1
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Rodionova IA, Lim HG, Gao Y, Rodionov DA, Hutchison Y, Szubin R, Dalldorf C, Monk J, Palsson BO. CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli. Commun Biol 2024; 7:1160. [PMID: 39289465 PMCID: PMC11408624 DOI: 10.1038/s42003-024-06831-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/30/2024] [Indexed: 09/19/2024] Open
Abstract
Hydrogen sulfide (H2S), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress and potentially increases antimicrobial resistance (AMR). CyuR is a Cys-dependent transcription regulator, responsible for the activation of the cyuPA operon and generation of H2S. Despite its potential importance, its regulatory network remains poorly understood. In this study, we investigate the roles of the CyuR regulon in a Cys-dependent AMR mechanism in E. coli strains. We show: (1) Generation of H2S from Cys affects the sensitivities to growth inhibitors; (2) Cys supplementation decreases stress responses; (3) CyuR negatively controls the expression of mdlAB encoding a potential transporter for antibiotics; (4) CyuR binds to a DNA sequence motif 'GAAwAAATTGTxGxxATTTsyCC' in the absence of Cys; and (5) CyuR may regulate 25 additional genes which were not reported previously. Collectively, our findings expand the understanding of the biological roles of CyuR relevant to antibiotic resistance associated with Cys.
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Affiliation(s)
- Irina A Rodionova
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Hyun Gyu Lim
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Korea
| | - Ye Gao
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
- The Second Hospital of Shandong University, Jinan, Shandong, PR China
| | - Dmitry A Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ying Hutchison
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Monk
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, Division of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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2
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Lee Y, Choe D, Palsson BO, Cho BK. Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403912. [PMID: 39264300 DOI: 10.1002/advs.202403912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/26/2024] [Indexed: 09/13/2024]
Abstract
Streptomyces produces diverse secondary metabolites of biopharmaceutical importance, yet the rate of biosynthesis of these metabolites is often hampered by complex transcriptional regulation. Therefore, a fundamental understanding of transcriptional regulation in Streptomyces is key to fully harness its genetic potential. Here, independent component analysis (ICA) of 454 high-quality gene expression profiles of the model species Streptomyces coelicolor is performed, of which 249 profiles are newly generated for S. coelicolor cultivated on 20 different carbon sources and 64 engineered strains with overexpressed sigma factors. ICA of the transcriptome dataset reveals 117 independently modulated groups of genes (iModulons), which account for 81.6% of the variance in the dataset. The genes in each iModulon are involved in specific cellular responses, which are often transcriptionally controlled by specific regulators. Also, iModulons accurately predict 25 secondary metabolite biosynthetic gene clusters encoded in the genome. This systemic analysis leads to reveal the functions of previously uncharacterized genes, putative regulons for 40 transcriptional regulators, including 30 sigma factors, and regulation of secondary metabolism via phosphate- and iron-dependent mechanisms in S. coelicolor. ICA of large transcriptomic datasets thus enlightens a new and fundamental understanding of transcriptional regulation of secondary metabolite synthesis along with interconnected metabolic processes in Streptomyces.
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Affiliation(s)
- Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
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3
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Champie A, Lachance JC, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques PÉ, Palsson BO, Rodrigue S. Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298. mBio 2024:e0087324. [PMID: 39207109 DOI: 10.1128/mbio.00873-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Microorganisms with simplified genomes represent interesting cell chassis for systems and synthetic biology. However, genome reduction can lead to undesired traits, such as decreased growth rate and metabolic imbalances. To investigate the impact of genome reduction on Escherichia coli strain DGF-298, a strain in which ~ 36% of the genome has been removed, we reconstructed a strain-specific metabolic model (iAC1061), investigated the regulation of gene expression using iModulon-based transcriptome analysis, and performed adaptive laboratory evolution to let the strain correct potential imbalances that arose during its simplification. The model notably predicted that the removal of all three key pathways for glycolaldehyde disposal in this microorganism would lead to a metabolic bottleneck through folate starvation. Glycolaldehyde is also known to cause self-generation of reactive oxygen species, as evidenced by the increased expression of oxidative stress resistance genes in the SoxS iModulon. The reintroduction of the aldA gene, responsible for one native glycolaldehyde disposal route, alleviated the constitutive oxidative stress response. Our results suggest that systems-level approaches and adaptive laboratory evolution have additive benefits when trying to repair and optimize genome-engineered strains. IMPORTANCE Genomic streamlining can be employed in model organisms to reduce complexity and enhance strain predictability. One of the most striking examples is the bacterial strain Escherichia coli DGF-298, notable for having over one-third of its genome deleted. However, such extensive genome modifications raise the question of how similar this simplified cell remains when compared with its parent, and what are the possible unintended consequences of this simplification. In this study, we used metabolic modeling along with iModulon-based transcriptomic analysis in different growth conditions to assess the impact of genome reduction on metabolism and gene regulation. We observed little impact of genomic reduction on the regulatory network of E. coli DGF-298 and identified a potential metabolic bottleneck leading to the constitutive activity of the SoxS iModulon. We then leveraged the model's predictions to successfully restore SoxS activity to the basal level.
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Affiliation(s)
- Antoine Champie
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Anand Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Dominick Matteau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Frédéric Grenier
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Cameron R Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Simon Jeanneau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | | | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Sébastien Rodrigue
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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4
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Shin J, Zielinski DC, Palsson BO. Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic Acids Res 2024:gkae742. [PMID: 39193902 DOI: 10.1093/nar/gkae742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Synthetic biology enables the reprogramming of cellular functions for various applications. However, challenges in scalability and predictability persist due to context-dependent performance and complex circuit-host interactions. This study introduces an iModulon-based engineering approach, utilizing machine learning-defined co-regulated gene groups (iModulons) as design parts containing essential genes for specific functions. This approach identifies the necessary components for genetic circuits across different contexts, enhancing genome engineering by improving target selection and predicting module behavior. We demonstrate several distinct uses of iModulons: (i) discovery of unknown iModulons to increase protein productivity, heat tolerance and fructose utilization; (ii) an iModulon boosting approach, which amplifies the activity of specific iModulons, improved cell growth under osmotic stress with minimal host regulation disruption; (iii) an iModulon rebalancing strategy, which adjusts the activity levels of iModulons to balance cellular functions, significantly increased oxidative stress tolerance while minimizing trade-offs and (iv) iModulon-based gene annotation enabled natural competence activation by predictably rewiring iModulons. Comparative experiments with traditional methods showed our approach offers advantages in efficiency and predictability of strain engineering. This study demonstrates the potential of iModulon-based strategies to systematically and predictably reprogram cellular functions, offering refined and adaptable control over complex regulatory networks.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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5
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Hua C, Huang J, Sun Y, Wang T, Li Y, Cui Z, Deng X. Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen. Cell Rep 2024; 43:114544. [PMID: 39052478 DOI: 10.1016/j.celrep.2024.114544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/27/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and -deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.
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Affiliation(s)
- Canfeng Hua
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jiadai Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yue Sun
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Tingting Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Youyue Li
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Zining Cui
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Center, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong, China; Tung Biomedical Sciences Center, City University of Hong Kong, Hong Kong, China.
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6
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Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024; 15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05782 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02306 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108570 Japan Agency for Medical Research and Development (AMED)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP22K20765 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K14173 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2178 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- Pioneering Project MEXT | RIKEN
- RIKEN TRIP initiative "TRIP-AGIS" MEXT | RIKEN
- Pioneering Project MEXT | RIKEN
- JPMJBS2418 MEXT | Japan Science and Technology Agency (JST)
- JPMJFR226F MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 2024; 9:e0030524. [PMID: 38829048 PMCID: PMC11264592 DOI: 10.1128/msystems.00305-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth in E. coli has been termed the fear versus greed (f/g) tradeoff. Two specific RNA polymerase (RNAP) mutations observed in adaptation to fast growth have been previously shown to affect the f/g tradeoff, suggesting that genetic adaptations may be primed to control f/g resource allocation. Here, we conduct a greatly expanded study of the genetic control of the f/g tradeoff across diverse conditions. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and obtained expression profiles of each. We found that these single RNAP mutation strains resulted in large shifts in the f/g tradeoff primarily in the RpoS regulon and ribosomal genes, likely through modifying RNAP-DNA interactions. Two of these mutations additionally caused condition-specific transcriptional adaptations. While this tradeoff was previously characterized by the RpoS regulon and ribosomal expression, we find that the GAD regulon plays an important role in stress readiness and ppGpp in translation activity, expanding the scope of the tradeoff. A phylogenetic analysis found the greed-related genes of the tradeoff present in numerous bacterial species. The results suggest that the f/g tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.IMPORTANCETo increase growth, E. coli must raise ribosomal content at the expense of non-growth functions. Previous studies have linked RNAP mutations to this transcriptional shift and increased growth but were focused on only two mutations found in the protein's central region. RNAP mutations, however, commonly occur over a large structural range. To explore RNAP mutations' impact, we have introduced 12 RNAP mutations found in laboratory evolution experiments and obtained expression profiles of each. The mutations nearly universally increased growth rates by adjusting said tradeoff away from non-growth functions. In addition to this shift, a few caused condition-specific adaptations. We explored the prevalence of this tradeoff across phylogeny and found it to be a widespread and conserved trend among bacteria.
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Affiliation(s)
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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8
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Shin J, Zielinski DC, Palsson BO. Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering. Metab Eng 2024; 84:34-47. [PMID: 38825177 DOI: 10.1016/j.ymben.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of Vibrio natriegens to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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9
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Kim K, Choe D, Kang M, Cho SH, Cho S, Jeong KJ, Palsson B, Cho BK. Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli. Metab Eng 2024; 83:160-171. [PMID: 38636729 DOI: 10.1016/j.ymben.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/31/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Microbes have inherent capacities for utilizing various carbon sources, however they often exhibit sub-par fitness due to low metabolic efficiency. To test whether a bacterial strain can optimally utilize multiple carbon sources, Escherichia coli was serially evolved in L-lactate and glycerol. This yielded two end-point strains that evolved first in L-lactate then in glycerol, and vice versa. The end-point strains displayed a universal growth advantage on single and a mixture of adaptive carbon sources, enabled by a concerted action of carbon source-specialists and generalist mutants. The combination of just four variants of glpK, ppsA, ydcI, and rph-pyrE, accounted for more than 80% of end-point strain fitness. In addition, machine learning analysis revealed a coordinated activity of transcriptional regulators imparting condition-specific regulation of gene expression. The effectiveness of the serial adaptive laboratory evolution (ALE) scheme in bioproduction applications was assessed under single and mixed-carbon culture conditions, in which serial ALE strain exhibited superior productivity of acetoin compared to ancestral strains. Together, systems-level analysis elucidated the molecular basis of serial evolution, which hold potential utility in bioproduction applications.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang-Hyeok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Ki Jun Jeong
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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10
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Menon ND, Poudel S, Sastry AV, Rychel K, Szubin R, Dillon N, Tsunemoto H, Hirose Y, Nair BG, Kumar GB, Palsson BO, Nizet V. Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant Acinetobacter baumannii. mSystems 2024; 9:e0060623. [PMID: 38189271 PMCID: PMC10878099 DOI: 10.1128/msystems.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Acinetobacter baumannii causes severe infections in humans, resists multiple antibiotics, and survives in stressful environmental conditions due to modulations of its complex transcriptional regulatory network (TRN). Unfortunately, our global understanding of the TRN in this emerging opportunistic pathogen is limited. Here, we apply independent component analysis, an unsupervised machine learning method, to a compendium of 139 RNA-seq data sets of three multidrug-resistant A. baumannii international clonal complex I strains (AB5075, AYE, and AB0057). This analysis allows us to define 49 independently modulated gene sets, which we call iModulons. Analysis of the identified A. baumannii iModulons reveals validating parallels to previously defined biological operons/regulons and provides a framework for defining unknown regulons. By utilizing the iModulons, we uncover potential mechanisms for a RpoS-independent general stress response, define global stress-virulence trade-offs, and identify conditions that may induce plasmid-borne multidrug resistance. The iModulons provide a model of the TRN that emphasizes the importance of transcriptional regulation of virulence phenotypes in A. baumannii. Furthermore, they suggest the possibility of future interventions to guide gene expression toward diminished pathogenic potential.IMPORTANCEThe rise in hospital outbreaks of multidrug-resistant Acinetobacter baumannii infections underscores the urgent need for alternatives to traditional broad-spectrum antibiotic therapies. The success of A. baumannii as a significant nosocomial pathogen is largely attributed to its ability to resist antibiotics and survive environmental stressors. However, there is limited literature available on the global, complex regulatory circuitry that shapes these phenotypes. Computational tools that can assist in the elucidation of A. baumannii's transcriptional regulatory network architecture can provide much-needed context for a comprehensive understanding of pathogenesis and virulence, as well as for the development of targeted therapies that modulate these pathways.
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Affiliation(s)
- Nitasha D. Menon
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Nicholas Dillon
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Biological Sciences, University of Texas at Dallas, Dallas, Texas, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yujiro Hirose
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
| | - Bipin G. Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Geetha B. Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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11
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Heom KA, Wangsanuwat C, Butkovich LV, Tam SC, Rowe AR, O'Malley MA, Dey SS. Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures. mSystems 2023; 8:e0028123. [PMID: 37855606 PMCID: PMC10734481 DOI: 10.1128/msystems.00281-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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Affiliation(s)
- Kellie A. Heom
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chatarin Wangsanuwat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Scott C. Tam
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Annette R. Rowe
- Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
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12
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Hirose Y, Poudel S, Sastry AV, Rychel K, Lamoureux CR, Szubin R, Zielinski DC, Lim HG, Menon ND, Bergsten H, Uchiyama S, Hanada T, Kawabata S, Palsson BO, Nizet V. Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins. mSystems 2023; 8:e0024723. [PMID: 37278526 PMCID: PMC10308926 DOI: 10.1128/msystems.00247-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. An underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each unique host environment. Consequently, an in-depth understanding of the comprehensive dynamics of the S. pyogenes TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA sequencing data sets of invasive S. pyogenes serotype M1 and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained the nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated the nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, altering bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify the interpretation of noisy bacterial transcriptome data at the infection site. IMPORTANCE S. pyogenes is a pre-eminent human bacterial pathogen that causes a wide variety of acute infections throughout the body of its host. Understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Since at least 43 S. pyogenes transcriptional regulators are known, it is often difficult to interpret transcriptomic data from regulon annotations. This study shows the novel ICA-based framework to elucidate the underlying regulatory structure of S. pyogenes allows us to interpret the transcriptome profile using data-driven regulons (iModulons). Additionally, the observations of the iModulon architecture lead us to identify the multiple regulatory inputs governing the expression of a virulence-related operon. The iModulons identified in this study serve as a powerful guidepost to further our understanding of S. pyogenes TRN structure and dynamics.
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Affiliation(s)
- Yujiro Hirose
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Anand V. Sastry
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Cameron R. Lamoureux
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Biological Engineering, Inha University, Michuhol-gu, Incheon, South Korea
| | - Nitasha D. Menon
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California, USA
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Helena Bergsten
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California, USA
| | - Satoshi Uchiyama
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California, USA
| | - Tomoki Hanada
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Graduate School of Dentistry, Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Suita, Osaka, Japan
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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13
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Shin J, Rychel K, Palsson BO. Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome. Cell Rep 2023; 42:112619. [PMID: 37285268 DOI: 10.1016/j.celrep.2023.112619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens's transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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14
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Rodionova IA, Lim HG, Rodionov DA, Hutchison Y, Dalldorf C, Gao Y, Monk J, Palsson BO. CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541025. [PMID: 37292663 PMCID: PMC10245726 DOI: 10.1101/2023.05.16.541025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hydrogen sulfide (H 2 S), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress. This mitigation of oxidative stress was suggested to be an important survival mechanism to achieve antimicrobial resistance (AMR) in many pathogenic bacteria. CyuR (known as DecR or YbaO) is a recently characterized Cys-dependent transcription regulator, responsible for the activation of the cyuAP operon and generation of hydrogen sulfide from Cys. Despite its potential importance, the regulatory network of CyuR remains poorly understood. In this study, we investigated the roles of the CyuR regulon in a Cys-dependent AMR mechanism in E. coli strains. We found: 1) Cys metabolism has a significant role in AMR and its effect is conserved in many E. coli strains, including clinical isolates; 2) CyuR negatively controls the expression of mdlAB encoding a transporter that exports antibiotics such as cefazolin and vancomycin; 3) CyuR binds to a DNA sequence motif 'GAAwAAATTGTxGxxATTTsyCC' in the absence of Cys, confirmed by an in vitro binding assay; and 4) CyuR may regulate 25 additional genes as suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings expanded the understanding of the biological roles of CyuR relevant to antibiotic resistance associated with Cys.
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15
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. RESEARCH SQUARE 2023:rs.3.rs-2729651. [PMID: 37090546 PMCID: PMC10120744 DOI: 10.21203/rs.3.rs-2729651/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced twelve RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations resulted in large shifts in the fear vs. greed tradeoff, likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that often have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species. The results suggest that the fear vs. greed tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
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Affiliation(s)
- Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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16
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Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum. Proc Natl Acad Sci U S A 2023; 120:e2216244120. [PMID: 36716373 PMCID: PMC9963998 DOI: 10.1073/pnas.2216244120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acetogenic bacteria are a unique biocatalyst that highly promises to develop the sustainable bioconversion of carbon oxides (e.g., CO and CO2) into multicarbon biochemicals. Genotype-phenotype relationships are important for engineering their metabolic capability to enhance their biocatalytic performance; however, systemic investigation on the fitness contribution of individual gene has been limited. Here, we report genome-scale CRISPR interference screening using 41,939 guide RNAs designed from the E. limosum genome, one of the model acetogenic species, where all genes were targeted for transcriptional suppression. We investigated the fitness contributions of 96% of the total genes identified, revealing the gene fitness and essentiality for heterotrophic and autotrophic metabolisms. Our data show that the Wood-Ljungdahl pathway, membrane regeneration, membrane protein biosynthesis, and butyrate synthesis are essential for autotrophic acetogenesis in E. limosum. Furthermore, we discovered genes that are repression targets that unbiasedly increased autotrophic growth rates fourfold and acetoin production 1.5-fold compared to the wild-type strain under CO2-H2 conditions. These results provide insight for understanding acetogenic metabolism and genome engineering in acetogenic bacteria.
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17
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Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. mSystems 2022; 7:e0048022. [PMID: 36321827 PMCID: PMC9765215 DOI: 10.1128/msystems.00480-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
Abstract
The complex cross talk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the Staphylococcus aureus USA300 strain by applying independent component analysis (ICA) to 385 RNA sequencing samples. We then combined the modular TRN model with a metabolic model to study the regulation of carbon and amino acid metabolism. Our analysis showed that regulation of central carbon metabolism by CcpA and amino acid biosynthesis by CodY are closely coordinated. In general, S. aureus increases the expression of CodY-regulated genes in the presence of preferred carbon sources such as glucose. This transcriptional coordination was corroborated by metabolic model simulations that also showed increased amino acid biosynthesis in the presence of glucose. Further, we found that CodY and CcpA cooperatively regulate the expression of ribosome hibernation-promoting factor, thus linking metabolic cues with translation. In line with this hypothesis, expression of CodY-regulated genes is tightly correlated with expression of genes encoding ribosomal proteins. Together, we propose a coarse-grained model where expression of S. aureus genes encoding enzymes that control carbon flux and nitrogen flux through the system is coregulated with expression of translation machinery to modularly control protein synthesis. While this work focuses on three key regulators, the full TRN model we present contains 76 total independently modulated sets of genes, each with the potential to uncover other complex regulatory structures and interactions. IMPORTANCE Staphylococcus aureus is a versatile pathogen with an expanding antibiotic resistance profile. The biology underlying its clinical success emerges from an interplay of many systems such as metabolism and gene regulatory networks. This work brings together models for these two systems to establish fundamental principles governing the regulation of S. aureus central metabolism and protein synthesis. Studies of these fundamental biological principles are often confined to model organisms such as Escherichia coli. However, expanding these models to pathogens can provide a framework from which complex and clinically important phenotypes such as virulence and antibiotic resistance can be better understood. Additionally, the expanded gene regulatory network model presented here can deconvolute the biology underlying other important phenotypes in this pathogen.
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Affiliation(s)
- Saugat Poudel
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Anand Sastry
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
| | - Ye Gao
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Department of Biological Sciences, University of California San Diego, San Diego, California, USA
| | - Victor Nizet
- Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, San Diego, California, USA
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18
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David BM, Jensen PA. Improving an rRNA depletion protocol with statistical design of experiments. SLAS Technol 2022. [DOI: 10.1016/j.slast.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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