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Kim YY, Kim JC, Kim S, Yang JE, Kim HM, Park HW. Heterotypic stress-induced adaptive evolution enhances freeze-drying tolerance and storage stability of Leuconostoc mesenteroides WiKim33. Food Res Int 2024; 175:113731. [PMID: 38128991 DOI: 10.1016/j.foodres.2023.113731] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Lactic acid bacteria (LAB) are currently being investigated for their potential use as probiotics and starter cultures. Researchers have developed powdering processes for the commercialization of LAB. Previous studies have focused on identifying innovative cryoprotective agents and freeze-drying (FD) techniques to enhance the stability of LAB. In this study, adaptive laboratory evolution (ALE) was employed to develop a strain with high FD tolerance and enhanced storage stability. Leuconostoc mesenteroids WiKim33 was subjected to heterotypic shock (heat and osmosis shock) to induce the desired phenotype and genotype. An FD-tolerant enhanced Leu. mesenteroides WiKim33 strain (ALE50) was obtained, which harbored a modified fatty acid composition and cell envelope characteristics. Specifically, ALE50 showed a lower unsaturated fatty acid (UFA)/saturated fatty acid (SFA) ratio and a higher cyclic fatty acid (CFA) composition. Moreover, the exopolysaccharide (EPS) thickness increased significantly by 331% compared to that of the wild type (WT). FD tolerance, which was evaluated using viability testing after FD, was enhanced by 33.4%. Overall, we demonstrated the feasibility of ALE to achieve desirable characteristics and provided insights into the mechanisms underlying increased FD tolerance.
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Affiliation(s)
- Yeong Yeol Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea; Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong-Cheol Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Seulbi Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea; Division of Applied Bioscience & Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jung Eun Yang
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Ho Myeong Kim
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
| | - Hae Woong Park
- Technology Innovation Research Division, World Institute of Kimchi, Gwangju 61755, Republic of Korea.
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2
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Lorenzetti APR, Kusebauch U, Zaramela LS, Wu WJ, de Almeida JPP, Turkarslan S, L. G. de Lomana A, Gomes-Filho JV, Vêncio RZN, Moritz RL, Koide T, Baliga NS. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. mSystems 2023; 8:e0081622. [PMID: 36912639 PMCID: PMC10134880 DOI: 10.1128/msystems.00816-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net). IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).
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Affiliation(s)
- Alan P. R. Lorenzetti
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Institute for Systems Biology, Seattle, Washington, USA
| | | | - Lívia S. Zaramela
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, Washington, USA
| | - João P. P. de Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | - José V. Gomes-Filho
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Z. N. Vêncio
- Department of Computation and Mathematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Tie Koide
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
- Lawrence Berkeley National Lab, Berkeley, California, USA
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3
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Gelsinger DR, Reddy R, Whittington K, Debic S, DiRuggiero J. Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea. RNA Biol 2021; 18:1867-1881. [PMID: 33522404 PMCID: PMC8583180 DOI: 10.1080/15476286.2021.1874717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the processes regulating this remarkable response is lacking. Oxidative stress-responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volc anii, but targets and mechanisms have not been elucidated. Using a combination of high throughput and reverse molecular genetic approaches, we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, named Small RNA in Haloferax Oxidative Stress (SHOxi). SHOxi was predicted to form a stable secondary structure with a conserved stem-loop region as the potential binding site for trans-targets. NAD-dependent malic enzyme mRNA, identified as a putative target of SHOxi, interacted directly with a putative 'seed' region within the predicted stem loop of SHOxi. Malic enzyme catalyzes the oxidative decarboxylation of malate into pyruvate using NAD+ as a cofactor. The destabilization of malic enzyme mRNA, and the decrease in the NAD+/NADH ratio, resulting from the direct RNA-RNA interaction between SHOxi and its trans-target was essential for the survival of H. volcanii to oxidative stress. These findings indicate that SHOxi likely regulates redox homoeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. SHOxi-mediated regulation provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.
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Affiliation(s)
| | - Rahul Reddy
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Sara Debic
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Jocelyne DiRuggiero
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
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Ibrahim AGAER, Vêncio RZN, Lorenzetti APR, Koide T. Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites. Genes (Basel) 2021; 12:genes12071018. [PMID: 34209065 PMCID: PMC8303175 DOI: 10.3390/genes12071018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 01/15/2023] Open
Abstract
Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.
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Affiliation(s)
- Amr Galal Abd El-Raheem Ibrahim
- Department of Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil; (A.G.A.E.-R.I.); (R.Z.N.V.)
| | - Ricardo Z. N. Vêncio
- Department of Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil; (A.G.A.E.-R.I.); (R.Z.N.V.)
| | - Alan P. R. Lorenzetti
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil;
| | - Tie Koide
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil;
- Correspondence: ; Tel.: +55-16-3315-3107
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5
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Gomes-Filho JV, Zaramela LS, Italiani VCDS, Baliga NS, Vêncio RZN, Koide T. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol 2016; 12:490-500. [PMID: 25806405 PMCID: PMC4615843 DOI: 10.1080/15476286.2015.1019998] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.
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Affiliation(s)
- José Vicente Gomes-Filho
- a Department of Biochemistry and Immunology ; Ribeirão Preto Medical School ; University of São Paulo ; Ribeirão Preto , Brazil
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6
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Gamba P, Jonker MJ, Hamoen LW. A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence. PLoS Genet 2015; 11:e1005047. [PMID: 26110430 PMCID: PMC4482431 DOI: 10.1371/journal.pgen.1005047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/01/2015] [Indexed: 01/25/2023] Open
Abstract
Gene expression can be highly heterogeneous in isogenic cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by specific genetic circuits in order to obtain a bimodal response. A classical model of bimodal differentiation is the activation of genetic competence in Bacillus subtilis. The competence transcription factor ComK activates transcription of its own gene, and an intricate regulatory network controls the switch to competence and ensures its reversibility. However, it is noise in ComK expression that determines which cells activate the ComK autostimulatory loop and become competent for genetic transformation. Despite its important role in bimodal gene expression, noise remains difficult to investigate due to its inherent stochastic nature. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators to screen for possible factors that affect noise. This led to the identification of a novel protein Kre (YkyB) that controls the bimodal regulation of ComK. Interestingly, Kre appears to modulate the induction of ComK by affecting the stability of comK mRNA. The protein influences the expression of many genes, however, Kre is only found in bacteria that contain a ComK homologue and, importantly, kre expression itself is downregulated by ComK. The evolutionary significance of this new feedback loop for the reduction of transcriptional noise in comK expression is discussed. Our findings show the importance of mRNA stability in bimodal regulation, a factor that requires more attention when studying and modelling this non-deterministic developmental mechanism. Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.
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Affiliation(s)
- Pamela Gamba
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail: (PG); (LWH)
| | - Martijs J. Jonker
- MicroArray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Leendert W. Hamoen
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (PG); (LWH)
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7
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Abstract
Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology.
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Affiliation(s)
- Fred D Mast
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
| | - Alexander V Ratushny
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
| | - John D Aitchison
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
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8
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Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS. A system-level model for the microbial regulatory genome. Mol Syst Biol 2014; 10:740. [PMID: 25028489 PMCID: PMC4299497 DOI: 10.15252/msb.20145160] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
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Affiliation(s)
- Aaron N Brooks
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | - Antoine Allard
- Département de Physique, de Génie Physique et d'Optique, Université Laval, Québec, QC, Canada
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA, USA
| | - Diego M Salvanha
- Institute for Systems Biology, Seattle, WA, USA LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil
| | | | | | - Min Pan
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA Lawrence Berkeley National Laboratories, Berkeley, CA, USA
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