1
|
Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol 2024; 121:742-766. [PMID: 38204420 PMCID: PMC11023807 DOI: 10.1111/mmi.15225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
Collapse
Affiliation(s)
- Rylee K. Hackley
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Sungmin Hwang
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Jake T. Herb
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Preeti Bhanap
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Katie Lam
- Biology Department, Duke University, Durham, North Carolina, USA
| | | | | | | | - Johnathan H. Martin
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Amy K. Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| |
Collapse
|
2
|
Schiller H, Hong Y, Kouassi J, Rados T, Kwak J, DiLucido A, Safer D, Marchfelder A, Pfeiffer F, Bisson A, Schulze S, Pohlschroder M. Identification of structural and regulatory cell-shape determinants in Haloferax volcanii. Nat Commun 2024; 15:1414. [PMID: 38360755 PMCID: PMC10869688 DOI: 10.1038/s41467-024-45196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative proteomics, genetics, and live-cell imaging to identify mutants that only form rods or disks. We compared the proteomes of the mutants with wild-type cells across growth phases, thereby distinguishing between protein abundance changes specific to cell shape and those related to growth phases. The results identified a diverse set of proteins, including predicted transporters, transducers, signaling components, and transcriptional regulators, as important for cell-shape determination. Through phenotypic characterization of deletion strains, we established that rod-determining factor A (RdfA) and disk-determining factor A (DdfA) are required for the formation of rods and disks, respectively. We also identified structural proteins, including an actin homolog that plays a role in disk-shape morphogenesis, which we named volactin. Using live-cell imaging, we determined volactin's cellular localization and showed its dynamic polymerization and depolymerization. Our results provide insights into archaeal cell-shape determination, with possible implications for understanding the evolution of cell morphology regulation across domains.
Collapse
Affiliation(s)
- Heather Schiller
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Yirui Hong
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Joshua Kouassi
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Theopi Rados
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Jasmin Kwak
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Anthony DiLucido
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Daniel Safer
- University of Pennsylvania, Department of Physiology, Philadelphia, PA, 19104, USA
| | | | - Friedhelm Pfeiffer
- Biology II, Ulm University, 89069, Ulm, Germany
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Alexandre Bisson
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA.
| | - Stefan Schulze
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA.
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, 14623, USA.
| | | |
Collapse
|
3
|
Gomes-Filho JV, Breuer R, Morales-Filloy HG, Pozhydaieva N, Borst A, Paczia N, Soppa J, Höfer K, Jäschke A, Randau L. Identification of NAD-RNA species and ADPR-RNA decapping in Archaea. Nat Commun 2023; 14:7597. [PMID: 37989750 PMCID: PMC10663502 DOI: 10.1038/s41467-023-43377-x] [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: 11/08/2022] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.
Collapse
Affiliation(s)
| | - Ruth Breuer
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | | | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Lennart Randau
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany.
| |
Collapse
|
4
|
Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ. The chromatin landscape of the euryarchaeon Haloferax volcanii. Genome Biol 2023; 24:253. [PMID: 37932847 PMCID: PMC10626798 DOI: 10.1186/s13059-023-03095-5] [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: 02/14/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes, not all archaea possess histones and it is not clear if histones are a main packaging component for all that do. Despite increased interest in archaeal chromatin in recent years, its properties have been little studied using genomic tools. RESULTS Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that while H. volcanii promoters exist in a preferentially accessible state, unlike most eukaryotes, modulation of transcriptional activity is not associated with changes in promoter accessibility. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii and find that Haloferax chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. CONCLUSIONS Our results provide the first comprehensive maps of chromatin accessibility and active transcription in Haloferax across conditions and thus a foundation for future functional studies of archaeal chromatin.
Collapse
Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Tong Wu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
5
|
Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564843. [PMID: 37961278 PMCID: PMC10634947 DOI: 10.1101/2023.10.30.564843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
Collapse
Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California, USA
| |
Collapse
|
6
|
Xu Q, Du Q, Gao J, Chen L, Dong X, Li J. A robust genetic toolbox for fine-tuning gene expression in the CO 2-Fixing methanogenic archaeon Methanococcus maripaludis. Metab Eng 2023; 79:130-145. [PMID: 37495072 DOI: 10.1016/j.ymben.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Libraries of well-characterized genetic elements for fine-tuning gene expression are essential for biological and biotechnological research and applications. The fast-growing and genetically tractable methanogen, Methanococcus maripaludis, is a promising host organism for biotechnological conversion of carbon dioxide and renewable hydrogen into fuels and value-added products, as well as fundamental biological studies of archaea. However, the lack of molecular tools for gene expression has hindered its application as a workhorse to fine-tune gene and metabolic pathway expressions. In this study, we developed a genetic toolbox, including libraries of promoters, ribosome binding sites (RBS), and neutral sites for chromosomal integration, to facilitate precise gene expression in M. maripaludis. We generated a promoter library consisting of 81 constitutive promoters with expression strengths spanning a ∼104-fold dynamic range. Importantly, we identified a base composition rule for strong archaeal promoters and successfully remodeled weak promoters, enhancing their activities by up to 120-fold. We also established an RBS library containing 42 diverse RBS sequences with translation strengths covering a ∼100-fold dynamic range. Additionally, we identified eight neutral sites and developed a one-step, Cas9-based marker-less knock-in approach for chromosomal integration. We successfully applied the characterized promoter and RBS elements to significantly improve recombinant protein expression by 41-fold and modulate essential gene expression to generate corresponding physiological changes in M. maripaludis. Therefore, this work establishes a solid foundation for utilizing this autotrophic methanogen as an ideal workhorse for archaeal biology and biotechnological studies and applications.
Collapse
Affiliation(s)
- Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Du
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Jian Gao
- School of Basic Medical Sciences and School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
| |
Collapse
|
7
|
Zehentner B, Scherer S, Neuhaus K. Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers. BMC Microbiol 2023; 23:243. [PMID: 37653502 PMCID: PMC10469882 DOI: 10.1186/s12866-023-02988-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.
Collapse
Affiliation(s)
- Barbara Zehentner
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
| |
Collapse
|
8
|
Sharma D, Sharma K, Mishra A, Siwach P, Mittal A, Jayaram B. Molecular dynamics simulation-based trinucleotide and tetranucleotide level structural and energy characterization of the functional units of genomic DNA. Phys Chem Chem Phys 2023; 25:7323-7337. [PMID: 36825435 DOI: 10.1039/d2cp04820e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Genomes of most organisms on earth are written in a universal language of life, made up of four units - adenine (A), thymine (T), guanine (G), and cytosine (C), and understanding the way they are put together has been a great challenge to date. Multiple efforts have been made to annotate this wonderfully engineered string of DNA using different methods but they lack a universal character. In this article, we have investigated the structural and energetic profiles of both prokaryotes and eukaryotes by considering two essential genomic sites, viz., the transcription start sites (TSS) and exon-intron boundaries. We have characterized these sites by mapping the structural and energy features of DNA obtained from molecular dynamics simulations, which considers all possible trinucleotide and tetranucleotide steps. For DNA, these physicochemical properties show distinct signatures at the TSS and intron-exon boundaries. Our results firmly convey the idea that DNA uses the same dialect for prokaryotes and eukaryotes and that it is worth going beyond sequence-level analyses to physicochemical space to determine the functional destiny of DNA sequences.
Collapse
Affiliation(s)
- Dinesh Sharma
- Supercomputing Facility for Bioinformatics & Computational Biology, Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Kopal Sharma
- Supercomputing Facility for Bioinformatics & Computational Biology, Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Aditya Mittal
- Supercomputing Facility for Bioinformatics & Computational Biology, Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India.,Department of Chemistry, Indian Institute of Technology, Delhi, India.
| |
Collapse
|
9
|
Machine learning and statistics shape a novel path in archaeal promoter annotation. BMC Bioinformatics 2022; 23:171. [PMID: 35538405 PMCID: PMC9087966 DOI: 10.1186/s12859-022-04714-x] [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: 12/16/2021] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background Archaea are a vast and unexplored domain. Bioinformatic techniques might enlighten the path to a higher quality genome annotation in varied organisms. Promoter sequences of archaea have the action of a plethora of proteins upon it. The conservation found in a structural level of the binding site of proteins such as TBP, TFB, and TFE aids RNAP-DNA stabilization and makes the archaeal promoter prone to be explored by statistical and machine learning techniques. Results and discussions In this study, experimentally verified promoter sequences of the organisms Haloferax volcanii, Sulfolobus solfataricus, and Thermococcus kodakarensis were converted into DNA duplex stability attributes (i.e. numerical variables) and were classified through Artificial Neural Networks and an in-house statistical method of classification, being tested with three forms of controls. The recognition of these promoters enabled its use to validate unannotated promoter sequences in other organisms. As a result, the binding site of basal transcription factors was located through a DNA duplex stability codification. Additionally, the classification presented satisfactory results (above 90%) among varied levels of control. Concluding remarks The classification models were employed to perform genomic annotation into the archaea Aciduliprofundum boonei and Thermofilum pendens, from which potential promoters have been identified and uploaded into public repositories. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04714-x.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Choe D, Kim K, Kang M, Lee SG, Cho S, Palsson B, Cho BK. Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli. Nucleic Acids Res 2022; 50:4171-4186. [PMID: 35357499 PMCID: PMC9023263 DOI: 10.1093/nar/gkac206] [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: 09/07/2021] [Revised: 03/12/2022] [Accepted: 03/29/2022] [Indexed: 11/15/2022] Open
Abstract
As the design of genetic circuitry for synthetic biology becomes more sophisticated, diverse regulatory bioparts are required. Despite their importance, well-characterized 3′-untranslated region (3′-UTR) bioparts are limited. Thus, transcript 3′-ends require further investigation to understand the underlying regulatory role and applications of the 3′-UTR. Here, we revisited the use of Term-Seq in the Escherichia coli strain K-12 MG1655 to enhance our understanding of 3′-UTR regulatory functions and to provide a diverse collection of tunable 3′-UTR bioparts with a wide termination strength range. Comprehensive analysis of 1,629 transcript 3′-end positions revealed multiple 3′-termini classes generated through transcription termination and RNA processing. The examination of individual Rho-independent terminators revealed a reduction in downstream gene expression over a wide range, which led to the design of novel synthetic metabolic valves that control metabolic fluxes in branched pathways. These synthetic metabolic valves determine the optimal balance of heterologous pathways for maximum target biochemical productivity. The regulatory strategy using 3′-UTR bioparts is advantageous over promoter- or 5′-UTR-based transcriptional control as it modulates gene expression at transcription levels without trans-acting element requirements (e.g. transcription factors). Our results provide a foundational platform for 3′-UTR engineering in synthetic biology applications.
Collapse
Affiliation(s)
- Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| |
Collapse
|
12
|
Gelsinger DR, DiRuggiero J. Small RNA-Sequencing Library Preparation for the Halophilic Archaeon Haloferax volcanii. Methods Mol Biol 2022; 2522:243-254. [PMID: 36125754 DOI: 10.1007/978-1-0716-2445-6_15] [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] [Indexed: 06/15/2023]
Abstract
Posttranscriptional regulation actuated by small RNAs (sRNAs) plays essential roles in a wide variety of cellular processes, especially in stress responses and environmental signaling. Hundreds of sRNAs have recently been discovered in archaea using genome-wide approaches but the molecular mechanisms of only a few have been characterized experimentally. Here, we describe how to build sRNA sequencing libraries using size-selected total RNA in the model archaeon, Haloferax volcanii , to provide a tool to further characterize sRNAs in archaea.
Collapse
Affiliation(s)
- Diego Rivera Gelsinger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Jocelyne DiRuggiero
- Department of Biology and Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
13
|
Manning RJ, Tschurtschenthaler M, Sabitzer S, Witte A. Manipulation of viral protein production using the PCNA of halovirus фCh1 via alternative start codon usage. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
|
14
|
The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress. Microorganisms 2021; 10:microorganisms10010014. [PMID: 35056463 PMCID: PMC8779481 DOI: 10.3390/microorganisms10010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of the ribosome as an additional player in regulating gene expression is only beginning to emerge. Ribosome-interacting proteins are central to this translational regulation and include universally conserved ribosome interacting proteins, such as the ATPase YchF (Ola1 in eukaryotes). In both eukaryotes and bacteria, the cellular concentrations of YchF/Ola1 determine the ability to cope with different stress conditions and are linked to several pathologies in humans. The available data indicate that YchF/Ola1 regulates the stress response via controlling non-canonical translation initiation and via protein degradation. Although the molecular mechanisms appear to be different between bacteria and eukaryotes, increased non-canonical translation initiation is a common consequence of YchF/Ola1 regulated translational control in E. coli and H. sapiens. In this review, we summarize recent insights into the role of the universally conserved ATPase YchF/Ola1 in adapting translation to unfavourable conditions.
Collapse
|
15
|
Gemayel K, Lomsadze A, Borodovsky M. StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. FRONTIERS IN BIOINFORMATICS 2021; 1:704157. [PMID: 36303749 PMCID: PMC9581028 DOI: 10.3389/fbinf.2021.704157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3'ends. Nonetheless, predictions of gene starts would not match for 15-25% of genes in a genome. This discrepancy is a serious issue that is difficult to be resolved due to the absence of sufficiently large sets of genes with experimentally verified starts. We have introduced StartLink that infers gene starts from conservation patterns revealed by multiple alignments of homologous nucleotide sequences. We also have introduced StartLink+ combining both ab initio and alignment-based methods. The ability of StartLink to predict the start of a given gene is restricted by the availability of homologs in a database. We observed that StartLink made predictions for 85% of genes per genome on average. The StartLink+ accuracy was shown to be 98-99% on the sets of genes with experimentally verified starts. In comparison with database annotations, we observed that the annotated gene starts deviated from the StartLink+ predictions for ∼5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes on average. The use of StartLink+ has a potential to significantly improve gene start annotation in genomic databases.
Collapse
Affiliation(s)
- Karl Gemayel
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
| | - Alexandre Lomsadze
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
| | - Mark Borodovsky
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| |
Collapse
|
16
|
Halovirus HF2 Intergenic Repeat Sequences Carry Promoters. Viruses 2021; 13:v13122388. [PMID: 34960657 PMCID: PMC8707807 DOI: 10.3390/v13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.
Collapse
|
17
|
Schramm F, Borst A, Linne U, Soppa J. Elucidation of the Translation Initiation Factor Interaction Network of Haloferax volcanii Reveals Coupling of Transcription and Translation in Haloarchaea. Front Microbiol 2021; 12:742806. [PMID: 34764944 PMCID: PMC8576121 DOI: 10.3389/fmicb.2021.742806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/29/2021] [Indexed: 02/04/2023] Open
Abstract
Translation is an important step in gene expression. Initiation of translation is rate-limiting, and it is phylogenetically more diverse than elongation or termination. Bacteria contain only three initiation factors. In stark contrast, eukaryotes contain more than 10 (subunits of) initiation factors (eIFs). The genomes of archaea contain many genes that are annotated to encode archaeal homologs of eukaryotic initiation factors (aIFs). However, experimental characterization of aIFs is scarce and mostly restricted to very few species. To broaden the view, the protein-protein interaction network of aIFs in the halophilic archaeon Haloferax volcanii has been characterized. To this end, tagged versions of 14 aIFs were overproduced, affinity isolated, and the co-isolated binding partners were identified by peptide mass fingerprinting and MS/MS analyses. The aIF-aIF interaction network was resolved, and it was found to contain two interaction hubs, (1) the universally conserved factor aIF5B, and (2) a protein that has been annotated as the enzyme ribose-1,5-bisphosphate isomerase, which we propose to rename to aIF2Bα. Affinity isolation of aIFs also led to the co-isolation of many ribosomal proteins, but also transcription factors and subunits of the RNA polymerase (Rpo). To analyze a possible coupling of transcription and translation, seven tagged Rpo subunits were overproduced, affinity isolated, and co-isolated proteins were identified. The Rpo interaction network contained many transcription factors, but also many ribosomal proteins as well as the initiation factors aIF5B and aIF2Bα. These results showed that transcription and translation are coupled in haloarchaea, like in Escherichia coli. It seems that aIF5B and aIF2Bα are not only interaction hubs in the translation initiation network, but also key players in the transcription-translation coupling.
Collapse
Affiliation(s)
- Franziska Schramm
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Phillipps University Marburg, Marburg, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Abstract
Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the Earth’s magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense, all steps of magnetosome formation are tightly controlled by >30 specific genes arranged in several gene clusters. However, the transcriptional organization of the magnetosome gene clusters has remained poorly understood. Here, by applying Cappable-seq and whole-transcriptome shotgun RNA sequencing, we show that mamGFDCop and feoAB1op are transcribed as single transcriptional units, whereas multiple transcription start sites (TSS) are present in mms6op, mamXYop, and the long (>16 kb) mamABop. Using a bioluminescence reporter assay and promoter knockouts, we demonstrate that most of the identified TSS originate from biologically meaningful promoters which mediate production of multiple transcripts and are functionally relevant for proper magnetosome biosynthesis. In addition, we identified a strong promoter in a large intergenic region within mamXYop, which likely drives transcription of a noncoding RNA important for gene expression in this operon. In summary, our data suggest a more complex transcriptional architecture of the magnetosome operons than previously recognized, which is largely conserved in other magnetotactic Magnetospirillum species and, thus, is likely fundamental for magnetosome biosynthesis in these organisms. IMPORTANCE Magnetosomes have emerged as a model system to study prokaryotic organelles and a source of biocompatible magnetic nanoparticles for various biomedical applications. However, the lack of knowledge about the transcriptional organization of magnetosome gene clusters has severely impeded the engineering, manipulation, and transfer of this highly complex biosynthetic pathway into other organisms. Here, we provide a high-resolution image of the previously unappreciated transcriptional landscape of the magnetosome operons. Our findings are important for further unraveling the complex genetic framework of magnetosome biosynthesis. In addition, they will facilitate the rational reengineering of magnetic bacteria for improved bioproduction of tunable magnetic nanoparticles, as well as transplantation of magnetosome biosynthesis into foreign hosts by synthetic biology approaches. Overall, our study exemplifies how a genetically complex pathway is orchestrated at the transcriptional level to ensure the balanced expression of the numerous constituents required for the proper assembly of one of the most intricate prokaryotic organelles.
Collapse
|
20
|
Martinez GS, Sarkar S, Kumar A, Pérez‐Rueda E, de Avila e Silva S. Characterization of promoters in archaeal genomes based on DNA structural parameters. Microbiologyopen 2021; 10:e1230. [PMID: 34713600 PMCID: PMC8553660 DOI: 10.1002/mbo3.1230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/10/2022] Open
Abstract
The transcription machinery of archaea can be roughly classified as a simplified version of eukaryotic organisms. The basal transcription factor machinery binds to the TATA box found around 28 nucleotides upstream of the transcription start site; however, some transcription units lack a clear TATA box and still have TBP/TFB binding over them. This apparent absence of conserved sequences could be a consequence of sequence divergence associated with the upstream region, operon, and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared with a simple sequence inspection. In this work, we evaluated and coded 3630 archaeal promoter sequences of three organisms, Haloferax volcanii, Thermococcus kodakarensis, and Sulfolobus solfataricus into DNA duplex stability, enthalpy, curvature, and bendability parameters. We also split our dataset into conserved TATA and degenerated TATA promoters to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoter architecture, that is, a distinctive signal is observed in the TFB, TBP, and TFE binding sites independently of these being TATA-conserved or TATA-degenerated. In addition, the promoter encountering method was validated with upstream regions of 13 other archaea, suggesting that there might be promoter sequences among them. Therefore, we suggest a novel method for locating promoters within the genome of archaea based on DNA energetic/structural features.
Collapse
Affiliation(s)
| | - Sharmilee Sarkar
- Department of Molecular Biology and BiotechnologyTezpur UniversityTezpurAssamIndia
| | - Aditya Kumar
- Department of Molecular Biology and BiotechnologyTezpur UniversityTezpurAssamIndia
| | - Ernesto Pérez‐Rueda
- Unidad Académica de YucatánInstituto de Investigaciones en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoMéridaYucatánMéxico
| | | |
Collapse
|
21
|
Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, Sun Z, Guan S, Corrêa IR. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Res 2021; 50:e2. [PMID: 34581823 PMCID: PMC8754658 DOI: 10.1093/nar/gkab861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Template-switching reverse transcription is widely used in RNA sequencing for low-input and low-quality samples, including RNA from single cells or formalin-fixed paraffin-embedded (FFPE) tissues. Previously, we identified the native eukaryotic mRNA 5′ cap as a key structural element for enhancing template switching efficiency. Here, we introduce CapTS-seq, a new strategy for sequencing small RNAs that combines chemical capping and template switching. We probed a variety of non-native synthetic cap structures and found that an unmethylated guanosine triphosphate cap led to the lowest bias and highest efficiency for template switching. Through cross-examination of different nucleotides at the cap position, our data provided unequivocal evidence that the 5′ cap acts as a template for the first nucleotide in reverse transcriptase-mediated post-templated addition to the emerging cDNA—a key feature to propel template switching. We deployed CapTS-seq for sequencing synthetic miRNAs, human total brain and liver FFPE RNA, and demonstrated that it consistently improves library quality for miRNAs in comparison with a gold standard template switching-based small RNA-seq kit.
Collapse
Affiliation(s)
- Madalee G Wulf
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Alice Blondel
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Dora Posfai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Zhiyi Sun
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| |
Collapse
|
22
|
Bharmal MHM, Gega A, Schrader JM. A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation. NAR Genom Bioinform 2021; 3:lqab081. [PMID: 34568822 PMCID: PMC8459731 DOI: 10.1093/nargab/lqab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/03/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial translation is thought to initiate by base pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA's 5' untranslated region (UTR). However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5' UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using these data, a simple computational model was built based on the combinatorial relationship of these mRNA features that can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.
Collapse
Affiliation(s)
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
23
|
Abstract
Transcriptional regulators that integrate cellular and environmental signals to control cell division are well known in bacteria and eukaryotes, but their existence is poorly understood in archaea. We identified a conserved gene (cdrS) that encodes a small protein and is highly transcribed in the model archaeon Haloferax volcanii. The cdrS gene could not be deleted, but CRISPR interference (CRISPRi)-mediated repression of the cdrS gene caused slow growth and cell division defects and changed the expression of multiple genes and their products associated with cell division, protein degradation, and metabolism. Consistent with this complex regulatory network, overexpression of cdrS inhibited cell division, whereas overexpression of the operon encoding both CdrS and a tubulin-like cell division protein (FtsZ2) stimulated division. Chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) identified 18 DNA-binding sites of the CdrS protein, including one upstream of the promoter for a cell division gene, ftsZ1, and another upstream of the essential gene dacZ, encoding diadenylate cyclase involved in c-di-AMP signaling, which is implicated in the regulation of cell division. These findings suggest that CdrS is a transcription factor that plays a central role in a regulatory network coordinating metabolism and cell division. IMPORTANCE Cell division is a central mechanism of life and is essential for growth and development. Members of the Bacteria and Eukarya have different mechanisms for cell division, which have been studied in detail. In contrast, cell division in members of the Archaea is still understudied, and its regulation is poorly understood. Interestingly, different cell division machineries appear in members of the Archaea, with the Euryarchaeota using a cell division apparatus based on the tubulin-like cytoskeletal protein FtsZ, as in bacteria. Here, we identify the small protein CdrS as essential for survival and a central regulator of cell division in the euryarchaeon Haloferax volcanii. CdrS also appears to coordinate other cellular pathways, including synthesis of signaling molecules and protein degradation. Our results show that CdrS plays a sophisticated role in cell division, including regulation of numerous associated genes. These findings are expected to initiate investigations into conditional regulation of division in archaea.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry. Nat Microbiol 2021; 6:746-756. [PMID: 33958766 PMCID: PMC7612053 DOI: 10.1038/s41564-021-00898-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Transcription initiates at promoters, DNA regions recognized by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters from which the direction of transcription was unclear. In the present study, we show that more than half of these promoters are bidirectional and drive divergent transcription. Using genome-scale approaches, we demonstrate that 19% of all transcription start sites detected in E. coli are associated with a bidirectional promoter. Bidirectional promoters are similarly common in diverse bacteria and archaea, and have inherent symmetry: specific bases required for transcription initiation are reciprocally co-located on opposite DNA strands. Bidirectional promoters enable co-regulation of divergent genes and are enriched in both intergenic and horizontally acquired regions. Divergent transcription is conserved among bacteria, archaea and eukaryotes, but the underlying mechanisms for bidirectionality are different.
Collapse
|
26
|
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.
Collapse
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
| | | |
Collapse
|
27
|
Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus methanolicus. Int J Mol Sci 2021; 22:ijms22094686. [PMID: 33925231 PMCID: PMC8124236 DOI: 10.3390/ijms22094686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 12/05/2022] Open
Abstract
Genome-wide transcriptomic data obtained in RNA-seq experiments can serve as a reliable source for identification of novel regulatory elements such as riboswitches and promoters. Riboswitches are parts of the 5′ untranslated region of mRNA molecules that can specifically bind various metabolites and control gene expression. For that reason, they have become an attractive tool for engineering biological systems, especially for the regulation of metabolic fluxes in industrial microorganisms. Promoters in the genomes of prokaryotes are located upstream of transcription start sites and their sequences are easily identifiable based on the primary transcriptome data. Bacillus methanolicus MGA3 is a candidate for use as an industrial workhorse in methanol-based bioprocesses and its metabolism has been studied in systems biology approaches in recent years, including transcriptome characterization through RNA-seq. Here, we identify a putative lysine riboswitch in B. methanolicus, and test and characterize it. We also select and experimentally verify 10 putative B. methanolicus-derived promoters differing in their predicted strength and present their functionality in combination with the lysine riboswitch. We further explore the potential of a B. subtilis-derived purine riboswitch for regulation of gene expression in the thermophilic B. methanolicus, establishing a novel tool for inducible gene expression in this bacterium.
Collapse
|
28
|
Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen HM, Quax TEF. Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1. Front Microbiol 2021; 12:625599. [PMID: 33664716 PMCID: PMC7921747 DOI: 10.3389/fmicb.2021.625599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/28/2021] [Indexed: 01/14/2023] Open
Abstract
Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus–host studies in euryarchaea.
Collapse
Affiliation(s)
- Colin Tittes
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabine Schwarzer
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| |
Collapse
|
29
|
Schwarz TS, Berkemer SJ, Bernhart SH, Weiß M, Ferreira-Cerca S, Stadler PF, Marchfelder A. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. Front Microbiol 2020; 11:594838. [PMID: 33329479 PMCID: PMC7714728 DOI: 10.3389/fmicb.2020.594838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
In all three domains of life, tRNA genes contain introns that must be removed to yield functional tRNA. In archaea and eukarya, the first step of this process is catalyzed by a splicing endonuclease. The consensus structure recognized by the splicing endonuclease is a bulge-helix-bulge (BHB) motif which is also found in rRNA precursors. So far, a systematic analysis to identify all biological substrates of the splicing endonuclease has not been carried out. In this study, we employed CRISPRi to repress expression of the splicing endonuclease in the archaeon Haloferax volcanii to identify all substrates of this enzyme. Expression of the splicing endonuclease was reduced to 1% of its normal level, resulting in a significant extension of lag phase in H. volcanii growth. In the repression strain, 41 genes were down-regulated and 102 were up-regulated. As an additional approach in identifying new substrates of the splicing endonuclease, we isolated and sequenced circular RNAs, which identified excised introns removed from tRNA and rRNA precursors as well as from the 5' UTR of the gene HVO_1309. In vitro processing assays showed that the BHB sites in the 5' UTR of HVO_1309 and in a 16S rRNA-like precursor are processed by the recombinant splicing endonuclease. The splicing endonuclease is therefore an important player in RNA maturation in archaea.
Collapse
Affiliation(s)
| | - Sarah J Berkemer
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions, Leipzig University, Leipzig, Germany
| | - Stephan H Bernhart
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Matthias Weiß
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Peter F Stadler
- Bioinformatics, Department of Computer Science, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Santa Fe Institute, Santa Fe, NM, United States
| | | |
Collapse
|
30
|
Mishra A, Dhanda S, Siwach P, Aggarwal S, Jayaram B. A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics. Bioinformatics 2020; 36:2375-2384. [PMID: 31909789 DOI: 10.1093/bioinformatics/btz941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/08/2019] [Accepted: 01/02/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Despite conservation in general architecture of promoters and protein-DNA interaction interface of RNA polymerases among various prokaryotes, identification of promoter regions in the whole genome sequences remains a daunting challenge. The available tools for promoter prediction do not seem to address the problem satisfactorily, apparently because the biochemical nature of promoter signals is yet to be understood fully. Using 28 structural and 3 energetic parameters, we found that prokaryotic promoter regions have a unique structural and energy state, quite distinct from that of coding regions and the information for this signature state is in-built in their sequences. We developed a novel promoter prediction tool from these 31 parameters using various statistical techniques. RESULTS Here, we introduce SEProm, a novel tool that is developed by studying and utilizing the in-built structural and energy information of DNA sequences, which is applicable to all prokaryotes including archaea. Compared to five most recent, diverged and current best available tools, SEProm performs much better, predicting promoters with an 'F-value' of 82.04 and 'Precision' of 81.08. The next best 'F-value' was obtained with PromPredict (72.14) followed by BProm (68.37). On the basis of 'Precision' value, the next best 'Precision' was observed for Pepper (75.39) followed by PromPredict (72.01). SEProm maintained the lead even when comparison was done on two test organisms (not involved in training for SEProm). AVAILABILITY AND IMPLEMENTATION The software is freely available with easy to follow instructions (www.scfbio-iitd.res.in/software/TSS_Predict.jsp). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology.,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Sahil Dhanda
- Supercomputing Facility for Bioinformatics & Computational Biology
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology.,Department of Biotechnology, Chaudhary Devi Lal University, Sirsa 125055, India
| | - Shruti Aggarwal
- Supercomputing Facility for Bioinformatics & Computational Biology
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology.,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India.,Department of Chemistry, Indian Institute of Technology, New Delhi 110016, India
| |
Collapse
|
31
|
Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J. Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from
Haloferax volcanii. FEBS J 2020; 288:2042-2062. [DOI: 10.1111/febs.15559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Sebastian Zahn
- Institute for Molecular Biosciences Goethe‐University Frankfurt Germany
| | - Nina Kubatova
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance Goethe‐University Frankfurt/Main Germany
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance Goethe‐University Frankfurt/Main Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance Goethe‐University Frankfurt/Main Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐Universität zu Kiel Kiel Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance Goethe‐University Frankfurt/Main Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences Goethe‐University Frankfurt Germany
- Johann Wolfgang Goethe‐Universität Frankfurt am Main Germany
| |
Collapse
|
32
|
Schmitt E, Coureux PD, Kazan R, Bourgeois G, Lazennec-Schurdevin C, Mechulam Y. Recent Advances in Archaeal Translation Initiation. Front Microbiol 2020; 11:584152. [PMID: 33072057 PMCID: PMC7531240 DOI: 10.3389/fmicb.2020.584152] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed. However, even if the general principles are the same in the three domains of life, the molecular mechanisms are different in bacteria, eukaryotes, and archaea and may also vary depending on the mRNA. Because TI mechanisms have evolved lately, their studies bring important information about the evolutionary relationships between extant organisms. In this context, recent structural data on ribosomal complexes and genome-wide studies are particularly valuable. This review focuses on archaeal translation initiation highlighting its relationships with either the eukaryotic or the bacterial world. Eukaryotic features of the archaeal small ribosomal subunit are presented. Ribosome evolution and TI mechanisms diversity in archaeal branches are discussed. Next, the use of leaderless mRNAs and that of leadered mRNAs having Shine-Dalgarno sequences is analyzed. Finally, the current knowledge on TI mechanisms of SD-leadered and leaderless mRNAs is detailed.
Collapse
Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France
| |
Collapse
|
33
|
Soutourina O, Dubois T, Monot M, Shelyakin PV, Saujet L, Boudry P, Gelfand MS, Dupuy B, Martin-Verstraete I. Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile. Front Microbiol 2020; 11:1939. [PMID: 32903654 PMCID: PMC7438776 DOI: 10.3389/fmicb.2020.01939] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
The emerging human enteropathogen Clostridioides difficile is the main cause of diarrhea associated with antibiotherapy. Regulatory pathways underlying the adaptive responses remain understudied and the global view of C. difficile promoter structure is still missing. In the genome of C. difficile 630, 22 genes encoding sigma factors are present suggesting a complex pattern of transcription in this bacterium. We present here the first transcriptional map of the C. difficile genome resulting from the identification of transcriptional start sites (TSS), promoter motifs and operon structures. By 5′-end RNA-seq approach, we mapped more than 1000 TSS upstream of genes. In addition to these primary TSS, this analysis revealed complex structure of transcriptional units such as alternative and internal promoters, potential RNA processing events and 5′ untranslated regions. By following an in silico iterative strategy that used as an input previously published consensus sequences and transcriptomic analysis, we identified candidate promoters upstream of most of protein-coding and non-coding RNAs genes. This strategy also led to refine consensus sequences of promoters recognized by major sigma factors of C. difficile. Detailed analysis focuses on the transcription in the pathogenicity locus and regulatory genes, as well as regulons of transition phase and sporulation sigma factors as important components of C. difficile regulatory network governing toxin gene expression and spore formation. Among the still uncharacterized regulons of the major sigma factors of C. difficile, we defined the SigL regulon by combining transcriptome and in silico analyses. We showed that the SigL regulon is largely involved in amino-acid degradation, a metabolism crucial for C. difficile gut colonization. Finally, we combined our TSS mapping, in silico identification of promoters and RNA-seq data to improve gene annotation and to suggest operon organization in C. difficile. These data will considerably improve our knowledge of global regulatory circuits controlling gene expression in C. difficile and will serve as a useful rich resource for scientific community both for the detailed analysis of specific genes and systems biology studies.
Collapse
Affiliation(s)
- Olga Soutourina
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France.,Institut Universitaire de France, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Thomas Dubois
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | | | - Laure Saujet
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Pierre Boudry
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems, Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Bruno Dupuy
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France.,Institut Universitaire de France, Paris, France
| |
Collapse
|
34
|
Niessen N, Soppa J. Regulated Iron Siderophore Production of the Halophilic Archaeon Haloferax volcanii. Biomolecules 2020; 10:biom10071072. [PMID: 32709147 PMCID: PMC7407949 DOI: 10.3390/biom10071072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
Iron is part of many redox and other enzymes and, thus, it is essential for all living beings. Many oxic environments have extremely low concentrations of free iron. Therefore, many prokaryotic species evolved siderophores, i.e., small organic molecules that complex Fe3+ with very high affinity. Siderophores of bacteria are intensely studied, in contrast to those of archaea. The haloarchaeon Haloferax volcanii contains a gene cluster that putatively encodes siderophore biosynthesis genes, including four iron uptake chelate (iuc) genes. Underscoring this hypothesis, Northern blot analyses revealed that a hexacistronic transcript is generated that is highly induced under iron starvation. A quadruple iuc deletion mutant was generated, which had a growth defect solely at very low concentrations of Fe3+, not Fe2+. Two experimental approaches showed that the wild type produced and exported an Fe3+-specific siderophore under low iron concentrations, in contrast to the iuc deletion mutant. Bioinformatic analyses revealed that haloarchaea obtained the gene cluster by lateral transfer from bacteria and enabled the prediction of enzymatic functions of all six gene products. Notably, a biosynthetic pathway is proposed that starts with aspartic acid, uses several group donors and citrate, and leads to the hydroxamate siderophore Schizokinen.
Collapse
Affiliation(s)
- Natalie Niessen
- Institute for Molecular Biosciences, Goethe-University, Biocentre, Max-von-Laue-str. 9, D-60439 Frankfurt, Germany;
- Campus Callaghan, Faculty of Health and Medicine, School of Medicine and Public Health, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe-University, Biocentre, Max-von-Laue-str. 9, D-60439 Frankfurt, Germany;
- Correspondence:
| |
Collapse
|
35
|
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 2020; 11:3145. [PMID: 32561711 PMCID: PMC7305310 DOI: 10.1038/s41467-020-16784-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
Abstract
While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
Collapse
|
36
|
Gelsinger DR, Dallon E, Reddy R, Mohammad F, Buskirk A, DiRuggiero J. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res 2020; 48:5201-5216. [PMID: 32382758 PMCID: PMC7261190 DOI: 10.1093/nar/gkaa304] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/09/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.
Collapse
Affiliation(s)
| | - Emma Dallon
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Rahul Reddy
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jocelyne DiRuggiero
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
- Department of Earth and Planetary Sciences, the Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
37
|
Lee STM, Ding JY, Chiang PW, Dyall-Smith M, Tang SL. Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica. Microbiologyopen 2020; 9:e1016. [PMID: 32212320 PMCID: PMC7221443 DOI: 10.1002/mbo3.1016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/16/2023] Open
Abstract
Gene expression in Haloarcula hispanica cells infected with the gammapleolipovirus His2 was studied using a custom DNA microarray. Total RNA from cells sampled at 0, 1, 2, 3, and 4.5 hr postinfection was reverse‐transcribed into labeled cDNA and hybridized to microarrays, revealing temporal and differential expression in both host and viral genes. His2 gene expression occurred in three main phases (early, middle, and late), and by 4.5 hr p.i. the majority of genes were actively transcribed, including those encoding the major structural proteins. Eighty host genes were differentially regulated ≥twofold postinfection, with most of them predicted to be involved in transport, translation, and metabolism. Differentially expressed host genes could also be grouped into early‐, middle‐, and late‐expressed genes based on the timing of their up‐ and downregulation postinfection. The altered host transcriptional pattern suggests regulation by His2 infection, which may reprogram host metabolism to facilitate its own DNA replication and propagation. This study enhances the characterization of many hypothetical viral genes and provides insights into the interaction between His2 and its host.
Collapse
Affiliation(s)
- Sonny T M Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, United States
| | - Jiun-Yan Ding
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mike Dyall-Smith
- Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany.,Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic., Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
38
|
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]
|
39
|
Adams PP, Storz G. Prevalence of small base-pairing RNAs derived from diverse genomic loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194524. [PMID: 32147527 DOI: 10.1016/j.bbagrm.2020.194524] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
Collapse
Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| |
Collapse
|
40
|
Berkemer SJ, Maier LK, Amman F, Bernhart SH, Wörtz J, Märkle P, Pfeiffer F, Stadler PF, Marchfelder A. Identification of RNA 3´ ends and termination sites in Haloferax volcanii. RNA Biol 2020; 17:663-676. [PMID: 32041469 PMCID: PMC7237163 DOI: 10.1080/15476286.2020.1723328] [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] [Indexed: 12/22/2022] Open
Abstract
Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea, Methanosarcina mazei and Sulfolobus acidocaldarius. In this study, only regions directly downstream of annotated genes were analysed, and thus, only part of the genome had been investigated. Here, we developed a novel algorithm (Internal Enrichment-Peak Calling) that allows an unbiased, genome-wide identification of RNA 3´ termini independent of annotation. In an RNA fraction enriched for primary transcripts by terminator exonuclease (TEX) treatment we identified 1,543 RNA 3´ termini. Approximately half of these were located in intergenic regions, and the remainder were found in coding regions. A strong sequence signature consistent with known termination events at intergenic loci indicates a clear enrichment for native TTS among them. Using these data we determined distinct putative termination motifs for intergenic (a T stretch) and coding regions (AGATC). In vivo reporter gene tests of selected TTS confirmed termination at these sites, which exemplify the different motifs. For several genes, more than one termination site was detected, resulting in transcripts with different lengths of the 3´ untranslated region (3´ UTR).
Collapse
Affiliation(s)
- Sarah J Berkemer
- Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | | | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Division of Cell and Developmental Biology, Medical University Vienna, Vienna, Austria
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Transcriptome Bioinformatics, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | | | | | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Center for RNA in Technology and Health, University Copenhagen, Frederiksberg C, Denmark.,Santa Fe Institute, Santa Fe, NM, USA.,German Centre for Integrative Biodiversity Research (iDiv), Halle, Jena and Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions, and Leipzig, Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
| | | |
Collapse
|
41
|
Wolters M, Borst A, Pfeiffer F, Soppa J. Bioinformatic and genetic characterization of three genes localized adjacent to the major replication origin of Haloferax volcanii. FEMS Microbiol Lett 2019; 366:5643889. [DOI: 10.1093/femsle/fnz238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/25/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
In haloarchaea, a cluster of three genes is localized directly adjacent to the major replication origin, and, hence, the encoded proteins were annotated as ‘origin-associated proteins’ (Oap). However, prior to this study, no experimental data were available for these conserved hypothetical proteins. Bioinformatic analyses were performed, which unraveled, 1) that the amino acid composition of all three proteins deviate from the average, 2) that OapA is a GTP-binding protein, 3) that OapC has an N-terminal zinc-finger motif, and 4) that the sequences of OapA and OapB are highly conserved while OapC conservation is restricted to short terminal regions. Surprisingly, transcript analyses revealed a complex expression pattern of the oap genes, despite their close proximity. Based on the high degree of conservation in haloarchaea it could be expected that one or more of the oap genes might be essential. However, in frame deletion mutants of all three genes could be readily generated, were viable, and had no growth phenotype. In addition, quantification of the chromsome copy numbers revealed no significant differences between the wild-type and the three mutants. In summary, experimental evidence is inconsistent with Oap proteins being essential for or involved in key steps of DNA replication.
Collapse
Affiliation(s)
- Maike Wolters
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany
| | - Andreas Borst
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, Frankfurt D-60438, Germany
| |
Collapse
|
42
|
Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Res 2019; 47:10477-10488. [PMID: 31602466 PMCID: PMC6847099 DOI: 10.1093/nar/gkz855] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
In all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine-Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position -3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
Collapse
Affiliation(s)
- William D Baez
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ralf Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
43
|
Hocher A, Rojec M, Swadling JB, Esin A, Warnecke T. The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog. eLife 2019; 8:52542. [PMID: 31710291 PMCID: PMC6877293 DOI: 10.7554/elife.52542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023] Open
Abstract
Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
Collapse
Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Maria Rojec
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Jacob B Swadling
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Alexander Esin
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College, London, United Kingdom
| |
Collapse
|
44
|
Jevtić Ž, Stoll B, Pfeiffer F, Sharma K, Urlaub H, Marchfelder A, Lenz C. The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label-Free Mass Spectrometry. Proteomics 2019; 19:e1800491. [PMID: 31502396 DOI: 10.1002/pmic.201800491] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 08/27/2019] [Indexed: 01/23/2023]
Abstract
In-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii has been performed under standard, low/high salt, and low/high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high-pH/reversed-phase fractionated samples indicates 61.1% proteome coverage (2509 proteins), which is close to the maximum recorded values in archaea. Identified proteins match to the predicted proteome in their physicochemical properties, with only a small bias against low-molecular-weight and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress are quantitatively compared to standard cultures by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 2244 proteins, or 54.7% of the predicted proteome, are quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2034 are significantly regulated under at least one stress condition. KEGG pathway enrichment analysis shows that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, and tryptophan) are affected by temperature stress. The most strongly downregulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, are found oppositely regulated to their immediate genetic neighbors from the same operon.
Collapse
Affiliation(s)
- Živojin Jevtić
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany
| | | | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany.,Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
| | | | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany.,Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
| |
Collapse
|
45
|
Translational coupling via termination-reinitiation in archaea and bacteria. Nat Commun 2019; 10:4006. [PMID: 31488843 PMCID: PMC6728339 DOI: 10.1038/s41467-019-11999-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 08/12/2019] [Indexed: 11/18/2022] Open
Abstract
The genomes of many prokaryotes contain substantial fractions of gene pairs with overlapping stop and start codons (ATGA or TGATG). A potential benefit of overlapping gene pairs is translational coupling. In 720 genomes of archaea and bacteria representing all major phyla, we identify substantial, albeit highly variable, fractions of co-directed overlapping gene pairs. Various patterns are observed for the utilization of the SD motif for de novo initiation at upstream genes versus reinitiation at overlapping gene pairs. We experimentally test the predicted coupling in 9 gene pairs from the archaeon Haloferax volcanii and 5 gene pairs from the bacterium Escherichia coli. In 13 of 14 cases, translation of both genes is strictly coupled. Mutational analysis of SD motifs located upstream of the downstream genes indicate that the contribution of the SD to translational coupling widely varies from gene to gene. The nearly universal, abundant occurrence of overlapping gene pairs suggests that tight translational coupling is widespread in archaea and bacteria. Archaea and bacteria often have gene pairs with overlapping stop and start codons, suggesting translational coupling. Here, Huber et al. analyse overlapping gene pairs from 720 genomes, and validate translational coupling via termination-reinitiation for 14 gene pairs in Haloferax volcanii and Escherichia coli.
Collapse
|
46
|
Ju X, Li D, Liu S. Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. Nat Microbiol 2019; 4:1907-1918. [PMID: 31308523 PMCID: PMC6814526 DOI: 10.1038/s41564-019-0500-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/29/2019] [Indexed: 12/18/2022]
Abstract
The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5' and 3' termini of the same transcript remain scarce. In the present study, simultaneous 5' and 3' end sequencing (SEnd-seq)-a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution-is presented. Using this method, a comprehensive view of the Escherichia coli transcriptome was obtained, which displays an unexpected level of complexity. SEnd-seq notably expands the catalogue of transcription start sites and termination sites, defines unique transcription units and detects prevalent antisense RNA. Strikingly, the results of the present study unveil widespread overlapping bidirectional terminators located between opposing gene pairs. Furthermore, it has been shown that convergent transcription is a major contributor to highly efficient bidirectional termination both in vitro and in vivo. This finding highlights an underappreciated role of RNA polymerase conflicts in shaping transcript boundaries and suggests an evolutionary strategy for modulating transcriptional output by arranging gene orientation.
Collapse
Affiliation(s)
- Xiangwu Ju
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Dayi Li
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.,The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
47
|
Grünberger F, Reichelt R, Bunk B, Spröer C, Overmann J, Rachel R, Grohmann D, Hausner W. Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription. Front Microbiol 2019; 10:1603. [PMID: 31354685 PMCID: PMC6640164 DOI: 10.3389/fmicb.2019.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/26/2019] [Indexed: 01/07/2023] Open
Abstract
Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100°C. The genome was sequenced about 18 years ago. However, some publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced the genome using third generation sequencing techniques. The new de novo assembled genome is 1,889,914 bp in size and exhibits high sequence identity to the published sequence. However, two major deviations were detected: (1) The genome is 18,342 bp smaller than the NCBI reference genome due to a recently described deletion. (2) The region between PF0349 and PF0388 is inverted most likely due an assembly problem for the original sequence. In addition, numerous minor variations, ranging from single nucleotide exchanges, deletions or insertions were identified. The total number of insertion sequence (IS) elements is also reduced from 30 to 24 in the new sequence. Re-sequencing of a 2-year-old “lab culture” using Nanopore sequencing confirmed the overall stability of the P. furiosus DSM 3638 genome even under normal lab conditions without taking any special care. To improve genome annotation, the updated DNA sequence was combined with an RNA sequencing approach. Here, RNAs from eight different growth conditions were pooled to increase the number of detected transcripts. Furthermore, a differential RNA-Seq approach was employed for the identification of transcription start sites (TSSs). In total, 2515 TSSs were detected and classified into 834 primary (pTSS), 797 antisense (aTSS), 739 internal and 145 secondary TSSs. Our analysis of the upstream regions revealed a well conserved archaeal promoter structure. Interrogation of the distances between pTSSs and aTSSs revealed a significant number of antisense transcripts, which are a result of bidirectional transcription from the same TATA box. This mechanism of antisense transcript production could be further confirmed by in vitro transcription experiments. We assume that bidirectional transcription gives rise to non-functional antisense RNAs and that this is a widespread phenomenon in archaea due to the architecture of the TATA element and the symmetric structure of the TATA-binding protein.
Collapse
Affiliation(s)
- Felix Grünberger
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| |
Collapse
|
48
|
Schwarz TS, Wäber NB, Feyh R, Weidenbach K, Schmitz RA, Marchfelder A, Hartmann RK. Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei. IUBMB Life 2019; 71:1109-1116. [PMID: 31283101 DOI: 10.1002/iub.2122] [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: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 01/20/2023]
Abstract
The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.
Collapse
Affiliation(s)
| | - Nadine B Wäber
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Katrin Weidenbach
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | | | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| |
Collapse
|
49
|
Kliemt J, Jaschinski K, Soppa J. A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions. Front Microbiol 2019; 10:1219. [PMID: 31231327 PMCID: PMC6560208 DOI: 10.3389/fmicb.2019.01219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/15/2019] [Indexed: 11/26/2022] Open
Abstract
The haloarchaeon Haloferax volcanii contains nearly 2800 small non-coding RNAs (sRNAs). One intergenic sRNA, sRNA132, was chosen for a detailed characterization. A deletion mutant had a growth defect and thus underscored the importance of sRNA132. A microarray analysis identified the transcript of an operon for a phosphate-specific ABC transporter as a putative target of sRNA132. Both the sRNA132 and the operon transcript accumulated under low phosphate concentrations, indicating a positive regulatory role of sRNA132. A kinetic analysis revealed that sRNA132 is essential shortly after the onset of phosphate starvation, while other regulatory processes take over after several hours. Comparison of the transcriptomes of wild-type and the sRNA132 gene deletion mutant 30 min after the onset of phosphate starvation revealed that sRNA132 controls a regulon of about 40 genes. Remarkably, the regulon included a second operon for a phosphate-specific ABC transporter, which also depended on sRNA132 for rapid induction in the absence of phosphate. Competitive growth experiments of the wild-type and ABC transporter operon deletion mutants underscored the importance of both transporters for growth at low phosphate concentrations. Northern blot analyses of four additional members of the sRNA132 regulon verified that all four transcripts depended on sRNA132 for rapid regulation after the onset of phosphate starvation. Importantly, this is the first example for the transient importance of a sRNA for any archaeal and bacterial species. In addition, this study unraveled the first sRNA regulon for haloarchaea.
Collapse
Affiliation(s)
- Jana Kliemt
- Biocentre, Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Katharina Jaschinski
- Biocentre, Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
50
|
Nagel C, Machulla A, Zahn S, Soppa J. Several One-Domain Zinc Finger µ-Proteins of Haloferax Volcanii Are Important for Stress Adaptation, Biofilm Formation, and Swarming. Genes (Basel) 2019; 10:genes10050361. [PMID: 31083437 PMCID: PMC6562870 DOI: 10.3390/genes10050361] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
Zinc finger domains are highly structured and can mediate interactions to DNA, RNA, proteins, lipids, and small molecules. Accordingly, zinc finger proteins are very versatile and involved in many biological functions. Eukaryotes contain a wealth of zinc finger proteins, but zinc finger proteins have also been found in archaea and bacteria. Large zinc finger proteins have been well studied, however, in stark contrast, single domain zinc finger µ-proteins of less than 70 amino acids have not been studied at all, with one single exception. Therefore, 16 zinc finger µ-proteins of the haloarchaeon Haloferax volcanii were chosen and in frame deletion mutants of the cognate genes were generated. The phenotypes of mutants and wild-type were compared under eight different conditions, which were chosen to represent various pathways and involve many genes. None of the mutants differed from the wild-type under optimal or near-optimal conditions. However, 12 of the 16 mutants exhibited a phenotypic difference under at least one of the four following conditions: Growth in synthetic medium with glycerol, growth in the presence of bile acids, biofilm formation, and swarming. In total, 16 loss of function and 11 gain of function phenotypes were observed. Five mutants indicated counter-regulation of a sessile versus a motile life style in H. volcanii. In conclusion, the generation and analysis of a set of deletion mutants demonstrated the high importance of zinc finger µ-proteins for various biological functions, and it will be the basis for future mechanistic insight.
Collapse
Affiliation(s)
- Chantal Nagel
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Anja Machulla
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Sebastian Zahn
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| | - Jörg Soppa
- Department of Biosciences, Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.
| |
Collapse
|