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Hackley RK, Vreugdenhil-Hayslette A, Darnell CL, Schmid AK. A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities. PLoS Genet 2024; 20:e1011115. [PMID: 38227606 PMCID: PMC10817205 DOI: 10.1371/journal.pgen.1011115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 12/22/2023] [Indexed: 01/18/2024] Open
Abstract
Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica, to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica, TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum, activation of ppsA and repression of pykA, is absent in Har. hispanica. Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica. Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
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Affiliation(s)
- Rylee K. Hackley
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | | | - Cynthia L. Darnell
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, United States of America
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2
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Buda DM, Szekeres E, Tudoran LB, Esclapez J, Banciu HL. Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T. BMC Microbiol 2023; 23:381. [PMID: 38049746 PMCID: PMC10694973 DOI: 10.1186/s12866-023-03133-z] [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: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance. RESULTS The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data. CONCLUSIONS Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.
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Grants
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- VIGRO-016 Vicerrectorado de Investigación y Transferencia de Conocimiento of the University of Alicante
- Ministry of Research, Innovation and Digitization, CNCS/CCCDI – UEFISCD
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Affiliation(s)
- Doriana Mădălina Buda
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Edina Szekeres
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Lucian Barbu Tudoran
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Julia Esclapez
- Biochemistry and Molecular Biology and Soil and Agricultural Chemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Alicante, Spain
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania.
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3
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Pastor MM, Sakrikar S, Rodriguez DN, Schmid AK. Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. Biomolecules 2022; 12:biom12050682. [PMID: 35625610 PMCID: PMC9138242 DOI: 10.3390/biom12050682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80–90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.
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Affiliation(s)
- Mar Martinez Pastor
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
| | - Saaz Sakrikar
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | | | - Amy K. Schmid
- Biology Department, Duke University, Durham, NC 27708, USA; (M.M.P.); (S.S.)
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
- Correspondence: ; Tel.: +919-613-4464
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4
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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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5
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Rodríguez-Herrero V, Peris A, Camacho M, Bautista V, Esclapez J, Bonete MJ. Novel Glutamate-Putrescine Ligase Activity in Haloferax mediterranei: A New Function for glnA-2 Gene. Biomolecules 2021; 11:biom11081156. [PMID: 34439822 PMCID: PMC8394153 DOI: 10.3390/biom11081156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/25/2021] [Accepted: 07/31/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of the halophilic archaea Haloferax mediterranei contains three ORFs that show homology with glutamine synthetase (GS) (glnA-1, glnA-2, and glnA-3). Previous studies have focused on the role of GlnA-1, suggesting that proteins GlnA-2 and GlnA-3 could play a different role to that of GS. Glutamine synthetase (EC 6.3.1.2) belongs to the class of ligases, including 20 subclasses of other different enzymes, such as aspartate–ammonia ligase (EC 6.3.1.1), glutamate–ethylamine ligase (EC 6.3.1.6), and glutamate–putrescine ligase (EC 6.3.1.11). The reaction catalyzed by glutamate–putrescine ligase is comparable to the reaction catalyzed by glutamine synthetase (GS). Both enzymes can bind a glutamate molecule to an amino group: ammonium (GS) or putrescine (glutamate–putrescine ligase). In addition, they present the characteristic catalytic domain of GS, showing significant similarities in their structure. Although these proteins are annotated as GS, the bioinformatics and experimental results obtained in this work indicate that the GlnA-2 protein (HFX_1688) is a glutamate–putrescine ligase, involved in polyamine catabolism. The most significant results are those related to glutamate–putrescine ligase’s activity and the analysis of the transcriptional and translational expression of the glnA-2 gene in the presence of different nitrogen sources. This work confirms a new metabolic pathway in the Archaea domain which extends the knowledge regarding the utilization of alternative nitrogen sources in this domain.
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Affiliation(s)
- Verónica Rodríguez-Herrero
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Arnau Peris
- Institute for Integrative Systems Biology, I2SysBio, Campus Burjassot, University of Valencia-CSIC, 46908 Valencia, Spain;
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Division, Faculty of Science, University of Alicante, 03080 Alicante, Spain; (V.R.-H.); (M.C.); (V.B.)
- Correspondence: (J.E.); (M.-J.B.); Tel.: +34-965-903-880 (J.E. & M.-J.B.)
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6
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Payá G, Bautista V, Camacho M, Bonete MJ, Esclapez J. Functional analysis of Lsm protein under multiple stress conditions in the extreme haloarchaeon Haloferax mediterranei. Biochimie 2021; 187:33-47. [PMID: 33992715 DOI: 10.1016/j.biochi.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/24/2023]
Abstract
The Sm, like-Sm, and Hfq proteins belonging to the Sm superfamily of proteins are represented in all domains of life. These proteins are involved in several RNA metabolism pathways. The functions of bacterial Hfq and eukaryotic Sm proteins have been described, but knowledge about the in vivo functions of archaeal Sm proteins remains limited. This study aims to improve the understanding of Lsm proteins and their role using the haloarchaeon Haloferax mediterranei as a model microorganism. The Haloferax mediterranei genome contains one lsm gene that overlaps with the rpl37e gene. To determine the expression of lsm and rpl37e genes and the co-transcription of both, reverse transcription-polymerase chain reaction (RT-PCR) analyses were performed under different standard and stress conditions. The results suggest that the expression of lsm and rpl37e is constitutive. Co-transcription occurs at sub-optimal salt concentrations and temperatures, depending on the growth phase. The halophilic Lsm protein contains two Sm motifs, Sm1 and Sm2, and the sequence encoding the Sm2 motif also constitutes the promoter of the rpl37e gene. To investigate their biological functions, the lsm deletion mutant and the Sm1 motif deletion mutant, where the Sm2 motif remained intact, were generated and characterised. Comparison of the lsm deletion mutant, Sm1 deletion mutant, and the parental strain HM26 under standard and stress growth conditions revealed growth differences. Finally, swarming assays in complex and defined media showed greater swarming capacity in the deletion mutants.
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Affiliation(s)
- Gloria Payá
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
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7
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Märkle P, Maier LK, Maaß S, Hirschfeld C, Bartel J, Becher D, Voß B, Marchfelder A. A Small RNA Is Linking CRISPR-Cas and Zinc Transport. Front Mol Biosci 2021; 8:640440. [PMID: 34055875 PMCID: PMC8155600 DOI: 10.3389/fmolb.2021.640440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon Haloferax volcanii, a plethora of sRNAs have been identified; however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from Haloferax volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, and the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild-type Haloferax cells and the deletion mutant revealed upregulation of six genes in the deletion strain, showing that this sRNA has a clearly defined function. Three of the six upregulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, and ZnuC1) suggesting the involvement of s479 in the regulation of zinc transport. Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. Furthermore, electrophoretic mobility shift assays demonstrate a direct interaction of s479 with the target znuC1 mRNA. Proteome comparison of wild-type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. Interestingly, s479 is not only encoded next to CRISPR-cas genes, but the mature s479 contains a crRNA-like 5' handle, and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. Together, this might suggest that the CRISPR-Cas system is involved in s479 function.
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Affiliation(s)
- Pascal Märkle
- Department of Biology II, Ulm University, Ulm, Germany
| | | | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Björn Voß
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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8
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Pastor-Soler S, Camacho M, Bautista V, Bonete MJ, Esclapez J. Towards the Elucidation of Assimilative nasABC Operon Transcriptional Regulation in Haloferax mediterranei. Genes (Basel) 2021; 12:genes12050619. [PMID: 33921943 PMCID: PMC8143581 DOI: 10.3390/genes12050619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 11/22/2022] Open
Abstract
The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the regulation at the transcriptional level of the assimilative nasABC operon (HFX_2002 to HFX_2004) through different approaches. Characterization of its promoter region using β-galactosidase as a reporter gene and site-directed mutagenesis has allowed us to identify possible candidate binding regions for a transcriptional factor. The identification of a potential transcriptional regulator related to nitrogen metabolism has become a real challenge due to the lack of information on haloarchaea. The investigation of protein–DNA binding by streptavidin bead pull-down analysis combined with mass spectrometry resulted in the in vitro identification of a transcriptional regulator belonging to the Lrp/AsnC family, which binds to the nasABC operon promoter (p.nasABC). To our knowledge, this study is the first report to suggest the AsnC transcriptional regulator as a powerful candidate to play a regulatory role in nasABC gene expression in Hfx. mediterranei and, in general, in the assimilatory nitrogen pathway.
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9
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New proposal of nitrogen metabolism regulation by small RNAs in the extreme halophilic archaeon Haloferax mediterranei. Mol Genet Genomics 2020; 295:775-785. [DOI: 10.1007/s00438-020-01659-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/27/2020] [Indexed: 12/16/2022]
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10
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Hwang S, Chavarria NE, Hackley RK, Schmid AK, Maupin-Furlow JA. Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. Int J Mol Sci 2019; 20:ijms20194784. [PMID: 31561502 PMCID: PMC6801745 DOI: 10.3390/ijms20194784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Haloferax volcanii, a well-developed model archaeon for genomic, transcriptomic, and proteomic analyses, can grow on a defined medium of abundant and intermediate levels of fixed nitrogen. Here we report a global profiling of gene expression of H. volcanii grown on ammonium as an abundant source of fixed nitrogen compared to l-alanine, the latter of which exemplifies an intermediate source of nitrogen that can be obtained from dead cells in natural habitats. By comparing the two growth conditions, 30 genes were found to be differentially expressed, including 16 genes associated with amino acid metabolism and transport. The gene expression profiles contributed to mapping ammonium and l-alanine usage with respect to transporters and metabolic pathways. In addition, conserved DNA motifs were identified in the putative promoter regions and transcription factors were found to be in synteny with the differentially expressed genes, leading us to propose regulons of transcriptionally co-regulated operons. This study provides insight to how H. volcanii responds to and utilizes intermediate vs. abundant sources of fixed nitrogen for growth, with implications for conserved functions in related halophilic archaea.
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Affiliation(s)
- Sungmin Hwang
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | - Nikita E Chavarria
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA.
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA.
- Center for Genomics and Computational Biology, Duke University, Duke University, Durham, NC 27708, USA.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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11
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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12
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Musa H, Kasim FH, Gunny AAN, Gopinath SCB, Chinni SV, Ahmad MA. Whole genome sequence of moderate halophilic marine bacterium Marinobacter litoralis SW-45: Abundance of non-coding RNAs. Int J Biol Macromol 2019; 133:1288-1298. [PMID: 31055112 DOI: 10.1016/j.ijbiomac.2019.05.003] [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: 01/23/2019] [Revised: 05/01/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022]
Abstract
A report on the de novo Whole Genome Sequence (WGS) of Marinobacter litoralis SW-45, a moderately salt-tolerant bacterium isolated from the seawater in Malaysia is presented. The strain has a genome size of 3.45 Mb and is capable of producing halophilic lipase, protease and esterase enzymes. Computational prediction of non-coding RNA (ncRNA) genes in M. litoralis SW-45 was performed using standalone software known as the non-coding RNA characterization (nocoRNAc). In addition, a phylogenetic tree showing the evolutionary relationship between the strain and other members of the genus Marinobacter was constructed using 16SrRNA sequence information. A total of 385 ncRNA transcripts, 1124 terminator region, and 2350 Stress Induced Duplex Destabilization sites were predicted. The current WGS shotgun project has provided the relevant genetic information that may be useful for the strain's improvement studies. This manuscript gives the first description of M. litoralis with a complete genome.
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Affiliation(s)
- Haliru Musa
- School of Bioprocess Engineering, Universiti Malaysia Perlis UNIMAP, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600, Malaysia; Centre of Excellence for Biomass Utilization, School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600 Malaysia.
| | - Farizul Hafiz Kasim
- School of Bioprocess Engineering, Universiti Malaysia Perlis UNIMAP, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600, Malaysia; Centre of Excellence for Biomass Utilization, School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600 Malaysia.
| | - Ahmad Anas Nagoor Gunny
- Centre of Excellence for Biomass Utilization, School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600 Malaysia; Department of Chemical Engineering Technology, Faculty of Engineering Technology, Universiti Malaysia Perlis, Kampus UniCITI Alam, Sungai Chuchuh, Padang Besar 02100, Perlis, Malaysia.
| | - Subash C B Gopinath
- School of Bioprocess Engineering, Universiti Malaysia Perlis UNIMAP, Kompleks Pusat Pengajian Jejawi 3, Arau, Perlis, 02600, Malaysia.
| | - Suresh V Chinni
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, 08100, Malaysia.
| | - Mohd Azmier Ahmad
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, Seri Ampangan, Nibong Tebai, Penang, 14300, Malaysia.
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Olaya-Abril A, Luque-Almagro VM, Pérez MD, López CM, Amil F, Cabello P, Sáez LP, Moreno-Vivián C, Roldán MD. Putative small RNAs controlling detoxification of industrial cyanide-containing wastewaters by Pseudomonas pseudoalcaligenes CECT5344. PLoS One 2019; 14:e0212032. [PMID: 30735537 PMCID: PMC6368324 DOI: 10.1371/journal.pone.0212032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/26/2019] [Indexed: 11/21/2022] Open
Abstract
The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 uses free cyanide and several metal−cyanide complexes as the sole nitrogen source and tolerates high concentrations of metals like copper, zinc and iron, which are present in the jewelry wastewaters. To understand deeply the regulatory mechanisms involved in the transcriptional regulation of cyanide-containing wastewaters detoxification by P. pseudoalcaligenes CECT5344, RNA-Seq has been performed from cells cultured with a cyanide-containing jewelry wastewater, sodium cyanide or ammonium chloride as the sole nitrogen source. Small RNAs (sRNAs) that may have potential regulatory functions under cyanotrophic conditions were identified. In total 20 sRNAs were identified to be differentially expressed when compared the jewelry residue versus ammonium as nitrogen source, 16 of which could be amplified successfully by RT-PCR. As predicted targets of these 16 sRNAs were several components of the nit1C gene cluster encoding the nitrilase NitC essential for cyanide assimilation, the cioAB gene cluster that codes for the cyanide-insensitive cytochrome bd-type terminal oxidase, the medium length-polyhydroxyalkanoates (ml-PHAs) gene cluster, and gene clusters related with a global nitrogen limitation response like those coding for glutamine synthase and urease. Other targets were non-clustered genes (or their products) involved in metal resistance and iron acquisition, such as metal extrusion systems and the ferric uptake regulatory (Fur) protein, and a GntR-like regulatory family member probably involved in the regulation of the cyanide assimilation process in the strain CECT5344. Induction of genes targeted by sRNAs in the jewelry residue was demonstrated by qRT-PCR.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor Manuel Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Pérez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Cristina María López
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Francisco Amil
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Campus de Rabanales, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara Paloma Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
- * E-mail:
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14
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Gómez-Villegas P, Vigara J, León R. Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain). Mar Drugs 2018; 16:md16090332. [PMID: 30213145 PMCID: PMC6164061 DOI: 10.3390/md16090332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 12/11/2022] Open
Abstract
The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.
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Affiliation(s)
- Patricia Gómez-Villegas
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Javier Vigara
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Rosa León
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
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