" rid="F4">Figures 4A</xref>, <xref ref-type="fig" rid="F5">5A</xref>). Overall OD<sub>600</sub> measurements indicated similar initial growth patterns before the first feeding, but after feeding, OD<sub>600</sub> measurements did not appreciably increase further and instead we detected overflow metabolite accumulation above 10&#xa0;g/L of succinate and acetate (<xref ref-type="fig" rid="F4">Figure&#x20;4A</xref>). The control reactor decreased in OD<sub>600</sub> from a high of 49 to a 21 OD<sub>600</sub>. The [Ch][Lys] reactor also decreased in OD<sub>600</sub>, but from a similar high of 50 to 36 OD<sub>600</sub> (<xref ref-type="sec" rid="s10">Supplementary Figure S2</xref>). We correlated gene expression changes during this campaign for both reactors using RNAseq analysis to understand how glucose was redirected from growth to the generation of these overflow metabolites (<xref ref-type="sec" rid="s10">Supplementary Dataset&#x20;S2</xref>).</p>
<fig id="F4" position="float">
<label>FIGURE 4</label>
<caption>
<p>Growth of engineered <italic>C. glutamicum</italic> for IP in a control stir tank bioreactor, <bold>(A)</bold> HPLC analysis of glucose and organic acids detected in the 2&#xa0;L stirred tank bioreactor. Cells were harvested from the indicated time points with (&#x2a;). Refer to <xref ref-type="fig" rid="F5">Figure&#x20;5A</xref> for the [Ch][Lys] treated bioreactor. <bold>(B)</bold> Shared and unique differentially expressed genes. Venn diagrams indicate the number of Upregulated (<italic>left)</italic> and downregulated (<italic>right)</italic> genes at the indicated time points, <bold>(C)</bold> Hierarchical cluster analysis of the top 181 differentially expressed genes at the 65-h time point vs. the 6.5&#xa0;h time point for both up or down regulation. A number of genes that are highly expressed only in stationary phase <italic>vs</italic> constitutively expressed are observed.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g004.tif"/>
</fig>
<fig id="F5" position="float">
<label>FIGURE 5</label>
<caption>
<p>Differential expression of genes in response to 50&#xa0;mM of [Ch][Lys], <bold>(A)</bold> HPLC analysis of glucose and organic acids detected in the 2-L stirred tank bioreactor of cells grown in the presence of an initial concentration of 50&#xa0;mM [Ch][Lys]. Cells were harvested from the indicated time points with (&#x2a;). Refer to <xref ref-type="fig" rid="F4">Figure&#x20;4A</xref> for the control bioreactor. The glucose and organic acid values for the time course in this figure panel have been previously described in <xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>, <bold>(B)</bold> Volcano plots of differentially expressed genes for each time point. Genes which have confidence values or log<sub>2</sub> ratios greater than the maximum value on each axis are plotted on a discontinuous portion of the axis as indicated with a line break. c) Shared and unique differentially expressed genes in response to [Ch][Lys]. Very few differences were detected in the 6 and 16.5&#xa0;h time points and are not included in the Venn diagram. DEG was calculated as the ratio between the treated reactor and its corresponding time-matched sample in the other control reactor. Venn diagrams indicate the number of upregulated (<italic>left)</italic> and downregulated (<italic>right)</italic> genes at the indicated time points.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g005.tif"/>
</fig>
<sec id="s2-4-1">
<title>Differentially Expressed Metabolic Genes</title>
<p>We observed several genes encoding metabolic processes related to succinate and acetate metabolism were downregulated in the time course, such as <italic>ptaA, ackA</italic> and <italic>sucC.</italic> Decreasing their gene expression suggests a decrease in activity, enabling greater succinate or acetate accumulation due to fewer competing reactions for these metabolites as precursors. Cgl2211, a putative succinate exporter (<xref ref-type="bibr" rid="B24">Huhn et&#x20;al., 2011</xref>; <xref ref-type="bibr" rid="B44">Litsanov et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B55">Prell et&#x20;al., 2020</xref>) was upregulated at 65&#xa0;h, that might explain higher succinate excretion profile for the fed-batch cultivation in the absence of the IL (<xref ref-type="fig" rid="F4">Figure&#x20;4A</xref>). The higher acetate secretion in this bioreactor correlated with upregulated Cgl2066 transcripts at 24 and 41&#xa0;h, which encodes a putative acyl phosphatase that converts acetyl phosphate to acetate. At the last phase of cultivation Cgl2380/<italic>mdh</italic> was upregulated (log<sub>2</sub> ratio of 3.14) with 12-fold over expression. Malate dehydrogenase, <italic>mdh</italic>, is involved in a NADH based reversible reaction in TCA and is responsible for NADH balance maintenance and succinate formation. The malic enzyme, Cgl3007/<italic>mez,</italic> was downregulated across all later time points (log<sub>2</sub> ratio of &#x2212;3.1 to &#x2212;7.65), with 10-fold decrease in expression in the last time point alone. Malic enzyme, upregulated during transition from shake flask to a bioreactor scale (log<sub>2</sub> ratio of 5.11 at 6.5&#xa0;h), is involved in gluconeogenesis important for NADPH regeneration for anabolic processes and pyruvate flux at the cost of carbon loss as 1&#xa0;mole of CO<sub>2</sub>. The later time points (24&#xa0;h and later) had many shared downregulated genes (211 genes), indicating a phenotypic similarity (<xref ref-type="fig" rid="F4">Figure&#x20;4B</xref>). We also observed significant downregulation of <italic>adhA</italic>, <italic>ald</italic>, <italic>sucCD</italic>, <italic>malE/mez</italic> (<xref ref-type="fig" rid="F4">Figure&#x20;4C</xref>, blue colored genes)<italic>,</italic> which were previously reported during microaerobic aeration in a bioreactor cultivation of <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B40">Lange et&#x20;al., 2018</xref>).</p>
</sec>
<sec id="s2-4-2">
<title>Differentially Expressed Transporter Genes</title>
<p>A more comprehensive analysis of differential gene expression indicated that many transporters were upregulated in these bioreactor time points (<xref ref-type="fig" rid="F4">Figure&#x20;4C</xref>, red colored genes). These included ABC transporters for phosphonate (<italic>pctABCD</italic>); sn-glycerol-3-phosphate (<italic>ugpABCE</italic>) and phosphate (<italic>pstSCAB),</italic> a branched chain amino acid and methionine exporter (Cgl0258/<italic>brnF</italic>); Cgl0968/<italic>lysI</italic>, which encodes a protein involved in lysine uptake (<xref ref-type="bibr" rid="B68">Seep-Feldhaus et&#x20;al., 1991</xref>). Cgl1502, a putative MFS transporter (PTS based sugar importer) was upregulated in all later bioreactor cultivation time points. A different complement of transport-related genes were also downregulated across all the later time points that included genes encoding for maltose and trehalose ABC transporter subunits (Cgl2460 and Cgl0727) and the entire glutamate ABC transporter operon <italic>gluABCD</italic>.</p>
</sec>
<sec id="s2-4-3">
<title>Overexpressed Regulatory Genes</title>
<p>Transcriptional regulators that were upregulated across all the later time points of the bioreactor cultivation and were associated with putative functions included Cgl2496/PucR family, Cgl0962/TetR family, Cgl2934/MarR family, Cgl1367/LacI family and Cgl2616/LysR family. Cgl2776 which is a putative XRE family transcriptional regulator MsrR was found to be upregulated from 24 to 65&#xa0;h. <italic>msrR</italic> is located downstream of the <italic>cmr</italic> gene that encodes for a MFS multidrug efflux protein and upstream of Cgl2775/<italic>sseA1</italic>, a sulfurtransferase and Cgl2774. These late-phase upregulated genes have been previously reported to be regulated by MsrR and overexpressed in response to oxidative stress response in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B69">Si et&#x20;al., 2020</xref>). Genes under the control of DtxR, a master regulator of iron homeostasis at late exponential phase (<xref ref-type="bibr" rid="B39">K&#xfc;berl et&#x20;al., 2020</xref>), and AmtR, a master regulator of nitrogen metabolism (<xref ref-type="bibr" rid="B8">Beckers et&#x20;al., 2005</xref>) were also upregulated at later time points compared to 6.5&#xa0;h. The iron homeostasis genes included Cgl0387 (putative membrane protein) and Cgl2035, an ABC-type cobalamin/Fe<sup>3&#x2b;</sup>-siderophores transporter. The nitrogen metabolism regulon included genes encoding for ammonium permease, <italic>amt</italic>; a predicted ornithine decarboxylase (<italic>ocd</italic>) and the ABC transporter for urea UrtABCDE. Ammonium is a critical precursor for growth and tetramethylpyrazine (TMP) production (<xref ref-type="bibr" rid="B78">Xiao et&#x20;al., 2014</xref>). A regulator involved in diverting acetyl CoA flux towards fatty acid biosynthesis, Cgl2490/<italic>fasR</italic> was constitutively expressed up until the last time point during bioreactor cultivation in absence of IL. This TetR type transcriptional regulator controls fatty acid biosynthesis and malonyl CoA formation from acetyl CoA and has been deleted for improving malonyl CoA production (<xref ref-type="bibr" rid="B47">Milke et&#x20;al., 2019</xref>). Our analysis correlated this repression by <italic>fasR</italic> with down regulated Cgl2495/<italic>fas-IA</italic> as well as downregulation of Cgl0700/<italic>accBC</italic>, Cgl0708/<italic>dtsR1</italic> and Cgl0707/<italic>dtsR2</italic> during later time points in absence of&#x20;IL.</p>
</sec>
<sec id="s2-4-4">
<title>Underexpressed Cell Division Genes</title>
<p>Genes encoding cell division proteins including <italic>mraZ, ftsX, ftsW, ftsE, sepF,</italic> were downregulated for later stage cultivation time points (24&#xa0;h and later) correlating with the lack of increased OD<sub>600</sub> after glucose was fed at the 24-h time&#x20;point.</p>
</sec>
<sec id="s2-4-5">
<title>Differentially Expressed Genes at Endpoint Bioreactor Cultivation</title>
<p>We observed a unique class of genes that were only expressed after high accumulation of succinate and acetate at the 65-h time point. At this time point, glucose consumption has stalled, and the overflow organic acids have plateaued at the &#x223c;10&#xa0;g/L concentration. Genes encoding for ROS detoxification including catalase gene Cgl0255/<italic>katA</italic>, superoxide dismutase gene Cgl2927/<italic>sod</italic> along with Cgl2003/<italic>gor,</italic> a mycothione reductase involved in arsenate detoxification were upregulated. DEGs that were downregulated included genes encoding for <italic>catA2, catC, nagI</italic>, <italic>qsuB, benC and benD.</italic> These are enzymes involved in aromatic compound degradation through beta-ketoadipate pathway that would reroute flux into TCA through succinate and acetyl&#x20;CoA.</p>
<p>Together the differential gene expression profile suggests that at the cell density reached by 20&#xa0;h, there was a general cell stress response and the activation of microaerobic-specific genes. The growth conditions did not promote additional cell growth due to the downregulation of cell division genes; glucose uptake genes were still highly active, enabling a significant conversion of glucose to organic acids but not biomass accumulation. We interpret the expression of these genes as indicative of the unfavorable growth conditions.</p>
</sec>
</sec>
<sec id="s2-5">
<title>
<italic>C. glutamicum</italic> Exhibits a Complex Response to the IL, Cholinium Lysinate Under Fed-Batch Cultivation in the Bioreactor</title>
<p>Next we analyzed differential gene expression when cells were grown in the presence of 50&#xa0;mM [Ch][Lys], simulating hydrolysate prepared under a water-conservation regimen (<xref ref-type="bibr" rid="B50">Neupane et&#x20;al., 2017</xref>). ILs have been reported to increase osmotic pressure, interact with lipid structures and consequently disrupt microbial membranes (<xref ref-type="bibr" rid="B71">Thuy Pham et&#x20;al., 2010</xref>; <xref ref-type="bibr" rid="B32">Khudyakov et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B79">Yu et&#x20;al., 2016</xref>). <italic>C. glutamicum</italic> exhibited differential expression of 727 genes (<xref ref-type="sec" rid="s10">Supplementary Dataset S3</xref>), during the [Ch][Lys] treated fed-batch bioreactor cultivation in comparison to the untreated culture at the time-matched samples (<xref ref-type="fig" rid="F5">Figure&#x20;5A</xref>). While both bioreactors consumed the initial glucose in the reactor at similar rates, their response to the first feeding at 24&#xa0;h differed. The [Ch][Lys] reactor showed maximum accumulation of 4&#xa0;g/L succinate and 6&#xa0;g/L acetate over the duration of this time course, a 4-fold decrease for both organic acids in the absence of [Ch][Lys] (compare <xref ref-type="fig" rid="F4">Figures 4A</xref>, <xref ref-type="fig" rid="F5">5A</xref>). In the presence of [Ch][Lys], genes encoding for succinate utilization such as <italic>sdhA</italic>, <italic>sdhB</italic> and <italic>sdhC</italic> were all upregulated at 24 and 41&#xa0;h in contrast to the control reactor. Similarly, genes encoding for pyruvate decarboxylation to acetyl CoA (instead of acetate) via <italic>aceE</italic> and <italic>aceF</italic> were also highly upregulated at later time points.</p>
<p>During the early cultivation time points (6.5&#x2013;16.5&#xa0;h), only 1.5% of the total pool of differentially expressed genes changed in response specifically to [Ch][Lys], but the datasets diverged after the first feeding at 24&#xa0;h as biomass formation reached its maximum (<xref ref-type="fig" rid="F5">Figure&#x20;5B</xref>). Only two genes were upregulated at the 6.5&#xa0;h time point: a MFS transporter (Cgl2611) and its transcriptional regulator (Cgl2612) (<xref ref-type="sec" rid="s10">Supplementary Dataset S3</xref>). The BRC-JBEI 1.1.2 homolog is 97.37% identical to Cgl2611 which exports cadaverine, a L-lysine derived product (<xref ref-type="bibr" rid="B34">Kind et&#x20;al., 2011</xref>; <xref ref-type="bibr" rid="B1">Adkins et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B29">Jones et&#x20;al., 2015</xref>; <xref ref-type="bibr" rid="B72">Tsuge et&#x20;al., 2016</xref>). Cgl2611 expression was not detected at the control 6.5&#xa0;h time point, but both genes are highly upregulated with or without [Ch][Lys] treatment in the remaining time points. Cgl1203, which encodes a phospho-N-acetylmuramoyl- pentapeptide-transferase associated with cell wall biosynthesis, was only upregulated at 16.5&#xa0;h.</p>
<p>Early transcriptome changes in <italic>C. glutamicum</italic> during bioreactor cultivation post [Chl][Lys] exposure included overexpression of MFS transporters along with repression of mechanosensitive channels that were consistent with IL tolerance mechanisms reported in other microbes (<xref ref-type="bibr" rid="B32">Khudyakov et&#x20;al., 2012</xref>; <xref ref-type="bibr" rid="B46">Martins et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B79">Yu et&#x20;al., 2016</xref>). Many genes were downregulated in response to exogenous [Ch][Lys] in the bioreactor and represented 25% of DEGs. Cgl0879/<italic>mscL</italic>, a large-conductance mechanosensitive channel, that is related to osmotic regulation (<xref ref-type="bibr" rid="B37">Kr&#xe4;mer, 2009</xref>), was uniquely downregulated at 16.5&#xa0;h.</p>
<p>A comprehensive analysis of upregulated DEGs at more than one time point represented around 59% of the total upregulated genes in the presence of IL (<xref ref-type="fig" rid="F5">Figure&#x20;5B</xref>). Nearly 15% of those genes showed consistent overexpression from 24&#xa0;h through 65&#xa0;h (<xref ref-type="fig" rid="F5">Figure&#x20;5C</xref>). This differential transcript profile reflects the metabolic perturbation over the course of the fed-batch cultivation after the initial glucose exhaustion followed by glucose pulse feeding and is depicted in <xref ref-type="fig" rid="F6">Figure&#x20;6</xref>. Prominent DEGs include those encoding for energy metabolism, amino acids biosynthesis, response to oxidative and other environmental stress conditions (<xref ref-type="sec" rid="s10">Supplementary Dataset&#x20;S4</xref>).</p>
<fig id="F6" position="float">
<label>FIGURE 6</label>
<caption>
<p>Differential transcript profiles of engineered <italic>C. glutamicum</italic> under fed-batch cultivation. Three DEGs corresponding to three discrete conditions that were analyzed are represented here: ST - scale transition from shake flask (SF) to early bioreactor cultivation (6.5&#xa0;h), BR - bioreactor later stage cultivation in the absence of IL and IL - bioreactor cultivation in the presence of IL compared to in the absence of IL. The heterologous pathway for IP production is shown in orange. Red crosses show the gene deletions in the <italic>C. glutamicum</italic> strain used in this study. Abbreviations: Acetyl-P, acetyl phosphate; Akg, alpha ketoglutarate; Arg, arginine; Asp, aspartate; <italic>atoB</italic>, acetyl-CoA acetyltransferase; Cit, citrate; Ch, cholinium; Cox, cytochrome oxidase; ETC, Electron transport chain; Fum, fumarate; Glx, glyoxylate; Glu, glutamate; Gln, glutamine; <italic>HMGS</italic>, hydroxymethylglutaryl-CoA synthase; <italic>HMGR</italic>, 3-hydroxy-3-methylglutaryl-CoA reductase; HMG CoA, 3-hydroxy-3-methyl-glutaryl-coenzyme A; Icit, isocitrate; IP, Isopentenol; Lys, lysine; Mal, malate; <italic>MK</italic>, mevalonate kinase; MVA, mevalonate; MVA-P, mevalonate; OAA, oxaloacetate; PMD, phosphomevalonate decarboxylase; Succ, succinate; Succ CoA, succinyl-CoA; Sdh, succinate dehydrogenase; TMP, tetramethylpyrazine.</p>
</caption>
<graphic xlink:href="fbioe-09-766674-g006.tif"/>
</fig>
<sec id="s2-5-1">
<title>Overexpressed Metabolic Genes</title>
<p>Genes involved in energy metabolism were highly upregulated during the later phase of fed-batch cultivation in the presence of IL compared to its absence. These included NADH dehydrogenase (Cgl1465), succinate dehydrogenase, <italic>sdhABC</italic> genes at 24 and 41&#xa0;h; cytochrome oxidase, <italic>ctaDCEF</italic>, cytochrome reductase, <italic>qcrCAB</italic> and the ATP synthase complex (Cgl1206 to Cgl1213) genes at 24, 41 and 65&#xa0;h. Amino acid biosynthetic genes upregulated at the later time points included the arginine biosynthetic genes <italic>argC, argJ, argB</italic> and <italic>argH</italic> at 65&#xa0;h and <italic>argG</italic> and <italic>argD</italic> at mid cultivation phase (41&#xa0;h). ArgJ protein was also enriched in the acetoin/TMP producing <italic>C. glutamicum</italic> strain (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>). Genes encoding for other amino acid biosynthesis included Cgl1139/<italic>metE</italic>, Cgl2446/<italic>metB</italic> and Cgl0653/<italic>metY</italic> at 24 and 41&#xa0;h from the methionine/homocysteine pathway; Cgl2204/<italic>ilvE</italic> at 24&#xa0;h and Cgl1273/<italic>ilvC</italic> at 24 and 41&#xa0;h in the branched amino acid pathway.</p>
</sec>
<sec id="s2-5-2">
<title>Overexpressed Genes Encoding Ribosomal Proteins</title>
<p>Several ribosomal proteins were significantly upregulated during the same cultivation phase (24 and 41&#xa0;h) including 30S ribosomal proteins S15 (Cgl1976/<italic>rpsO</italic>) and S18 (Cgl0866/<italic>rpsR</italic>); 50S ribosomal proteins L28 (Cgl0869/<italic>rpmB</italic>) and L15 (Cgl0542/<italic>rplO</italic>) along with the ribosome recycling factor Cgl2023/<italic>frr</italic>.</p>
</sec>
<sec id="s2-5-3">
<title>Overexpressed Transporter Genes</title>
<p>We also observed the upregulation of an ABC transporter (Cgl0946 and Cgl0947), a multidrug transport system (MTS) operon, in part regulated by its adjacent two-component system (TCS) (Cgl0948-Cgl0949, also upregulated). MTS offers a natural defense against toxic compounds and is reported to be upregulated in response to the non-ionic surfactant Tween 40 (<xref ref-type="bibr" rid="B27">Jiang et&#x20;al., 2020</xref>). Also, Cgl2312/<italic>ectP</italic>, a putative BCCT family transporter was overexpressed in the bioreactor with IL at 24&#xa0;h time point. This gene, an orthologue for <italic>betT</italic> gene in <italic>E.&#x20;coli</italic> and <italic>P. putida</italic>, was under-expressed in the bioreactor without IL at later time points (24 h, 41&#xa0;h). Betaine/carnitine/choline (BCCT) family transporters could enable cholinium uptake and catabolism. An array of other transporters and transcriptional regulators were also downregulated in the presence of IL (<xref ref-type="sec" rid="s10">Supplementary Dataset&#x20;S3</xref>).</p>
<p>While the analysis above compared matched time points with or without [Ch][Lys] treatment, we also included one additional analysis to examine DEGs from samples in the same reactor but as they progressed from the 41 to 65&#xa0;h time point (<xref ref-type="sec" rid="s10">Supplementary Figure S3</xref>, and <xref ref-type="sec" rid="s10">Supplementary Dataset S6</xref>). As observed from our earlier analysis in <xref ref-type="fig" rid="F4">Figure&#x20;4C</xref> a set of DEGs in the control bioreactor were detected, consistent with entry into the stationary phase. Significantly downregulated genes also included genes encoding for a stationary phase repressor protein/redox responsive transcription factor, <italic>whiB/</italic>Cgl0599 (<xref ref-type="bibr" rid="B74">Walter et&#x20;al., 2020</xref>) and a branched chain amino acid transporter (Cgl2250) (<xref ref-type="bibr" rid="B20">Graf et&#x20;al., 2019</xref>). Cgl2250 has been reported to be downregulated during the transition from exponential to stationary phase in <italic>C. glutamicum</italic> (<xref ref-type="bibr" rid="B41">Larisch et&#x20;al., 2007</xref>).</p>
</sec>
</sec>
<sec id="s2-6">
<title>Indication of Flux Rerouting in the Presence of IL Stress During Fed-Batch Bioreactor Cultivation</title>
<p>Our transcriptome analysis identified differential profiles for energy metabolism, amino acid biosynthesis and redox related genes as discussed in the previous section (<xref ref-type="fig" rid="F6">Figure&#x20;6</xref>). Several genes encoding for metabolic reactions related to acetoin and TMP accumulation were specifically upregulated in the presence of 50&#xa0;mM of [Ch][Lys] at the 24&#xa0;h or 41&#xa0;h time points (<xref ref-type="sec" rid="s10">Supplementary Dataset S3</xref>, <xref ref-type="sec" rid="s10">Supplementary Figure S4</xref>) when compared to the control samples at the same time points. Of the two subunits of the acetolactate synthase (ALS) <italic>ilvB and ilvN,</italic> the smaller regulatory subunit, Cgl1272/<italic>ilvN</italic> was upregulated in the presence of IL fed-batch cultivation when compared to the absence of IL at 24&#xa0;h. Acetolactate synthase in <italic>C. glutamicum</italic> takes part in diverting pyruvate flux towards branched chain amino acids biosynthesis and acetoin biosynthesis and could be a precursor to TMP (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>) (<xref ref-type="fig" rid="F5">Figure&#x20;5</xref>). Although branched chain amino acid biosynthesis has been extensively researched for engineering branched chain alcohol (e.g. isobutanol) producing <italic>C. glutamicum</italic> strains (<xref ref-type="bibr" rid="B22">Hasegawa et&#x20;al., 2020</xref>) the branched chain amino acid degradation towards isopentenol biosynthesis (through HMG-CoA) and TCA through acetyl CoA still remains to be fully investigated. The other proposed enzyme in TMP accumulation is the NADH consuming acetoin reductase (AR, Cgl2674) and was also significantly upregulated (log<sub>2</sub> &#x3e; 4) at 41&#xa0;h in presence of 50&#xa0;mM of [Ch][Lys] compared to fed-batch cultivation in the absence of IL at similar time points. Genes encoding mechanisms that divert pyruvate flux towards acetyl CoA (Cgl2248/<italic>aceE</italic> and Cgl2207/<italic>aceF</italic>) were also upregulated along with genes for pyruvate kinase (Cgl2089/<italic>pyk</italic>) and citrate synthase (Cgl0829/<italic>gltA</italic>).</p>
</sec>
</sec>
<sec sec-type="discussion" id="s3">
<title>Discussion</title>
<p>
<italic>C. glutamicum</italic> is a strong contender as a microbial chassis for IP production and is already used at commercial scales. To test IP production in stirred-tank bioreactors, we used process optimizations empirically identified for high IP titers in <italic>E. coli</italic> (<xref ref-type="bibr" rid="B30">Kang et&#x20;al., 2019</xref>). In <italic>E.&#x20;coli</italic>, Kang et&#x20;al. reported IP titers &#x3e; 3&#xa0;g/L in fed-batch mode production; in contrast, these process parameters led to much lower IP titers in <italic>C. glutamicum</italic>. It is possible that these optimizations were specific to <italic>E.&#x20;coli;</italic> the impact of this IP production pathway in <italic>C. glutamicum</italic> upon shifting from batch mode to fed-batch mode in a stirred tank bioreactor may have resulted in a different host-specific metabolic response.</p>
<p>What parameters are important in selecting one microbial host over another? From a genetic tractability perspective, <italic>C. glutamicum</italic>&#x2019;s biggest drawback <italic>vs.</italic> model microbes such as <italic>E.&#x20;coli</italic> could arise from its reduced transformation efficiency, which was lower by 3&#x2013;5 orders of magnitude (<xref ref-type="bibr" rid="B13">Chung et&#x20;al., 1989</xref>; <xref ref-type="bibr" rid="B26">Inoue et&#x20;al., 1990</xref>; <xref ref-type="bibr" rid="B61">Ruan et&#x20;al., 2015</xref>). However, Baumgart and coworkers made an astute observation; by using a methylation deficient strain of <italic>C. glutamicum</italic>, one could both improve transformation efficiency as well as plasmid copy number (<xref ref-type="bibr" rid="B6">Baumgart et&#x20;al., 2013</xref>). Improved pathway copy number (both genomically integrated or plasmid-borne) in <italic>E.&#x20;coli</italic> had already been shown to dramatically improve heterologous isoprenoid titers (<xref ref-type="bibr" rid="B19">Goyal et&#x20;al., 2018</xref>; <xref ref-type="bibr" rid="B11">Chatzivasileiou et&#x20;al., 2019</xref>). With this premise we initially used a methylation deficient strain as our starting host. However, the methylation deficient strain only produced trace titers of IP, but a related strain produced both improved IP titers 20x or a co-product, tetra-methylpyrazine. Understanding the genetic differences in this isolate BRC-JBEI 1.1.2 was the major thrust of this&#x20;study.</p>
<p>Leveraging strain isolate differences is already commonplace when analyzing natively expressed products, such as natural products from <italic>Streptomyces</italic> spp. or wine, beer, and baking in <italic>Saccharomyces</italic> spp. (<xref ref-type="bibr" rid="B49">Nepal and Wang, 2019</xref>; <xref ref-type="bibr" rid="B16">Gallone et&#x20;al., 2016</xref>). In <italic>E.&#x20;coli</italic>, the Hanahan cloning strain DH1 is the preferred strain for the production of many terpenes, but experimentally identified modifications are needed to translate port pathways to other <italic>E.&#x20;coli</italic> isolates as with the case for limonene production in <italic>E.&#x20;coli</italic> BL21 (DE3) (<xref ref-type="bibr" rid="B73">Tsuruta et&#x20;al., 2009</xref>; <xref ref-type="bibr" rid="B60">Rolf et&#x20;al., 2020</xref>). A potential explanation for DH1 being a more robust host may be due to its elevated number of ribosomes compared to strains DH10, BL21, or BW25113 (<xref ref-type="bibr" rid="B10">Cardinale et&#x20;al., 2013</xref>), which may indirectly help with heterologous pathway protein expression. Our whole-genome sequencing analysis identified a large number of genetic differences in our engineered isopentenol producing <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 isolate (many associated with metabolic functions) that are unaccounted for when using the reference <italic>C. glutamicum</italic> genome. Previously we used computationally driven maximum theoretical yields calculations for a product across several microbes to evaluate microbial potential for a specific product/substrate pair (<xref ref-type="bibr" rid="B3">Banerjee et&#x20;al., 2020</xref>). However, the accuracy of such predictions relies on the metabolic reactions curated for the reference strain and are challenging to apply in isolates used with differences at the genomic or metabolic level (refer to IP titers in <xref ref-type="fig" rid="F1">Figure&#x20;1A</xref>). Pan-genome assemblies and metabolic models can be applied to this situation (both for BRC-JBEI 1.1.2 and DH1) to more accurately account for these metabolic features (<xref ref-type="bibr" rid="B48">Monk et&#x20;al., 2013</xref>; <xref ref-type="bibr" rid="B51">Norsigian et&#x20;al., 2018</xref>).</p>
<p>For emerging processes using IL pretreated lignocellulosic biomass, <italic>C. glutamicum</italic> as the microbial IP producer for this process is compelling. To the best of our knowledge, this is the first transcriptomics analysis of an engineered isopentenol producing <italic>C. glutamicum</italic> strain in fed-batch conditions. Due to the relative similarity between this isolate to the type strain, we were able to use existing gene annotations with a fairly low homology cutoff (&#x3e; 70%) for the majority of detected transcripts in this study. A large number of significant DEGs identified in this analysis encode hypothetical proteins that lack functional information. These genes can be further characterized using functional genomics tools such as parallelized transposon mutant libraries (<xref ref-type="bibr" rid="B43">Lim et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B9">Cain et&#x20;al., 2020</xref>) or high throughput transcription factor characterization (<xref ref-type="bibr" rid="B56">Rajeev et&#x20;al., 2011</xref>; <xref ref-type="bibr" rid="B57">Rajeev et&#x20;al., 2014</xref>) to improve our understanding of these useful <italic>C. glutamicum</italic> isolates.</p>
<p>Our analysis here indicated a number of actionable targets for future studies to improve isopentenol titers under stirred tank fed-batch conditions. Deleting <italic>mdh</italic> could limit accumulation of succinate, a highly overexpressed gene. Deleting or down regulating <italic>gltA,</italic> Cgl2211, <italic>brnF</italic> and arginine biosynthesis genes that were also highly upregulated (<xref ref-type="fig" rid="F6">Figure&#x20;6</xref>); could enlarge the acetyl-CoA pool, in turn improving IP titers. Additional gene targets should include <italic>pta-ackA, poxB, actA</italic> and Cgl2066 to block acetate formation. These proposed targets are specific to <italic>C. glutamicum</italic> host engineering for isopentenol production. Our transcriptomics analysis also implicated <italic>ectP</italic>, a BCCT family transporter similar to <italic>E.&#x20;coli betT</italic> and <italic>P. putida betT-III,</italic> as a transporter for [Ch][Lys]; <italic>ectP</italic> was overexpressed in the presence of ILs<italic>.</italic> A BCCT transporter has been proposed to be involved in uptake and catabolism of the cholinium ion from [Ch][Lys] in both <italic>E.&#x20;coli</italic> and <italic>P. putida</italic> (<xref ref-type="bibr" rid="B53">Park et&#x20;al., 2020</xref>). Characterizing IL tolerance is an active research thrust in our laboratory.</p>
<p>In summary, our transcriptomic analysis under industrially relevant process conditions provides a toehold for future DBTL cycles. Future learn steps can leverage the information gleaned here to target the critical features implicated for improved <italic>C. glutamicum</italic> strain performance when producing desirable products, like isopentenol. Even accounting for potential increased cell heterogeneity in the bioreactor (<xref ref-type="bibr" rid="B76">Wehrs et&#x20;al., 2019</xref>), important features both common and unique to conditions allow a closer look into cell physiology.</p>
</sec>
<sec sec-type="materials|methods" id="s4">
<title>Materials and Methods</title>
<sec id="s4-1">
<title>Reagents and Experimental Conditions</title>
<p>In a previous report (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>), we referred to the IP producing <italic>C. glutamicum</italic> strain as ATCC 13032 NHRI 1.1.2, as indicated in our archival notes. As we cannot confirm the provenance of <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 and how it may have been derived from its closest relatives <italic>C. glutamicum</italic> SCgG1 or SCgG2, we opted to give this strain a unique identifier to avoid further confusion.</p>
<p>Unless indicated elsewhere, all reagents used were molecular biology grade or higher. Primers were synthesized by IDT DNA Technologies (Coralville, IA). CGXII media was prepared as previously described (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>; <xref ref-type="bibr" rid="B31">Keilhauer et&#x20;al., 1993</xref>). All strains and plasmids used in this study are described in <xref ref-type="sec" rid="s10">Supplementary Table S2</xref>. <italic>C. glutamicum</italic> strains were struck to single colonies from glycerol stock on LB plates containing the appropriate antibiotic and prepared for production runs as previously described (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>). The fed-batch cultivation with 50&#xa0;mM of [Ch][Lys] supplementation was previously described in (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>). The control bioreactor without [Ch][Lys] was conducted at the same time and the glucose feeding regime was identical to that of the ionic liquid (IL) supplemented reactor. For RNAseq extraction, 5&#xa0;ml culture samples were harvested in 1&#xa0;ml aliquots, collected by centrifugation at 14,000 &#xd7; <italic>g</italic> for 3&#xa0;min, and stored at &#x2212;80&#xb0;C until subsequent RNA extraction. The supernatant from one of the appropriate time point aliquots was processed for organic acid analysis as described previously (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>). Lab-scale IP production in deep well plates or 5&#xa0;ml culture tubes were conducted as previously described (<xref ref-type="bibr" rid="B15">Eng et&#x20;al., 2020</xref>). Isopentenol titers reported for the deep well plate format were corrected for evaporation at the 48&#xa0;h time point as conducted previously (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>). Exogenous [Ch][Lys] toxicity against <italic>C. glutamicum</italic> ATCC13032 and BRC-JBEI 1.1.2 was analyzed in a 48-well microtiter dish format. Cells were first adapted two times in CGXII minimal media with 4% (w/v) D-glucose. When cells were back diluted into fresh media in the microtiter dish, the starting Optical Density (OD) was set to 0.1 with a fill volume of 200&#xa0;&#x3bc;l. The plate was incubated with shaking at 30&#xb0;C and exogenous [Ch][Lys] added at the start of the time course. OD was monitored at 600&#xa0;nm on a Synergy 4 plate reader (BioTek Instruments, Winooski VT) with the continuous shaking setting.</p>
</sec>
<sec id="s4-2">
<title>Production Run With Ensiled Sorghum Hydrolysate</title>
<p>CGXII minimal media was supplemented with ensiled sorghum biomass hydrolysate to test the ability of <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 to utilize carbon sources from renewable feedstock pretreated with IL. Briefly, the forage sorghum (NK300 type, grown in Fresno, CA) was planted in Spring 2020 and harvested in Fall 2020. A forage harvester was used to both harvest and chop the sorghum biomass, which was then loaded in a silage pit, inoculated, and covered to maintain anaerobic conditions. The pit was opened in November 2020 and a sample of the ensiled material was collected, packed with dry ice while in transit, and stored at 4&#xb0;C. A 210&#xa0;L scale Andritz Hastelloy C276 pressure reactor (AG, Graz, Austria) with a helical impeller was utilized to process ensiled sorghum for the pretreatment and saccharification processes. Ensiled sorghum biomass was pretreated at 20% w/w solid loading with 10% w/w [Ch][Lys] at 140&#xb0;C for 3&#xa0;h with a mixing speed of 30&#xa0;rpm. Solid loading was calculated based on the dry matter content determined using a Binder VDL115 vacuum oven. After 3&#xa0;h at the target temperature, the reactor was cooled to room temperature before proceeding with the next steps. The Andritz reactor is sealed during this process, preventing contamination until further processing. Following pretreatment, the pretreated materials were adjusted to pH 5.1 using 50% v/v sulfuric acid and an enzyme cocktail of Novozyme, Inc. Cellic Ctec3 and Cellic Htec3 commercial enzymes in a ratio of 9:1 was added. Concentration of the commercial stocks were determined using Bradford assays and bovine serum albumin as a reference. Enzyme load was conducted at a ratio of 10&#xa0;mg enzyme per 1&#xa0;g of dry weight biomass. Following pH adjustment and enzyme addition, RODI water was added to obtain a final solid loading of 18.70%. Saccharification by enzymatic hydrolysis was operated at 50&#xb0;C, 30&#xa0;rpm for 70&#xa0;h (<xref ref-type="bibr" rid="B5">Barcelos et&#x20;al., 2021</xref>). The hydrolysate was then sequentially filtered using a filter press through 5, 1, and 0.25&#xa0;&#x3bc;m filters. Final filter sterilization was completed with a 0.2&#xa0;&#x3bc;m filter and stored at &#x2212;80&#xb0;C until further use. This hydrolysate was thawed and added in place of water in CGXII media (amounting to 2.8 % (w/v) glucose), pH was adjusted to 7.4 and filter sterilized one additional time before use. We make the assumption the hydrolysate contained no biologically available nitrogen. To maintain a C/N ratio of glucose/ammonium sulfate &#x2b; urea of 2.8, pure glucose powder was supplemented to the hydrolysate CGXII cultivation medium composition (<xref ref-type="bibr" rid="B65">Sasaki et&#x20;al., 2019</xref>).</p>
</sec>
<sec id="s4-3">
<title>DNA and RNA Isolation</title>
<p>Genomic DNA from <italic>C. glutamicum</italic> BRC-JBEI 1.1.2 was isolated with the following protocol. In brief, strains from glycerol stocks were struck to single colonies on LB plates grown at 30&#xb0;C overnight. A single colony was then inoculated into a 250&#xa0;ml shake flask with 25&#xa0;ml LB media and grown overnight to saturation. Cells were collected by centrifugation at 4,000 &#xd7; <italic>g</italic> for 5&#xa0;min. The cell pellet was then resuspended in 2&#xa0;ml lysis buffer (2&#xa0;mM EDTA, 250&#xa0;mM NaCl, 2% (w/v) SDS, 2% (v/v) Triton-X 100, 2% (v/v) Tween-80, 5&#xa0;mM DTT, 30 units Zymolase 100T, 1&#xa0;mg/ml RNaseA). Zymolyase was supplied by US Biological (Salem, MA). The cells were initially incubated at 50&#xb0;C for 30&#xa0;min to promote protease activity and then incubated for an additional 3&#xa0;h at 37&#xb0;C with occasional mixing, at which point the lysate became noticeably viscous. DNA was extracted following standard protocols for isolation of DNA using phenol chloroform: isoamyl alcohol and subsequent isopropanol precipitation (<xref ref-type="bibr" rid="B63">Sambrook and Russell, 2001</xref>).</p>
<p>RNA was extracted from <italic>C. glutamicum</italic> samples using a Direct-Zol RNA Kit (Zymo Research, Irvine, CA) following the manufacturer&#x2019;s protocol. <italic>C. glutamicum</italic> cells were lysed after initially resuspending the cell pellet in 500&#xa0;&#xb5;l TRI reagent and mixed with glass beads. This mixture was then subject to cell disruption using a bead-beater (Biospec Inc., Bartlesville, OK) with a 3-min homogenization time at maximum intensity. After bead beating, samples were collected following the manufacturer&#x2019;s protocol without any additional modifications. RNA quality was assessed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA) before RNA library preparation and downstream analysis.</p>
<p>For 16S ribosomal sequencing, <italic>C. glutamicum</italic> ATCC 13032&#x20;&#x2206;<italic>mrr</italic> and <italic>C. glutamicum</italic> JBEI-BRC 1.1.2 were struck from glycerol stocks to single colonies on LB plates and incubated overnight at 30&#xb0;C. A single colony was isolated and boiled in 50&#xa0;&#xb5;l dH<sub>2</sub>0 for 10&#xa0;min. 1&#xa0;&#xb5;l of the boiled colony was used for PCR with primer pair (JGI_27F: 5&#x2032;-AGAGTTTGATCCTGGCTCAG-3&#x2032; and JGI_1391R: 5&#x2032;-GACGGGCRGTGWGTRCA-3&#x2032;) with NEB Q5 Polymerase (New England Biolabs, Ipswitch, MA). The PCR amplicon was confirmed by agarose gel electrophoresis and the sequence was determined using conventional Sanger Sequencing (Genewiz LLC, Chelmsford,&#x20;MA).</p>
</sec>
<sec id="s4-4">
<title>PacBio Genome Assembly</title>
<p>DNA sequencing was generated at the DOE Joint Genome Institute (JGI) using the Pacific Biosciences (PacBio) sequencing technology. A Pacbio SMRTbell(tm) library was constructed and sequenced on the PacBio Sequel and PacBio RS II platforms, which generated 397,096 filtered subreads (1,418,602,725 subread bases) totaling 3,352,276&#xa0;bp. The mean coverage for this genome was 432.21x. All general aspects of library construction and sequencing performed at the JGI can be found at <ext-link ext-link-type="uri" xlink:href="http://www.jgi.doe.gov/">http://www.jgi.doe.gov</ext-link>.</p>
</sec>
<sec id="s4-5">
<title>RNAseq Library Generation and Processing for Illumina NGS</title>
<p>Stranded RNAseq library(s) were created and quantified by qPCR. Sequencing was performed using an Illumina instrument (refer to <xref ref-type="sec" rid="s10">Supplementary Table S3</xref> for specifics per library). Raw fastq file reads were filtered and trimmed using the JGI QC pipeline resulting in the filtered fastq file (&#x2a;.filter-RNA.gz files). Using BBDuk (<ext-link ext-link-type="uri" xlink:href="https://sourceforge.net/projects/bbmap/">https://sourceforge.net/projects/bbmap/</ext-link>), raw reads were evaluated for artifact sequence by kmer matching (kmer &#x3d; 25), allowing for 1 mismatch and detected artifacts which were trimmed from the 3&#x2032; end of the reads. RNA spike-in reads, PhiX reads and reads containing any Ns were removed. Quality trimming was performed using the phred trimming method set at Q6. Following trimming, reads that did not meet the length threshold of at least 50 bases were removed.</p>
<p>Filtered reads from each library were aligned to the reference genome using HISAT2 version 2.2.0 (<xref ref-type="bibr" rid="B33">Kim et&#x20;al., 2015</xref>). Strand-specific coverage bigWig files were generated using deepTools v3.1 (<xref ref-type="bibr" rid="B58">Ram&#xed;rez et&#x20;al., 2014</xref>). Next, featureCounts (<xref ref-type="bibr" rid="B42">Liao et&#x20;al., 2014</xref>) was used to generate the raw gene counts (counts.txt) file using gff3 annotations. Only primary hits assigned to the reverse strand were included in the raw gene counts (-s 2&#x20;-p --primary options). Raw gene counts were used to evaluate the level of correlation between biological replicates using Pearson&#x2019;s correlation and determine which replicates would be used in the DEG analysis (<xref ref-type="sec" rid="s10">Supplementary Figure S5</xref>). In the heatmap view, the libraries were ordered as groups of replicates. The cells containing the correlations between replicates have a purple (or white) border around them. For fragments per kilobase of transcript per million fragments mapped (FPKM) and TPM, normalized gene counts refer to SRA reads (Data availability section). A sample legend and description of RNAseq libraries used in this paper is described in <xref ref-type="sec" rid="s10">Supplementary Table&#x20;S3</xref>.</p>
</sec>
<sec id="s4-6">
<title>Transcriptome Analysis</title>
<p>Global transcriptome response under various experiment conditions were measured using Geneious Prime 2021 (<ext-link ext-link-type="uri" xlink:href="https://www.geneious.com/">https://www.geneious.com</ext-link>). The normalized expression was calculated and the differentially expressed genes (DEGs) were filtered for absolute log<sub>2</sub> ratio &#x3e;2 (i.e. a 4-fold up or down regulation), absolute confidence &#x3e;3 (<italic>p</italic>&#x20;&#x3c; 0.001) and &#x3e;90% sequence identity. The DEGs at various conditions were functionally annotated using Blast2GO suite (<xref ref-type="bibr" rid="B18">G&#xf6;tz et&#x20;al., 2008</xref>) to assign GO annotations (<xref ref-type="bibr" rid="B17">Galperin et&#x20;al., 2015</xref>). Each DEG was subjected to pathway analysis using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database (<ext-link ext-link-type="uri" xlink:href="http://www.kegg.jp/kegg/pathway.html">http://www.kegg.jp/kegg/pathway.html</ext-link>) to explore the biological implications. Biocyc (<ext-link ext-link-type="uri" xlink:href="https://biocyc.org/">https://biocyc.org/</ext-link>) was used to calculate pathway enrichment for the last 65&#xa0;h/41&#xa0;h time point and for additional gene orthologs identification. Pathways were considered significant if <italic>p</italic>&#x20;&#x3c; 0.05. Hierarchically clustered heat maps were generated with average linkage method and euclidean distance metric in Jupyter notebook using Python library Seaborn 0.11.1 (<xref ref-type="bibr" rid="B75">Waskom et&#x20;al., 2020</xref>).</p>
</sec>
</sec>
</body>
<back>
<sec id="s5">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov">https://www.ncbi.nlm.nih.gov</ext-link>/, PRJNA533344&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, GCA_011761195.1&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP23996&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239973&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239963&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239971&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239972&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239970&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP2399a68&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov">https://www.ncbi.nlm.nih.gov</ext-link>/, SRP239969&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239966&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239967&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239964&#x20;<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</ext-link>, SRP239965.</p>
</sec>
<sec id="s6">
<title>Author Contributions</title>
<p>Raised Funds: AM and BS. Conceptualization of the project: AM and TE. Strain construction, molecular biology, bioreactor sample collection and processing: YS, TE, RH, and JT. Analytical Chemistry, IP Production Assays, IL toxicity assays: YS, TE, and AS. Interpreted results: YS, DB, TE, and AM. Contributed critical reagents: NS, AO, CS, DP, TE, YS, JT, and BS. RNAseq library generation, data collection, validation: VS, YS, and TE. Drafted the manuscript: DB, TE, and AM. All authors read, contributed feedback, and approved the final manuscript for publication.</p>
</sec>
<sec id="s7">
<title>Funding</title>
<p>A portion of this work was conducted by the United&#x20;States Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported by the Office of Science of the United&#x20;States Department of Energy under Contract No. DE-AC02-05CH11231. Other portions of this work were part of the Joint Bioenergy Institute project, funded by the United&#x20;States Department of Energy, Office of Science, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the United&#x20;States Department of Energy.</p>
</sec>
<sec sec-type="COI-statement" id="s8">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec sec-type="disclaimer" id="s9">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<ack>
<p>We thank Andrew Lau for feedback on the figures. We also thank Venkata Ramana Reddy Pidatala and Alex Codik for technical assistance.</p>
</ack>
<sec id="s10">
<title>Supplementary Material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fbioe.2021.766674/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fbioe.2021.766674/full&#x23;supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="DataSheet1.PDF" id="SM1" mimetype="application/PDF" xmlns:xlink="http://www.w3.org/1999/xlink"/>
<supplementary-material xlink:href="DataSheet2.xlsx" id="SM2" mimetype="application/xlsx" xmlns:xlink="http://www.w3.org/1999/xlink"/>
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