1
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Üresin D, Schulte J, Morgner N, Soppa J. C(P)XCG Proteins of Haloferax volcanii with Predicted Zinc Finger Domains: The Majority Bind Zinc, but Several Do Not. Int J Mol Sci 2024; 25:7166. [PMID: 39000272 PMCID: PMC11241148 DOI: 10.3390/ijms25137166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
In recent years, interest in very small proteins (µ-proteins) has increased significantly, and they were found to fulfill important functions in all prokaryotic and eukaryotic species. The halophilic archaeon Haloferax volcanii encodes about 400 µ-proteins of less than 70 amino acids, 49 of which contain at least two C(P)XCG motifs and are, thus, predicted zinc finger proteins. The determination of the NMR solution structure of HVO_2753 revealed that only one of two predicted zinc fingers actually bound zinc, while a second one was metal-free. Therefore, the aim of the current study was the homologous production of additional C(P)XCG proteins and the quantification of their zinc content. Attempts to produce 31 proteins failed, underscoring the particular difficulties of working with µ-proteins. In total, 14 proteins could be produced and purified, and the zinc content was determined. Only nine proteins complexed zinc, while five proteins were zinc-free. Three of the latter could be analyzed using ESI-MS and were found to contain another metal, most likely cobalt or nickel. Therefore, at least in haloarchaea, the variability of predicted C(P)XCG zinc finger motifs is higher than anticipated, and they can be metal-free, bind zinc, or bind another metal. Notably, AlphaFold2 cannot correctly predict whether or not the four cysteines have the tetrahedral configuration that is a prerequisite for metal binding.
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Affiliation(s)
- Deniz Üresin
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
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2
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Genth J, Schäfer K, Cassidy L, Graspeuntner S, Rupp J, Tholey A. Identification of proteoforms of short open reading frame-encoded peptides in Blautia producta under different cultivation conditions. Microbiol Spectr 2023; 11:e0252823. [PMID: 37782090 PMCID: PMC10715070 DOI: 10.1128/spectrum.02528-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023] Open
Abstract
IMPORTANCE The identification of short open reading frame-encoded peptides (SEP) and different proteoforms in single cultures of gut microbes offers new insights into a largely neglected part of the microbial proteome landscape. This is of particular importance as SEP provide various predicted functions, such as acting as antimicrobial peptides, maintaining cell homeostasis under stress conditions, or even contributing to the virulence pattern. They are, thus, taking a poorly understood role in structure and function of microbial networks in the human body. A better understanding of SEP in the context of human health requires a precise understanding of the abundance of SEP both in commensal microbes as well as pathogens. For the gut beneficial B. producta, we demonstrate the importance of specific environmental conditions for biosynthesis of SEP expanding previous findings about their role in microbial interactions.
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Affiliation(s)
- Jerome Genth
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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3
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Elston R, Mulligan C, Thomas GH. Flipping the switch: dynamic modulation of membrane transporter activity in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37948297 DOI: 10.1099/mic.0.001412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The controlled entry and expulsion of small molecules across the bacterial cytoplasmic membrane is essential for efficient cell growth and cellular homeostasis. While much is known about the transcriptional regulation of genes encoding transporters, less is understood about how transporter activity is modulated once the protein is functional in the membrane, a potentially more rapid and dynamic level of control. In this review, we bring together literature from the bacterial transport community exemplifying the extensive and diverse mechanisms that have evolved to rapidly modulate transporter function, predominantly by switching activity off. This includes small molecule feedback, inhibition by interaction with small peptides, regulation through binding larger signal transduction proteins and, finally, the emerging area of controlled proteolysis. Many of these examples have been discovered in the context of metal transport, which has to finely balance active accumulation of elements that are essential for growth but can also quickly become toxic if intracellular homeostasis is not tightly controlled. Consistent with this, these transporters appear to be regulated at multiple levels. Finally, we find common regulatory themes, most often through the fusion of additional regulatory domains to transporters, which suggest the potential for even more widespread regulation of transporter activity in biology.
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Affiliation(s)
- Rory Elston
- Department of Biology, University of York, York, UK
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4
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Jiang S, Steup LC, Kippnich C, Lazaridi S, Malengo G, Lemmin T, Yuan J. The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensing. Proc Natl Acad Sci U S A 2023; 120:e2309607120. [PMID: 37792514 PMCID: PMC10576120 DOI: 10.1073/pnas.2309607120] [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: 06/07/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023] Open
Abstract
A large number of small membrane proteins have been uncovered in bacteria, but their mechanism of action has remained mostly elusive. Here, we investigate the mechanism of a physiologically important small protein, MgrB, which represses the activity of the sensor kinase PhoQ and is widely distributed among enterobacteria. The PhoQ/PhoP two-component system is a master regulator of the bacterial virulence program and interacts with MgrB to modulate bacterial virulence, fitness, and drug resistance. A combination of cross-linking approaches with functional assays and protein dynamic simulations revealed structural rearrangements due to interactions between MgrB and PhoQ near the membrane/periplasm interface and along the transmembrane helices. These interactions induce the movement of the PhoQ catalytic domain and the repression of its activity. Without MgrB, PhoQ appears to be much less sensitive to antimicrobial peptides, including the commonly used C18G. In the presence of MgrB, C18G promotes MgrB to dissociate from PhoQ, thus activating PhoQ via derepression. Our findings reveal the inhibitory mechanism of the small protein MgrB and uncover its importance in antimicrobial peptide sensing.
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Affiliation(s)
- Shan Jiang
- Max Planck Institute for Terrestrial Microbiology, 35043Marburg, Germany
- Center for Synthetic Microbiology, 35043Marburg, Germany
| | - Lydia C. Steup
- Max Planck Institute for Terrestrial Microbiology, 35043Marburg, Germany
- Center for Synthetic Microbiology, 35043Marburg, Germany
| | - Charlotte Kippnich
- Max Planck Institute for Terrestrial Microbiology, 35043Marburg, Germany
- Center for Synthetic Microbiology, 35043Marburg, Germany
| | - Symela Lazaridi
- Institute of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Bern, 3012Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012Bern, Switzerland
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology, 35043Marburg, Germany
- Center for Synthetic Microbiology, 35043Marburg, Germany
| | - Thomas Lemmin
- Institute of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Bern, 3012Bern, Switzerland
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, 35043Marburg, Germany
- Center for Synthetic Microbiology, 35043Marburg, Germany
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5
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Meier-Credo J, Heiniger B, Schori C, Rupprecht F, Michel H, Ahrens CH, Langer JD. Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics. Anal Chem 2023; 95:11892-11900. [PMID: 37535005 PMCID: PMC10433244 DOI: 10.1021/acs.analchem.3c00676] [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: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the cbb3-type oxidase that plays an essential role in adaptation to oxygen-limited conditions in Pseudomonas stutzeri (P. stutzeri), a model for the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. However, as no comprehensive data were available in P. stutzeri, we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond P. stutzeri, were predicted to form an operon with a conserved protein and may represent de novo genes. These data demonstrate the power of this combined approach to study small proteins in P. stutzeri and show its potential for other prokaryotes.
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Affiliation(s)
- Jakob Meier-Credo
- Proteomics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Benjamin Heiniger
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Christian Schori
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Fiona Rupprecht
- Proteomics, Max Planck Institute for Brain
Research, 60438 Frankfurt
am Main, Germany
| | - Hartmut Michel
- Department
of Molecular Membrane Biology, Max Planck
Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Christian H. Ahrens
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Julian D. Langer
- Proteomics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain
Research, 60438 Frankfurt
am Main, Germany
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6
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Ventroux M, Noirot-Gros MF. Prophage-encoded small protein YqaH counteracts the activities of the replication initiator DnaA in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748575 DOI: 10.1099/mic.0.001268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial genomes harbour cryptic prophages that are mostly transcriptionally silent with many unannotated genes. Still, cryptic prophages may contribute to their host fitness and phenotypes. In Bacillus subtilis, the yqaF-yqaN operon belongs to the prophage element skin, and is tightly repressed by the Xre-like repressor SknR. This operon contains several small ORFs (smORFs) potentially encoding small-sized proteins. The smORF-encoded peptide YqaH was previously reported to bind to the replication initiator DnaA. Here, using a yeast two-hybrid assay, we found that YqaH binds to the DNA binding domain IV of DnaA and interacts with Spo0A, a master regulator of sporulation. We isolated single amino acid substitutions in YqaH that abolished the interaction with DnaA but not with Spo0A. Then, using a plasmid-based inducible system to overexpress yqaH WT and mutant derivatives, we studied in B. subtilis the phenotypes associated with the specific loss-of-interaction with DnaA (DnaA_LOI). We found that expression of yqaH carrying DnaA_LOI mutations abolished the deleterious effects of yqaH WT expression on chromosome segregation, replication initiation and DnaA-regulated transcription. When YqaH was induced after vegetative growth, DnaA_LOI mutations abolished the drastic effects of YqaH WT on sporulation and biofilm formation. Thus, YqaH inhibits replication, sporulation and biofilm formation mainly by antagonizing DnaA in a manner that is independent of the cell cycle checkpoint Sda.
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Affiliation(s)
- Magali Ventroux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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7
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Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress. Mol Cell Proteomics 2022; 21:100423. [PMID: 36210010 PMCID: PMC9650054 DOI: 10.1016/j.mcpro.2022.100423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022] Open
Abstract
Organisms have developed different mechanisms to respond to stresses. However, the roles of small ORF-encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially because of the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.
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8
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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9
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Thousands of small, novel genes predicted in global phage genomes. Cell Rep 2022; 39:110984. [PMID: 35732113 DOI: 10.1016/j.celrep.2022.110984] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/14/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022] Open
Abstract
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.
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10
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Phylogenomic Analyses of
Snodgrassella
Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity. mSystems 2022; 7:e0150021. [PMID: 35604118 PMCID: PMC9239279 DOI: 10.1128/msystems.01500-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee’s microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.
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11
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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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12
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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13
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Vajjala M, Johnson B, Kasparek L, Leuze M, Yao Q. Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning. Front Genet 2022; 13:935351. [PMID: 35938008 PMCID: PMC9354662 DOI: 10.3389/fgene.2022.935351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.
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Affiliation(s)
- Mitra Vajjala
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Brady Johnson
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Lauren Kasparek
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Qiuming Yao
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
- *Correspondence: Qiuming Yao,
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14
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Dimonaco NJ, Aubrey W, Kenobi K, Clare A, Creevey CJ. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. Bioinformatics 2021; 38:1198-1207. [PMID: 34875010 PMCID: PMC8825762 DOI: 10.1093/bioinformatics/btab827] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/13/2021] [Accepted: 12/02/2021] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. This hinders the discovery of new genomic information as it results in predictions being biased towards existing knowledge. To date, users have lacked a systematic and replicable approach to identify the strengths and weaknesses of any CDS prediction tool and allow them to choose the right tool for their analysis. RESULTS We present an evaluation framework (ORForise) based on a comprehensive set of 12 primary and 60 secondary metrics that facilitate the assessment of the performance of CDS prediction tools. This makes it possible to identify which performs better for specific use-cases. We use this to assess 15 ab initio- and model-based tools representing those most widely used (historically and currently) to generate the knowledge in genomic databases. We find that the performance of any tool is dependent on the genome being analysed, and no individual tool ranked as the most accurate across all genomes or metrics analysed. Even the top-ranked tools produced conflicting gene collections, which could not be resolved by aggregation. The ORForise evaluation framework provides users with a replicable, data-led approach to make informed tool choices for novel genome annotations and for refining historical annotations. AVAILABILITY AND IMPLEMENTATION Code and datasets for reproduction and customisation are available at https://github.com/NickJD/ORForise. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicholas J Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, UK,To whom correspondence should be addressed.
| | - Wayne Aubrey
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - Kim Kenobi
- Department of Mathematics, Aberystwyth University, Aberystwyth SY23 3BZ, UK
| | - Amanda Clare
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
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15
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Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis. Commun Biol 2021; 4:1248. [PMID: 34728737 PMCID: PMC8563848 DOI: 10.1038/s42003-021-02759-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
Plague caused by Yersinia pestis is one of the deadliest diseases. However, many molecular mechanisms of bacterial virulence remain unclear. This study engaged in the discovery of small open reading frame (sORF)-encoded peptides (SEPs) in Y. pestis. An integrated proteogenomic pipeline was established, and an atlas containing 76 SEPs was described. Bioinformatic analysis indicated that 20% of these SEPs were secreted or localized to the transmembrane and that 33% contained functional domains. Two SEPs, named SEPs-yp1 and -yp2 and encoded in noncoding regions, were selected by comparative peptidomics analysis under host-specific environments and high-salinity stress. They displayed important roles in the regulation of antiphagocytic capability in a thorough functional assay. Remarkable attenuation of virulence in mice was observed in the SEP-deleted mutants. Further global proteomic analysis indicated that SEPs-yp1 and -yp2 affected the bacterial metabolic pathways, and SEP-yp1 was associated with the bacterial virulence by modulating the expression of key virulence factors of the Yersinia type III secretion system. Our study provides a rich resource for research on Y. pestis and plague, and the findings on SEP-yp1 and SEP-yp2 shed light on the molecular mechanism of bacterial virulence. Shiyang Cao, Xinyue Liu, Yin Huang, and Yanfeng Yan et al. utilized an integrated proteogenomic approach to describe an atlas of small open reading frame-encoded peptides (SEPs) in the pathogen, Yersinia pestis. They demonstrate that two of these SEPs are associated with regulation of bacterial virulence, and altogether develop a valuable resource for future research into Y. pestis physiology.
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16
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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.
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17
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Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA. High complexity of Glutamine synthetase regulation in
Methanosarcina mazei
: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J 2021; 288:5350-5373. [DOI: 10.1111/febs.15799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Gutt
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Britta Jordan
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Katrin Weidenbach
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Mirja Gudzuhn
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Claudia Kiessling
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Helbig
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Andreas Tholey
- AG Proteomics & Bioanalytics Institute for Experimental Medicine Christian‐Albrechts‐University Kiel Germany
| | - Dennis Joshua Pyper
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Nina Kubatova
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Johann Wolfgang Goethe University Frankfurt am Main Germany
| | - Ruth Anne Schmitz
- Institute for General Microbiology Christian‐Albrechts‐University Kiel Germany
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18
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Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. MICROBIOME 2021; 9:55. [PMID: 33622394 PMCID: PMC7903761 DOI: 10.1186/s40168-020-00981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
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Affiliation(s)
- Hannes Petruschke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian Schori
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Canzler
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Tina Segessemann
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Johannes Zimmerman
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
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19
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Schlesinger D, Elsässer SJ. Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins. FEBS J 2021; 289:53-74. [PMID: 33595896 DOI: 10.1111/febs.15769] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/17/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
Abstract
Short ORFs (sORFs), that is, occurrences of a start and stop codon within 100 codons or less, can be found in organisms of all domains of life, outnumbering annotated protein-coding ORFs by orders of magnitude. Even though functional proteins smaller than 100 amino acids are known, the coding potential of sORFs has often been overlooked, as it is not trivial to predict and test for functionality within the large number of sORFs. Recent advances in ribosome profiling and mass spectrometry approaches, together with refined bioinformatic predictions, have enabled a huge leap forward in this field and identified thousands of likely coding sORFs. A relatively low number of small proteins or microproteins produced from these sORFs have been characterized so far on the molecular, structural, and/or mechanistic level. These however display versatile and, in some cases, essential cellular functions, allowing for the exciting possibility that many more, previously unknown small proteins might be encoded in the genome, waiting to be discovered. This review will give an overview of the steadily growing microprotein field, focusing on eukaryotic small proteins. We will discuss emerging themes in the molecular action of microproteins, as well as advances and challenges in microprotein identification and characterization.
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Affiliation(s)
- Dörte Schlesinger
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
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20
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Westermann AJ, Vogel J. Cross-species RNA-seq for deciphering host-microbe interactions. Nat Rev Genet 2021; 22:361-378. [PMID: 33597744 DOI: 10.1038/s41576-021-00326-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
The human body is constantly exposed to microorganisms, which entails manifold interactions between human cells and diverse commensal or pathogenic bacteria. The cellular states of the interacting cells are decisive for the outcome of these encounters such as whether bacterial virulence programmes and host defence or tolerance mechanisms are induced. This Review summarizes how next-generation RNA sequencing (RNA-seq) has become a primary technology to study host-microbe interactions with high resolution, improving our understanding of the physiological consequences and the mechanisms at play. We illustrate how the discriminatory power and sensitivity of RNA-seq helps to dissect increasingly complex cellular interactions in time and space down to the single-cell level. We also outline how future transcriptomics may answer currently open questions in host-microbe interactions and inform treatment schemes for microbial disorders.
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Affiliation(s)
- Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
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21
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Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes. Cell Host Microbe 2020; 29:121-131.e4. [PMID: 33290720 DOI: 10.1016/j.chom.2020.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/26/2020] [Accepted: 11/07/2020] [Indexed: 01/21/2023]
Abstract
Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.
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22
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Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J. Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biol 2020; 18:1099-1110. [PMID: 33103565 PMCID: PMC8244752 DOI: 10.1080/15476286.2020.1827785] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As part of the ongoing renaissance of phage biology, more phage genomes are becoming available through DNA sequencing. However, our understanding of the transcriptome architecture that allows these genomes to be expressed during host infection is generally poor. Transcription start sites (TSSs) and operons have been mapped for very few phages, and an annotated global RNA map of a phage – alone or together with its infected host – is not available at all. Here, we applied differential RNA-seq (dRNA-seq) to study the early, host takeover phase of infection by assessing the transcriptome structure of Pseudomonas aeruginosa jumbo phage ɸKZ, a model phage for viral genetics and structural research. This map substantially expands the number of early expressed viral genes, defining TSSs that are active ten minutes after ɸKZ infection. Simultaneously, we record gene expression changes in the host transcriptome during this critical metabolism conversion. In addition to previously reported upregulation of genes associated with amino acid metabolism, we observe strong activation of genes with functions in biofilm formation (cdrAB) and iron storage (bfrB), as well as an activation of the antitoxin ParD. Conversely, ɸKZ infection rapidly down-regulates complexes IV and V of oxidative phosphorylation (atpCDGHF and cyoABCDE). Taken together, our data provide new insights into the transcriptional organization and infection process of the giant bacteriophage ɸKZ and adds a framework for the genome-wide transcriptomic analysis of phage–host interactions.
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Affiliation(s)
- Laura Wicke
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Lucas Coppens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
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23
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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
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24
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Wang B, Hao J, Pan N, Wang Z, Chen Y, Wan C. Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell. J Proteomics 2020; 230:103965. [PMID: 32891891 DOI: 10.1016/j.jprot.2020.103965] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023]
Abstract
The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.
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Affiliation(s)
- Bing Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Junhui Hao
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Ni Pan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Zhiwei Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Yinxuan Chen
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Cuihong Wan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China.
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25
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Garai P, Blanc‐Potard A. Uncovering small membrane proteins in pathogenic bacteria: Regulatory functions and therapeutic potential. Mol Microbiol 2020; 114:710-720. [DOI: 10.1111/mmi.14564] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Preeti Garai
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
| | - Anne Blanc‐Potard
- Laboratory of Pathogen‐Host Interactions Université de MontpellierCNRS‐UMR5235 Montpellier France
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26
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A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Nat Commun 2020; 11:3557. [PMID: 32678091 PMCID: PMC7366714 DOI: 10.1038/s41467-020-17348-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Bacteria of the genus Bacteroides are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species Bacteroides thetaiotaomicron has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ (www.helmholtz-hiri.de/en/datasets/bacteroides), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of N-acetyl-D-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of N-acetyl-D-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes. Bacteroides thetaiotaomicron is a human gut microbe and an emergent model organism. Here, Ryan et al. generate single-nucleotide resolution RNA-seq data for this bacterium and map transcription start sites and noncoding RNAs, one of which modulates expression of metabolic enzymes.
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27
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Yadavalli SS, Goh T, Carey JN, Malengo G, Vellappan S, Nickels BE, Sourjik V, Goulian M, Yuan J. Functional determinants of a small protein controlling a broadly conserved bacterial sensor kinase. J Bacteriol 2020; 202:JB.00305-20. [PMID: 32482726 PMCID: PMC8404706 DOI: 10.1128/jb.00305-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
The PhoQ/PhoP two-component system plays a vital role in the regulation of Mg2+ homeostasis, resistance to acid and hyperosmotic stress, cationic antimicrobial peptides, and virulence in Escherichia coli, Salmonella and related bacteria. Previous studies have shown that MgrB, a 47 amino acid membrane protein that is part of the PhoQ/PhoP regulon, inhibits the histidine kinase PhoQ. MgrB is part of a negative feedback loop modulating this two-component system that prevents hyperactivation of PhoQ and may also provide an entry point for additional input signals for the PhoQ/PhoP pathway. To explore the mechanism of action of MgrB, we have analyzed the effects of point mutations, C-terminal truncations and transmembrane region swaps on MgrB activity. In contrast with two other known membrane protein regulators of histidine kinases in E. coli, we find that the MgrB TM region is necessary for PhoQ inhibition. Our results indicate that the TM region mediates interactions with PhoQ and that W20 is a key residue for PhoQ/MgrB complex formation. Additionally, mutations of the MgrB cytosolic region suggest that the two N-terminal lysines play an important role in regulating PhoQ activity. Alanine scanning mutagenesis of the periplasmic region of MgrB further indicates that, with the exception of a few highly conserved residues, most residues are not essential for MgrB's function as a PhoQ inhibitor. Our results indicate that the regulatory function of the small protein MgrB depends on distinct contributions from multiple residues spread across the protein. Interestingly, the TM region also appears to interact with other non-cognate histidine kinases in a bacterial two-hybrid assay, suggesting a potential route for evolving new small protein modulators of histidine kinases.
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Affiliation(s)
- Srujana S Yadavalli
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ted Goh
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA
- Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Jeffrey N Carey
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Sangeevan Vellappan
- Molecular Biosciences Graduate Program, Rutgers University, Piscataway NJ 08854
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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28
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Wang B, Yang J, Xu C, Yi L, Wan C. Dynamic expression of intra‐ and extra‐cellular proteome and the influence of epiphytic bacteria for
Nostoc flagelliforme
in response to rehydration. Environ Microbiol 2020; 22:1251-1264. [DOI: 10.1111/1462-2920.14931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Bing Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Jingjing Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Chen Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Lanxing Yi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
| | - Cuihong Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal University No. 152 Luoyu Road, Wuhan 430079 People's Republic of China
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29
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Orr MW, Mao Y, Storz G, Qian SB. Alternative ORFs and small ORFs: shedding light on the dark proteome. Nucleic Acids Res 2020; 48:1029-1042. [PMID: 31504789 DOI: 10.1093/nar/gkz734] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/03/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Traditional annotation of protein-encoding genes relied on assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it is becoming clear that these initial assumptions are incorrect. The findings have led to the realization that genetic information is more densely coded and that the proteome is more complex than previously anticipated. As such, interest in the identification and characterization of the previously ignored 'dark proteome' is increasing, though we note that research in eukaryotes and bacteria has largely progressed in isolation. To bridge this gap and illustrate exciting findings emerging from studies of the dark proteome, we highlight recent advances in both eukaryotic and bacterial cells. We discuss progress in the detection of alternative ORFs as well as in the understanding of functions and the regulation of their expression and posit questions for future work.
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Affiliation(s)
- Mona Wu Orr
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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30
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Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships. J Proteome Res 2020; 19:1647-1662. [PMID: 32091902 DOI: 10.1021/acs.jproteome.9b00842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, but a proteogenomic resource that bridges the gap in our molecular understanding of the relationships between the Listeria genotypes and phenotypes via proteotypes is still missing. Here, we devised a next-generation proteogenomics strategy that enables the community to rapidly proteotype Listeria strains and relate this information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria model strains, EGD-e and ScottA, we established two comprehensive Listeria proteogenomic databases. A genome comparison established core- and strain-specific genes potentially responsible for virulence differences. Next, we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, that enables the reproducible, sensitive, and relative quantitative measurement of Listeria proteotypes. This reusable and publicly available DIA/SWATH library covers 70% of open reading frames of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 °C, which simulates conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 °C, this was an unexpected finding. The formation of flagella, which might have implications on infectivity, was validated by parallel reaction monitoring and light and scanning electron microscopy. flaA transcript levels did not change significantly upon exposure to bile salts at 37 °C, suggesting regulation at the post-transcriptional level. Together, these analyses provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
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Affiliation(s)
- Adithi R Varadarajan
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Maria P Pavlou
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Virginie Grosboillot
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Yang Shen
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Martin J Loessner
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
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31
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Bufe B, Teuchert Y, Schmid A, Pyrski M, Pérez-Gómez A, Eisenbeis J, Timm T, Ishii T, Lochnit G, Bischoff M, Mombaerts P, Leinders-Zufall T, Zufall F. Bacterial MgrB peptide activates chemoreceptor Fpr3 in mouse accessory olfactory system and drives avoidance behaviour. Nat Commun 2019; 10:4889. [PMID: 31653840 PMCID: PMC6814738 DOI: 10.1038/s41467-019-12842-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/02/2019] [Indexed: 12/31/2022] Open
Abstract
Innate immune chemoreceptors of the formyl peptide receptor (Fpr) family are expressed by vomeronasal sensory neurons (VSNs) in the accessory olfactory system. Their biological function and coding mechanisms remain unknown. We show that mouse Fpr3 (Fpr-rs1) recognizes the core peptide motif f-MKKFRW that is predominantly present in the signal sequence of the bacterial protein MgrB, a highly conserved regulator of virulence and antibiotic resistance in Enterobacteriaceae. MgrB peptide can be produced and secreted by bacteria, and is selectively recognized by a subset of VSNs. Exposure to the peptide also stimulates VSNs in freely behaving mice and drives innate avoidance. Our data shows that Fpr3 is required for neuronal detection and avoidance of peptides derived from a conserved master virulence regulator of enteric bacteria.
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Affiliation(s)
- Bernd Bufe
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany.,Molecular Immunology Section, Faculty of Computer Science and Microsystems Engineering, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482, Zweibrücken, Germany
| | - Yannick Teuchert
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany
| | - Andreas Schmid
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany
| | - Martina Pyrski
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany
| | - Anabel Pérez-Gómez
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany.,Department of Molecular Medicine, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Janina Eisenbeis
- Institute for Medical Microbiology and Hygiene, Saarland University, 66424, Homburg, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Tomohiro Ishii
- Max Planck Research Unit for Neurogenetics, Max-von-Laue-Strasse 4, 60438, Frankfurt, Germany.,Department of Cell Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Günter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygiene, Saarland University, 66424, Homburg, Germany
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Max-von-Laue-Strasse 4, 60438, Frankfurt, Germany
| | - Trese Leinders-Zufall
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany
| | - Frank Zufall
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66424, Homburg, Germany.
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32
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Synthetic hydrophobic peptides derived from MgtR weaken Salmonella pathogenicity and work with a different mode of action than endogenously produced peptides. Sci Rep 2019; 9:15253. [PMID: 31649255 PMCID: PMC6813294 DOI: 10.1038/s41598-019-51760-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/24/2019] [Indexed: 12/03/2022] Open
Abstract
Due to the antibiotic resistance crisis, novel therapeutic strategies need to be developed against bacterial pathogens. Hydrophobic bacterial peptides (small proteins under 50 amino acids) have emerged as regulatory molecules that can interact with bacterial membrane proteins to modulate their activity and/or stability. Among them, the Salmonella MgtR peptide promotes the degradation of MgtC, a virulence factor involved in Salmonella intramacrophage replication, thus providing the basis for an antivirulence strategy. We demonstrate here that endogenous overproduction of MgtR reduced Salmonella replication inside macrophages and lowered MgtC protein level, whereas a peptide variant of MgtR (MgtR-S17I), which does not interact with MgtC, had no effect. We then used synthetic peptides to evaluate their action upon exogenous addition. Unexpectedly, upon addition of synthetic peptides, both MgtR and its variant MgtR-S17I reduced Salmonella intramacrophage replication and lowered MgtC and MgtB protein levels, suggesting a different mechanism of action of exogenously added peptides versus endogenously produced peptides. The synthetic peptides did not act by reducing bacterial viability. We next tested their effect on various recombinant proteins produced in Escherichia coli and showed that the level of several inner membrane proteins was strongly reduced upon addition of both peptides, whereas cytoplasmic or outer membrane proteins remained unaffected. Moreover, the α-helical structure of synthetic MgtR is important for its biological activity, whereas helix-helix interacting motif is dispensable. Cumulatively, these results provide perspectives for new antivirulence strategies with the use of peptides that act by reducing the level of inner membrane proteins, including virulence factors.
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33
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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell 2019; 178:1245-1259.e14. [PMID: 31402174 DOI: 10.1016/j.cell.2019.07.016] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022]
Abstract
Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.
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34
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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.
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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.
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35
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Scheidler CM, Kick LM, Schneider S. Ribosomal Peptides and Small Proteins on the Rise. Chembiochem 2019; 20:1479-1486. [PMID: 30648812 DOI: 10.1002/cbic.201800715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/05/2022]
Abstract
Genetically encoded and ribosomally synthesised peptides and small proteins act as important regulators in fundamental cellular processes, including gene expression, development, signalling and metabolism. Moreover, they also play a crucial role in eukaryotic and prokaryotic defence against microorganisms. Extremely diverse in size and structure, they are often subject to extensive post-translational modification. Recent technological advances are now allowing the analysis of the whole cellular transcriptome and proteome, revealing the presence of hundreds of long-overlooked alternative and short open reading frames (short ORFs, or sORFs) in mRNA and supposedly noncoding RNAs. However, in many instances the biological roles of their translational products remain to be elucidated. Here we provide an overview on the intriguing structural and functional diversity of ribosomally synthesised peptides and newly discovered peptides and small proteins.
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Affiliation(s)
- Christopher M Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Leonhard M Kick
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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36
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Monson RE, Apagyi K, Bowden SD, Simpson N, Williamson NR, Cubitt MF, Harris S, Toth IK, Salmond GPC. The rsmS (ybaM) mutation causes bypass suppression of the RsmAB post-transcriptional virulence regulation system in enterobacterial phytopathogens. Sci Rep 2019; 9:4525. [PMID: 30872786 PMCID: PMC6418279 DOI: 10.1038/s41598-019-40970-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022] Open
Abstract
Plant cell wall degrading enzymes (PCWDEs) are the primary virulence determinants of soft rotting bacteria such as the potato pathogen, Pectobacterium atrosepticum. The regulation of secondary metabolite (Rsm) system controls production of PCWDEs in response to changing nutrient conditions. This work identified a new suppressor of an rsmB mutation - ECA1172 or rsmS (rsmB suppressor). Mutants defective in rsmB (encoding a small regulatory RNA), show reduced elaboration of the quorum sensing molecule (N-3-oxohexanoyl-homoserine lactone; OHHL) and PCWDEs. However, OHHL and PCWDE production were partially restored in an rsmB, rsmS double mutant. Single rsmS mutants, overproduced PCWDEs and OHHL relative to wild type P. atrosepticum and exhibited hypervirulence in potato. RsmS overproduction also resulted in increased PCWDEs and OHHL. Homology searches revealed rsmS conservation across pathogens such as Escherichia coli (ybaM), Dickeya solani, Klebsiella pneumoniae and Shigella flexneri. An rsmS mutant of Pectobacterium carotovorum ATCC39048 showed bypass of rsmB-dependent repression of PCWDEs and OHHL production. P. carotovorum ATCC39048 produces the β-lactam antibiotic, 1-carbapen-2-em-3-carboxylic acid (a carbapenem). Production of the antibiotic was repressed in an rsmB mutant but partially restored in an rsmB, rsmS double mutant. This work highlights the importance of RsmS, as a conserved pleiotropic regulator of virulence and antibiotic biosynthesis.
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Affiliation(s)
- Rita E Monson
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Katinka Apagyi
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
- Faculty of Medicine, School of Public Health, Imperial College, London, St Mary's Campus, Norfolk Place, W2 1PG, UK
| | - Steven D Bowden
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Natalie Simpson
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Neil R Williamson
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Marion F Cubitt
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Steve Harris
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, LE11 3TU, UK
| | - Ian K Toth
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - George P C Salmond
- Department of Biochemistry, Hopkins Building, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK.
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37
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Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E, Serrano L, Lluch-Senar M. Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol 2019; 15:e8290. [PMID: 30796087 PMCID: PMC6385055 DOI: 10.15252/msb.20188290] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool (RanSEPs) with “‐omics” approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in Mycoplasma pneumoniae proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16 ± 9% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non‐coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide‐binding categories. Additionally, 9.7% of the SEPs included a N‐terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.
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Affiliation(s)
- Samuel Miravet-Verde
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tony Ferrar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guadalupe Espadas-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anas Gharrab
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eduard Sabido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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38
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Yin X, Wu Orr M, Wang H, Hobbs EC, Shabalina SA, Storz G. The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels. Mol Microbiol 2018; 111:131-144. [PMID: 30276893 DOI: 10.1111/mmi.14143] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 01/04/2023]
Abstract
In response to low levels of magnesium (Mg2+ ), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pairs with the eptB mRNA thus affecting lipopolysaccharide modification. Surprisingly, we found overexpression of the MgtS protein also leads to induction of the PhoRB regulon. Studies to understand this activation showed that MgtS forms a complex with a second protein, PitA, a cation-phosphate symporter. Given that the additive effect of ∆mgtA and ∆mgtS mutations on intracellular Mg2+ concentrations seen previously is lost in the ∆pitA mutant, we suggest that MgtS binds to and prevents Mg2+ leakage through PitA under Mg2+ -limiting conditions. Consistent with a detrimental role of PitA in low Mg2+ , we also observe MgrR sRNA repression of PitA synthesis. Thus, PhoQP induces the expression of two convergent small genes in response to Mg2+ limitation whose products act to modulate PitA at different levels to increase intracellular Mg2+ .
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Affiliation(s)
- Xuefeng Yin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,Health Science Center, Peking University, Beijing, 100191, China
| | - Mona Wu Orr
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Hanbo Wang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Errett C Hobbs
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
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Investigation of amino acid specificity in the CydX small protein shows sequence plasticity at the functional level. PLoS One 2018; 13:e0198699. [PMID: 29912917 PMCID: PMC6005532 DOI: 10.1371/journal.pone.0198699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Small proteins are a new and expanding area of research. Many characterized small proteins are composed of a single hydrophobic α-helix, and the functional requirements of their limited amino acid sequence are not well understood. One hydrophobic small protein, CydX, has been shown to be a component of the cytochrome bd oxidase complex in Escherichia coli, and is required for enzyme function. To investigate small protein sequence specificity, an alanine scanning mutagenesis on the small protein CydX was conducted using mutant alleles expressed from the E. coli chromosome at the wild-type locus. The resulting mutant strains were assayed for CydX function. No single amino acid was required to maintain wild-type resistance to β-mercaptoethanol. However, substitutions of 10-amino acid blocks indicated that the N-terminus of the protein was required for wild-type CydX activity. A series of double mutants showed that multiple mutations at the N-terminus led to β-mercaptoethanol sensitivity in vivo. Triple mutants showed both in vivo and in vitro phenotypes. Together, these data provide evidence suggesting a high level of functional plasticity in CydX, in which multiple amino acids may work cooperatively to facilitate CydX function.
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