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Gu L, Zhao S, Tadesse BT, Zhao G, Solem C. Scrutinizing a Lactococcus lactis mutant with enhanced capacity for extracellular electron transfer reveals a unique role for a novel type-II NADH dehydrogenase. Appl Environ Microbiol 2024; 90:e0041424. [PMID: 38563750 PMCID: PMC11107169 DOI: 10.1128/aem.00414-24] [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: 03/04/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024] Open
Abstract
Lactococcus lactis, a lactic acid bacterium used in food fermentations and commonly found in the human gut, is known to possess a fermentative metabolism. L. lactis, however, has been demonstrated to transfer metabolically generated electrons to external electron acceptors, a process termed extracellular electron transfer (EET). Here, we investigated an L. lactis mutant with an unusually high capacity for EET that was obtained in an adaptive laboratory evolution (ALE) experiment. First, we investigated how global gene expression had changed, and found that amino acid metabolism and nucleotide metabolism had been affected significantly. One of the most significantly upregulated genes encoded the NADH dehydrogenase NoxB. We found that this upregulation was due to a mutation in the promoter region of NoxB, which abolished carbon catabolite repression. A unique role of NoxB in EET could be attributed and it was directly verified, for the first time, that NoxB could support respiration in L. lactis. NoxB, was shown to be a novel type-II NADH dehydrogenase that is widely distributed among gut microorganisms. This work expands our understanding of EET in Gram-positive electroactive microorganisms and the special significance of a novel type-II NADH dehydrogenase in EET.IMPORTANCEElectroactive microorganisms with extracellular electron transfer (EET) ability play important roles in biotechnology and ecosystems. To date, there have been many investigations aiming at elucidating the mechanisms behind EET, and determining the relevance of EET for microorganisms in different niches. However, how EET can be enhanced and harnessed for biotechnological applications has been less explored. Here, we compare the transcriptomes of an EET-enhanced L. lactis mutant with its parent and elucidate the underlying reason for its superior performance. We find that one of the most significantly upregulated genes is the gene encoding the NADH dehydrogenase NoxB, and that upregulation is due to a mutation in the catabolite-responsive element that abolishes carbon catabolite repression. We demonstrate that NoxB has a special role in EET, and furthermore show that it supports respiration to oxygen, which has never been done previously. In addition, a search reveals that this novel NoxB-type NADH dehydrogenase is widely distributed among gut microorganisms.
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Affiliation(s)
- Liuyan Gu
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Ge Zhao
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Castro-López C, Romero-Luna HE, García HS, Vallejo-Cordoba B, González-Córdova AF, Hernández-Mendoza A. Key Stress Response Mechanisms of Probiotics During Their Journey Through the Digestive System: A Review. Probiotics Antimicrob Proteins 2023; 15:1250-1270. [PMID: 36001271 DOI: 10.1007/s12602-022-09981-x] [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] [Accepted: 08/17/2022] [Indexed: 11/26/2022]
Abstract
The survival of probiotic microorganisms during their exposure to harsh environments plays a critical role in the fulfillment of their functional properties. In particular, transit through the human gastrointestinal tract (GIT) is considered one of the most challenging habitats that probiotics must endure, because of the particularly stressful conditions (e.g., oxygen level, pH variations, nutrient limitations, high osmolarity, oxidation, peristalsis) prevailing in the different sections of the GIT, which in turn can affect the growth, viability, physiological status, and functionality of microbial cells. Consequently, probiotics have developed a series of strategies, called "mechanisms of stress response," to protect themselves from these adverse conditions. Such mechanisms may include but are not limited to the induction of new metabolic pathways, formation/production of particular metabolites, and changes of transcription rates. It should be highlighted that some of such mechanisms can be conserved across several different strains or can be unique for specific genera. Hence, this review attempts to review the state-of-the-art knowledge of mechanisms of stress response displayed by potential probiotic strains during their transit through the GIT. In addition, evidence whether stress responses can compromise the biosafety of such strains is also discussed.
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Affiliation(s)
- Cecilia Castro-López
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Gustavo Enrique Astiazarán Rosas 46, Hermosillo, Sonora, 83304, México
| | - Haydee E Romero-Luna
- Instituto Tecnológico Superior de Xalapa/Tecnológico Nacional de México, Reserva Territorial s/n Sección 5, Santa Bárbara, Xalapa-Enríquez, Veracruz, 91096, México
| | - Hugo S García
- Unidad de Investigación Y Desarrollo de Alimentos, Instituto Tecnológico de Veracruz/Tecnológico Nacional de México, Miguel Ángel de Quevedo 2779, Veracruz, Veracruz, 91897, México
| | - Belinda Vallejo-Cordoba
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Gustavo Enrique Astiazarán Rosas 46, Hermosillo, Sonora, 83304, México
| | - Aarón F González-Córdova
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Gustavo Enrique Astiazarán Rosas 46, Hermosillo, Sonora, 83304, México
| | - Adrián Hernández-Mendoza
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Gustavo Enrique Astiazarán Rosas 46, Hermosillo, Sonora, 83304, México.
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3
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Huynh U, Nguyen HN, Trinh BK, Elhaj J, Zastrow ML. A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae. Metallomics 2023; 15:mfad044. [PMID: 37463796 PMCID: PMC10391621 DOI: 10.1093/mtomcs/mfad044] [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: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
As the second most abundant transition element and a crucial cofactor for many proteins, zinc is essential for the survival of all living organisms. To maintain required zinc levels and prevent toxic overload, cells and organisms have a collection of metal transport proteins for uptake and efflux of zinc. In bacteria, metal transport proteins are well defined for model organisms and many pathogens, but fewer studies have explored metal transport proteins, including those for zinc, in commensal bacteria from the gut microbiota. The healthy human gut microbiota comprises hundreds of species and among these, bacteria from the Lactobacillaceae family are well documented to have various beneficial effects on health. Furthermore, changes in dietary metal intake, such as for zinc and iron, are frequently correlated with changes in abundance of Lactobacillaceae. Few studies have explored zinc requirements and zinc homeostasis mechanisms in Lactobacillaceae, however. Here we applied a bioinformatics approach to identify and compare predicted zinc uptake and efflux proteins in several Lactobacillaceae genera of intestinal relevance. Few Lactobacillaceae had zinc transporters currently annotated in proteomes retrieved from the UniProt database, but protein sequence-based homology searches revealed that high-affinity ABC transporter genes are likely common, albeit with genus-specific domain features. P-type ATPase transporters are probably also common and some Lactobacillaceae genera code for predicted zinc efflux cation diffusion facilitators. This analysis confirms that Lactobacillaceae harbor genes for various zinc transporter homologs, and provides a foundation for systematic experimental studies to elucidate zinc homeostasis mechanisms in these bacteria.
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Affiliation(s)
- Uyen Huynh
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Brittany K Trinh
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Joanna Elhaj
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
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Li HK, Zhi X, Vieira A, Whitwell HJ, Schricker A, Jauneikaite E, Li H, Yosef A, Andrew I, Game L, Turner CE, Lamagni T, Coelho J, Sriskandan S. Characterization of emergent toxigenic M1 UK Streptococcus pyogenes and associated sublineages. Microb Genom 2023; 9:mgen000994. [PMID: 37093716 PMCID: PMC10210942 DOI: 10.1099/mgen.0.000994] [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: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 04/25/2023] Open
Abstract
Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterize M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of gldA in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs), respectively, that had failed to expand in the population. Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amelia Schricker
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
| | - Hanqi Li
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ahmed Yosef
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, South Yorkshire, UK
| | - Theresa Lamagni
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
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5
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Ercan O, den Besten HMW, Smid EJ, Kleerebezem M. The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:632-636. [PMID: 35445553 PMCID: PMC9544163 DOI: 10.1111/1758-2229.13073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Most microbes reside in oligotrophic environments for extended periods of time, requiring survival strategies that maintain proliferative capacity. We demonstrate that the non-spore-forming Lactococcus lactis KF147 progressively activates the expression of stress-associated functions in response to the declining growth rate elicited by prolonged retentostat cultivation, which coincides with up to 104 -fold increased stress tolerance. Our findings provide a quantified view of the transcription and stress-tolerance adaptations underlying the growth-survival trade-off in L. lactis, and exemplify the hard-wiring of this trade-off in the lactococcal gene regulation network.
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Affiliation(s)
- Onur Ercan
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- NIZO Food Research, P.O. Box 20Ede6710 BAThe Netherlands
| | - Heidy M. W. den Besten
- Laboratory of Food MicrobiologyWageningen University, P.O. Box 17Wageningen6700 AAThe Netherlands
| | - Eddy J. Smid
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- Laboratory of Food MicrobiologyWageningen University, P.O. Box 17Wageningen6700 AAThe Netherlands
| | - Michiel Kleerebezem
- TiFN, Agro Business Park 82Wageningen6708 PWThe Netherlands
- NIZO Food Research, P.O. Box 20Ede6710 BAThe Netherlands
- Host Microbe InteractomicsWageningen University, P.O. Box 338Wageningen6700 AHThe Netherlands
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6
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Zhao G, Kempen PJ, Shetty R, Gu L, Zhao S, Ruhdal Jensen P, Solem C. Harnessing cross-resistance - Sustainable nisin production from low-value food side streams using a Lactococcus lactis mutant with higher nisin-resistance obtained after prolonged chlorhexidine exposure. BIORESOURCE TECHNOLOGY 2022; 348:126776. [PMID: 35104649 DOI: 10.1016/j.biortech.2022.126776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Nisin has a tendency to associate with the cell wall of the producing strain, which inhibits growth and lowers the ceiling for nisin production. With the premise that resistance to the cationic chlorhexidine could reduce nisin binding, variants with higher tolerance to this compound were isolated. One of the resistant isolates, AT0606, had doubled its resistance to nisin, and produced three times more free nisin, when cultured in shake flasks. Characterization revealed that AT0606 had an overall less negatively charged and thicker cell wall, and these changes appeared to be linked to a defect high-affinity phosphate uptake system, and a mutation inactivating the oleate hydratase. Subsequently, the potential of using AT0606 for cost efficient production of nisin was explored, and it was possible to attain a high titer of 13181 IU/mL using a fermentation substrate based on molasses and a by-product from whey protein hydrolysate production.
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Affiliation(s)
- Ge Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Paul J Kempen
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Radhakrishna Shetty
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Liuyan Gu
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Ruhdal Jensen
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Christian Solem
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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7
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Monteiro GA, Duarte SOD. The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome. Microorganisms 2022; 10:microorganisms10020267. [PMID: 35208722 PMCID: PMC8877491 DOI: 10.3390/microorganisms10020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Lactococcus lactis is a food-grade, and generally recognized as safe, bacterium, which making it ideal for producing plasmid DNA (pDNA) or recombinant proteins for industrial or pharmaceutical applications. The present paper reviews the major findings from L. lactis transcriptome and proteome studies, with an overexpression of native or recombinant proteins. These studies should provide important insights on how to engineer the plasmid vectors and/or the strains in order to achieve high pDNA or recombinant proteins yields, with high quality standards. L. lactis harboring high copy numbers of plasmids for DNA vaccines production showed altered proteome profiles, when compared with a smaller copy number plasmid. For live mucosal vaccination applications, the cell-wall anchored antigens had shown more promising results, when compared with intracellular or secreted antigens. However, previous transcriptome and proteome studies demonstrated that engineering L. lactis to express membrane proteins, mainly with a eukaryotic background, increases the overall cellular burden. Genome engineering strategies could be used to knockout or overexpress the pinpointed genes, so as to increase the profitability of the process. Studies about the effect of protein overexpression on Escherichia coli and Bacillus subtillis transcriptome and proteome are also included.
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Affiliation(s)
- Gabriel A. Monteiro
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Sofia O. D. Duarte
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Correspondence:
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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10
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Liu G, Chang H, Qiao Y, Huang K, Zhang A, Zhao Y, Feng Z. Profiles of Small Regulatory RNAs at Different Growth Phases of Streptococcus thermophilus During pH-Controlled Batch Fermentation. Front Microbiol 2021; 12:765144. [PMID: 35035386 PMCID: PMC8753986 DOI: 10.3389/fmicb.2021.765144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 12/02/2022] Open
Abstract
Small regulatory RNA (sRNA) has been shown to play an important role under various stress conditions in bacteria, and it plays a vital role in regulating growth, adaptation and survival through posttranscriptional control of gene expression in bacterial cells. Streptococcus thermophilus is widely used as a starter culture in the manufacture of fermented dairy products. However, the lack of reliable information on the expression profiles and potential physiological functions of sRNAs in this species hinders our understanding of the importance of sRNAs in S. thermophilus. The present study was conducted to assess the expression profiles of sRNAs in S. thermophilus and to identify sRNAs that exhibited significant changes. A total of 530 potential sRNAs were identified, including 198 asRNAs, 135 sRNAs from intergenic regions, and 197 sRNAs from untranslated regions (UTRs). Significant changes occurred in the expression of 238, 83, 194, and 139 sRNA genes during the lag, early exponential growth, late exponential growth, and stationary phases, respectively. The expression of 14 of the identified sRNAs was verified by qRT-PCR. Predictions of the target genes of these candidate sRNAs showed that the primary metabolic pathways targeted were involved in carbon metabolism, biosynthesis of amino acids, ABC transporters, the metabolism of amino and nucleotide sugars, purine metabolism, and the phosphotransferase system. The expression of the predicted target genes was further analyzed to better understand the roles of sRNAs during different growth stages. The results suggested that these sRNAs play crucial roles by regulating biological pathways during different growth phases of S. thermophilus. According to the results, sRNAs sts141, sts392, sts318, and sts014 are involved in the regulation of osmotic stress. sRNAs sts508, sts087, sts372, sts141, sts375, and sts119 are involved in the regulation of starvation stress. sRNAs sts129, sts226, sts166, sts231, sts204, sts145, and sts236 are involved in arginine synthesis. sRNAs sts033, sts341, sts492, sts140, sts230, sts172, and sts377 are involved in the ADI pathway. The present study provided valuable information for the functional study of sRNAs in S. thermophilus and indicated a future research direction for sRNA in S. thermophilus. Overall, our results provided new insights for understanding the complex regulatory network of sRNAs in S. thermophilus.
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Affiliation(s)
- Gefei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
| | - Haode Chang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
| | - Yali Qiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
| | - Kai Huang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
| | - Ao Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
| | - Yu Zhao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
- Yu Zhao,
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Chanjiang Road,150030, Harbin, Heilongjiang, China
- College of Food and Biological Engineering, Qiqihar University, 42 Wenhua Road, 160006, Qiqihar, China
- *Correspondence: Zhen Feng,
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11
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Martínez B, Rodríguez A, Kulakauskas S, Chapot-Chartier MP. Cell wall homeostasis in lactic acid bacteria: threats and defences. FEMS Microbiol Rev 2021; 44:538-564. [PMID: 32495833 PMCID: PMC7476776 DOI: 10.1093/femsre/fuaa021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.
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Affiliation(s)
- Beatriz Martínez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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12
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Liu G, Qiao Y, Zhang Y, Leng C, Chen H, Sun J, Fan X, Li A, Feng Z. Metabolic Profiles of Carbohydrates in Streptococcus thermophilus During pH-Controlled Batch Fermentation. Front Microbiol 2020; 11:1131. [PMID: 32547529 PMCID: PMC7272703 DOI: 10.3389/fmicb.2020.01131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/05/2020] [Indexed: 02/05/2023] Open
Abstract
Revealing the metabolic profiles of carbohydrates with their regulatory genes and metabolites is conducive to understanding their mechanism of utilization in Streptococcus thermophilus MN-ZLW-002 during pH-controlled batch fermentation. Transcriptomics and metabolomics were used to study carbohydrate metabolism. More than 200 unigenes were involved in carbohydrate transport. Of these unigenes, 55 were involved in the phosphotransferase system (PTS), which had higher expression levels than those involved in ABC protein-dependent systems, permeases, and symporters. The expression levels of the genes involved in the carbohydrate transport systems and phosphate transport system were high at the end-lag and end-exponential growth phases, respectively. In addition, 166 differentially expressed genes (DEGs) associated with carbohydrate metabolism were identified. Most genes had their highest expression levels at the end-lag phase. The pfk, ldh, zwf, and E3.2.1.21 genes involved in the glycolytic pathway had higher expression levels at the end-exponential growth phase than the mid-exponential growth phase. The results showed high expression levels of lacZ and galKTM genes and reabsorption of extracellular galactose. S. thermophilus MN-ZLW-002 can metabolize and utilize galactose. Overall, this comprehensive network of carbohydrate metabolism is useful for further studies of the control of glycolytic pathway during the high-density culture of S. thermophilus.
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Affiliation(s)
- Gefei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yali Qiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yanjiao Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Cong Leng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Hongyu Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Jiahui Sun
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Aili Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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Andersen JM, Pedersen CM, Bang-Berthelsen CH. Omics-based comparative analysis of putative mobile genetic elements in Lactococcus lactis. FEMS Microbiol Lett 2019; 366:5487889. [PMID: 31074793 DOI: 10.1093/femsle/fnz102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/09/2019] [Indexed: 12/29/2022] Open
Abstract
Lactococcus lactis is globally used in food fermentation. Genomics is useful to investigate speciation and differential occurrence of (un)desired gene functions, often related to mobile DNA. This study investigates L. lactis for putative chromosomal mobile genetic elements through comparative genomics, and analyses how they contribute to chromosomal variation at strain level. Our work identified 95 loci that may range over 10% of the chromosome size when including prophages, and the loci display a marked differential occurrence in the analysed strains. Analysis of differential transcriptomics data revealed how mobile genetic elements may impact the host physiology in response to conditional changes. This insight in the genetic variation of mobile genetic elements in L. lactis holds potential to further identify important functions related to food and biotechnology applications within this important species.
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Affiliation(s)
- Joakim Mark Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
| | - Christine Møller Pedersen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 201, 2800 Kgs. Lyngby, Denmark
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Reverón I, Plaza-Vinuesa L, Franch M, de Las Rivas B, Muñoz R, López de Felipe F. Transcriptome-Based Analysis in Lactobacillus plantarum WCFS1 Reveals New Insights into Resveratrol Effects at System Level. Mol Nutr Food Res 2018; 62:e1700992. [PMID: 29573169 DOI: 10.1002/mnfr.201700992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/16/2018] [Indexed: 12/12/2022]
Abstract
SCOPE This study was undertaken to expand our insights into the mechanisms involved in the tolerance to resveratrol (RSV) that operate at system-level in gut microorganisms and advance knowledge on new RSV-responsive gene circuits. METHODS AND RESULTS Whole genome transcriptional profiling was used to characterize the molecular response of Lactobacillus plantarum WCFS1 to RSV. DNA repair mechanisms were induced by RSV and responses were triggered to decrease the load of copper, a metal required for RSV-mediated DNA cleavage, and H2 S, a genotoxic gas. To counter the effects of RSV, L. plantarum strongly up- or downregulated efflux systems and ABC transporters pointing to transport control of RSV across the membrane as a key mechanism for RSV tolerance. L. plantarum also downregulated tRNAs, induced chaperones, and reprogrammed its transcriptome to tightly control ammonia levels. RSV induced a probiotic effector gene and a likely deoxycholate transporter, two functions that improve the host health status. CONCLUSION Our data identify novel protective mechanisms involved in RSV tolerance operating at system level in a gut microbe. These insights could influence the way RSV is used for a better management of gut microbial ecosystems to obtain associated health benefits.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040, Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040, Madrid, Spain
| | - Mónica Franch
- National Center for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040, Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040, Madrid, Spain
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN-CSIC), 28040, Madrid, Spain
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