1
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Beggs GA, Bassler BL. Phage small proteins play large roles in phage-bacterial interactions. Curr Opin Microbiol 2024; 80:102519. [PMID: 39047312 PMCID: PMC11323111 DOI: 10.1016/j.mib.2024.102519] [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: 06/17/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/27/2024]
Abstract
Phages have wide influence on bacterial physiology, and likewise, bacterial processes impinge on phage biology. Key to these interactions are phage small proteins (<100 aa). Long underappreciated, recent work has revealed millions of phage small proteins, and increasingly, mechanisms by which they function to dictate phage and/or bacterial behavior and evolution. Here, we describe select phage small proteins that mediate phage-bacterial interactions by modulating phage lifestyle decision-making components or by altering host gene expression.
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Affiliation(s)
- Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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2
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Mohsen JJ, Mohsen MG, Jiang K, Landajuela A, Quinto L, Isaacs FJ, Karatekin E, Slavoff SA. Cellular function of the GndA small open reading frame-encoded polypeptide during heat shock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601336. [PMID: 38979229 PMCID: PMC11230408 DOI: 10.1101/2024.06.29.601336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Over the past 15 years, hundreds of previously undiscovered bacterial small open reading frame (sORF)-encoded polypeptides (SEPs) of fewer than fifty amino acids have been identified, and biological functions have been ascribed to an increasing number of SEPs from intergenic regions and small RNAs. However, despite numbering in the dozens in Escherichia coli, and hundreds to thousands in humans, same-strand nested sORFs that overlap protein coding genes in alternative reading frames remain understudied. In order to provide insight into this enigmatic class of unannotated genes, we characterized GndA, a 36-amino acid, heat shock-regulated SEP encoded within the +2 reading frame of the gnd gene in E. coli K-12 MG1655. We show that GndA pulls down components of respiratory complex I (RCI) and is required for proper localization of a RCI subunit during heat shock. At high temperature GndA deletion (ΔGndA) cells exhibit perturbations in cell growth, NADH+/NAD ratio, and expression of a number of genes including several associated with oxidative stress. These findings suggest that GndA may function in maintenance of homeostasis during heat shock. Characterization of GndA therefore supports the nascent but growing consensus that functional, overlapping genes occur in genomes from viruses to humans.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
| | - Michael G. Mohsen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
| | - Ane Landajuela
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Laura Quinto
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Systems Biology Institute, Yale University, West Haven, CT 06516
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511
- Systems Biology Institute, Yale University, West Haven, CT 06516
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
- Wu Tsai Institute, Yale University, New Haven, CT 06511
- Université de Paris, Saints-Pères Paris Institute for the Neurosciences (SPPIN), Centre National de la Recherche Scientifique (CNRS), 75006 Paris, France
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06511
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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3
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Coelho LP, Santos-Júnior CD, de la Fuente-Nunez C. Challenges in computational discovery of bioactive peptides in 'omics data. Proteomics 2024; 24:e2300105. [PMID: 38458994 DOI: 10.1002/pmic.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
Peptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well as in industry and agriculture. The increase in available 'omics data has recently provided a large opportunity for mining novel enzymes, biosynthetic gene clusters, and molecules. While these data primarily consist of DNA sequences, other types of data provide important complementary information. Due to their size, the approaches proven successful at discovering novel proteins of canonical size cannot be naïvely applied to the discovery of peptides. Peptides can be encoded directly in the genome as short open reading frames (smORFs), or they can be derived from larger proteins by proteolysis. Both of these peptide classes pose challenges as simple methods for their prediction result in large numbers of false positives. Similarly, functional annotation of larger proteins, traditionally based on sequence similarity to infer orthology and then transferring functions between characterized proteins and uncharacterized ones, cannot be applied for short sequences. The use of these techniques is much more limited and alternative approaches based on machine learning are used instead. Here, we review the limitations of traditional methods as well as the alternative methods that have recently been developed for discovering novel bioactive peptides with a focus on prokaryotic genomes and metagenomes.
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Affiliation(s)
- Luis Pedro Coelho
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
- Laboratory of Microbial Processes & Biodiversity - LMPB, Hydrobiology Department, Federal University of São Carlos - UFSCar, São Paulo, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. Mol Microbiol 2024; 121:152-166. [PMID: 38104967 PMCID: PMC10842292 DOI: 10.1111/mmi.15206] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.
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Affiliation(s)
- Zachary Wright
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Mackenzie Seymour
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Kalista Paszczak
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Taylor Truttmann
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Katherine Senn
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Samuel Stilp
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Nickolas Jansen
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Magdalyn Gosz
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Lindsay Goeden
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lauren S. Waters
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
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5
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Fuchs S, Engelmann S. Small proteins in bacteria - Big challenges in prediction and identification. Proteomics 2023; 23:e2200421. [PMID: 37609810 DOI: 10.1002/pmic.202200421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
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Affiliation(s)
- Stephan Fuchs
- Genome Competence Center (MF1), Department MFI, Robert-Koch-Institut, Berlin, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung GmbH, Braunschweig, Germany
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6
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Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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7
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Simoens L, Fijalkowski I, Van Damme P. Exposing the small protein load of bacterial life. FEMS Microbiol Rev 2023; 47:fuad063. [PMID: 38012116 PMCID: PMC10723866 DOI: 10.1093/femsre/fuad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.
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Affiliation(s)
- Laure Simoens
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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8
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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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9
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Schultz BJ, Snow ED, Walker S. Mechanism of D-alanine transfer to teichoic acids shows how bacteria acylate cell envelope polymers. Nat Microbiol 2023; 8:1318-1329. [PMID: 37308592 PMCID: PMC10664464 DOI: 10.1038/s41564-023-01411-0] [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: 10/26/2022] [Accepted: 05/17/2023] [Indexed: 06/14/2023]
Abstract
Bacterial cell envelope polymers are often modified with acyl esters that modulate physiology, enhance pathogenesis and provide antibiotic resistance. Here, using the D-alanylation of lipoteichoic acid (Dlt) pathway as a paradigm, we have identified a widespread strategy for how acylation of cell envelope polymers occurs. In this strategy, a membrane-bound O-acyltransferase (MBOAT) protein transfers an acyl group from an intracellular thioester onto the tyrosine of an extracytoplasmic C-terminal hexapeptide motif. This motif shuttles the acyl group to a serine on a separate transferase that moves the cargo to its destination. In the Dlt pathway, here studied in Staphylococcus aureus and Streptococcus thermophilus, the C-terminal 'acyl shuttle' motif that forms the crucial pathway intermediate is found on a transmembrane microprotein that holds the MBOAT protein and the other transferase together in a complex. In other systems, found in both Gram-negative and Gram-positive bacteria as well as some archaea, the motif is fused to the MBOAT protein, which interacts directly with the other transferase. The conserved chemistry uncovered here is widely used for acylation throughout the prokaryotic world.
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Affiliation(s)
- Bailey J Schultz
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Eric D Snow
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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10
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Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543501. [PMID: 37398132 PMCID: PMC10312517 DOI: 10.1101/2023.06.02.543501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Small proteins (< 50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance are poorly understood. Here we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments, but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene-neighborhoods support that MntS evolved from an ancestral SitA, acquiring a life of its own with a distinct function in Mn homeostasis. Significance This study demonstrates that the MntS small protein binds and inhibits the MntP Mn exporter, adding another layer to the complex regulation of Mn homeostasis. MntS also interacts with itself in cells with Mn, which could prevent it from regulating MntP. We propose that MntS and other small proteins might sense environmental signals and shut off their own regulation via binding to ligands (e.g., metals) or other proteins. We also provide evidence that MntS evolved from the signal peptide region of the Mn importer, SitA. Homologous SitA signal peptides can recapitulate MntS activities, showing that they have a second function beyond protein secretion. Overall, we establish that small proteins can emerge and develop novel functionalities from gene remnants.
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11
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Farid N, Waheed A, Motwani S. Synthetic and natural antimicrobials as a control against food borne pathogens: A review. Heliyon 2023; 9:e17021. [PMID: 37484319 PMCID: PMC10361103 DOI: 10.1016/j.heliyon.2023.e17021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 05/28/2023] [Accepted: 06/04/2023] [Indexed: 07/25/2023] Open
Abstract
Food borne pathogens are one of the most common yet concerning cause of illnesses around the globe. These microbes invade the body via food items, through numerous mediums of contamination and it is impossible to completely eradicate these organisms from food. Extensive research has been made regarding their treatment. Unfortunately, the only available treatment currently is by antibiotics. Recent exponential increase in antibiotic resistance and the side effect of synthetic compounds have established a need for alternate therapies that could be utilized either on their own or along with antibiotics to provide protection against food-borne diseases. The aim of this review is to provide information regarding some common food borne diseases, their current and possible natural treatment. It will include details regarding some common foodborne pathogens, the disease they cause, prevalence, manifestations and treatment of the respective disease. Some natural modes of potential treatment will be summarized, which including phytochemicals, derived from plants either as crude extracts or as purified form and Bacteriocins as microbial based treatment, obtained from various types of bacteria. The paper will describe their mechanism of action, classification, susceptible organisms, some antimicrobial compounds and producing organisms, application in food systems and as potential treatment. Along with that, synthetic treatment i.e., antibiotics will be discussed including the first-line treatment of some common food borne infections, prevalence and mechanism of resistance against antibiotics in the pathogens.
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Affiliation(s)
- Neha Farid
- Corresponding author. Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Pakistan.
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12
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Lei M, Trivedi VD, Nair NU, Lee K, Van Deventer JA. Flow cytometric evaluation of yeast-bacterial cell-cell interactions. Biotechnol Bioeng 2023; 120:399-408. [PMID: 36259110 PMCID: PMC10072783 DOI: 10.1002/bit.28253] [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: 06/10/2022] [Revised: 09/23/2022] [Accepted: 10/09/2022] [Indexed: 01/13/2023]
Abstract
Synthetic cell-cell interaction systems can be useful for understanding multicellular communities or for screening binding molecules. We adapt a previously characterized set of synthetic cognate nanobody-antigen pairs to a yeast-bacteria coincubation format and use flow cytometry to evaluate cell-cell interactions mediated by binding between surface-displayed molecules. We further use fluorescence-activated cell sorting to enrich a specific yeast-displayed nanobody within a mixed yeast-display population. Finally, we demonstrate that this system supports the characterization of a therapeutically relevant nanobody-antigen interaction: a previously discovered nanobody that binds to the intimin protein expressed on the surface of enterohemorrhagic Escherichia coli. Overall, our findings indicate that the yeast-bacteria format supports efficient evaluation of ligand-target interactions. With further development, this format may facilitate systematic characterization and high-throughput discovery of bacterial surface-binding molecules.
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Affiliation(s)
- Ming Lei
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Vikas D. Trivedi
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
| | - James A. Van Deventer
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155
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13
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Sur VP, Simonik O, Novotna M, Mazumdar A, Liska F, Vimberg V, Komrskova K. Dynamic study of small toxic hydrophobic proteins PepA1 and PepG1 of Staphylococcus aureus. Int J Biol Macromol 2022; 219:1360-1371. [PMID: 35932805 DOI: 10.1016/j.ijbiomac.2022.07.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022]
Abstract
Toxin-antitoxin (TA) systems are small genetic elements which encode toxin proteins that interfere with vital cellular functions. PepA1 and PepG1 toxin proteins, known also as SprA1 and SprG1, are type I TA. In Staphylococcus aureus (S. aureus), their expression without the antitoxin counterparts (SprA1AS and SprF1), is lethal to the pathogen. Molecular Dynamics (MD) simulation was performed for PepA1 and PepG1 to understand their dynamic state, conformational changes, and their toxicity. The protein structures were constructed and used for MD simulation and the conformational changes, stability, flexibility, fluctuations, hydrophobicity, and role of their dynamic state on function prediction were studied extensively by GROMACS MD simulation analysis tools. In silico study indicated that the PepA1 and PepG1 proteins change their structural conformation from an open to closed state where PepA1 conformational changes were faster (10 ns) than PepG1 (20 ns) while PepG1 exerted more stability and flexibility than PepA1. According to SASA values, PepG1 is more hydrophobic than the PepA1 and forms fewer hydrogen bonds than PepA1. The in vivo study with PepA1 and PepG1 proteins provided evidence that both the conformation changes between the open and closed states and the amino acid sequence are crucial for peptide toxicity.
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Affiliation(s)
- Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Ondrej Simonik
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic
| | - Michaela Novotna
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Aninda Mazumdar
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Frantisek Liska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Vladimir Vimberg
- Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Katerina Komrskova
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; Department of Zoology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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14
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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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15
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Genes Differentially Expressed by Haemophilus ducreyi during Anaerobic Growth Significantly Overlap Those Differentially Expressed during Experimental Infection of Human Volunteers. J Bacteriol 2022; 204:e0000522. [PMID: 35377183 DOI: 10.1128/jb.00005-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Haemophilus ducreyi causes cutaneous ulcers in children and the genital ulcer disease chancroid in adults. In humans, H. ducreyi is found in the anaerobic environment of an abscess; previous studies comparing bacterial gene expression levels in pustules with the inocula (∼4-h aerobic mid-log-phase cultures) identified several upregulated differentially expressed genes (DEGs) that are associated with anaerobic metabolism. To determine how H. ducreyi alters its gene expression in response to anaerobiosis, we performed RNA sequencing (RNA-seq) on both aerobic and anaerobic broth cultures harvested after 4, 8, and 18 h of growth. Principal-coordinate analysis (PCoA) plots showed that anaerobic growth resulted in distinct transcriptional profiles compared to aerobic growth. During anaerobic growth, early-time-point comparisons (4 versus 8 h) identified few DEGs at a 2-fold change in expression and a false discovery rate (FDR) of <0.01. By 18 h, we observed 18 upregulated and 16 downregulated DEGs. DEGs involved in purine metabolism, the uptake and use of alternative carbon sources, toxin production, nitrate reduction, glycine metabolism, and tetrahydrofolate synthesis were upregulated; DEGs involved in electron transport, thiamine biosynthesis, DNA recombination, peptidoglycan synthesis, and riboflavin synthesis or modification were downregulated. To examine whether transcriptional changes that occur during anaerobiosis overlap those that occur during infection of human volunteers, we compared the overlap of DEGs obtained from 4 h of aerobic growth to 18 h of anaerobic growth to those found between the inocula and pustules in previous studies; the DEGs significantly overlapped. Thus, a major component of H. ducreyi gene regulation in vivo involves adaptation to anaerobiosis. IMPORTANCE In humans, H. ducreyi resides in the anaerobic environment of an abscess and appears to upregulate genes involved in anaerobic metabolism. How anaerobiosis alone affects gene transcription in H. ducreyi is unknown. Using RNA-seq, we investigated how anaerobiosis affects gene transcription over time compared to aerobic growth. Our results suggest that a substantial component of H. ducreyi gene regulation in vivo overlaps the organism's response to anaerobiosis in vitro. Our data identify potential therapeutic targets that could be inhibited during in vivo growth.
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16
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Wittekind MA, Frey A, Bonsall AE, Briaud P, Keogh RA, Wiemels RE, Shaw LN, Carroll RK. The novel protein ScrA acts through the SaeRS two component system to regulate virulence gene expression in Staphylococcus aureus. Mol Microbiol 2022; 117:1196-1212. [PMID: 35366366 PMCID: PMC9324805 DOI: 10.1111/mmi.14901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a Gram‐positive commensal that can also cause a variety of infections in humans. S. aureus virulence factor gene expression is under tight control by a complex regulatory network, which includes, sigma factors, sRNAs, and two‐component systems (TCS). Previous work in our laboratory demonstrated that overexpression of the sRNA tsr37 leads to an increase in bacterial aggregation. Here, we demonstrate that the clumping phenotype is dependent on a previously unannotated 88 amino acid protein encoded within the tsr37 sRNA transcript (which we named ScrA for S. aureusclumping regulator A). To investigate the mechanism of action of ScrA we performed proteomics and transcriptomics in a ScrA overexpressing strain and show that a number of surface adhesins are upregulated, while secreted proteases are downregulated. Results also showed upregulation of the SaeRS TCS, suggesting that ScrA is influencing SaeRS activity. Overexpression of ScrA in a saeR mutant abrogates the clumping phenotype confirming that ScrA functions via the Sae system. Finally, we identified the ArlRS TCS as a positive regulator of scrA expression. Collectively, our results show that ScrA is an activator of the SaeRS system and suggests that ScrA may act as an intermediary between the ArlRS and SaeRS systems.
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Affiliation(s)
| | - Andrew Frey
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Abigail E Bonsall
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Paul Briaud
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Rebecca A Keogh
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA.,Current address: Department of Immunology & Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Richard E Wiemels
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA.,Infectious and Tropical Disease Institute, Ohio University, Athens, Ohio, USA
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17
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Nuti N, Rottmann P, Stucki A, Koch P, Panke S, Dittrich PS. A Multiplexed Cell‐Free Assay to Screen for Antimicrobial Peptides in Double Emulsion Droplets. Angew Chem Int Ed Engl 2022; 61:e202114632. [PMID: 34989471 PMCID: PMC9303939 DOI: 10.1002/anie.202114632] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 12/17/2022]
Abstract
The global surge in bacterial resistance against traditional antibiotics triggered intensive research for novel compounds, with antimicrobial peptides (AMPs) identified as a promising candidate. Automated methods to systematically generate and screen AMPs according to their membrane preference, however, are still lacking. We introduce a novel microfluidic system for the simultaneous cell‐free production and screening of AMPs for their membrane specificity. On our device, AMPs are cell‐free produced within water‐in‐oil‐in‐water double emulsion droplets, generated at high frequency. Within each droplet, the peptides can interact with different classes of co‐encapsulated liposomes, generating a membrane‐specific fluorescent signal. The double emulsions can be incubated and observed in a hydrodynamic trapping array or analyzed via flow cytometry. Our approach provides a valuable tool for the discovery and development of membrane‐active antimicrobials.
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Affiliation(s)
- Nicola Nuti
- Department of Biosystems Science and Engineering Bioanalytics Group ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Philipp Rottmann
- Department of Biosystems Science and Engineering Bioprocess Laboratory ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Ariane Stucki
- Department of Biosystems Science and Engineering Bioanalytics Group ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Philipp Koch
- Department of Biosystems Science and Engineering Bioprocess Laboratory ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering Bioprocess Laboratory ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering Bioanalytics Group ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
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18
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Yadavalli SS, Yuan J. Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer. J Bacteriol 2022; 204:e0034421. [PMID: 34516282 PMCID: PMC8765417 DOI: 10.1128/jb.00344-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.
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Affiliation(s)
- Srujana S. Yadavalli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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19
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Dittrich PS, Nuti N, Rottmann P, Stucki A, Koch P, Panke S. A Multiplexed Cell‐Free Assay to Screen for Antimicrobial Peptides in Double Emulsion Droplets. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Petra S Dittrich
- Eidgenossische Technische Hochschule Zurich Biosystems and Engineering Mattenstrasse 26 4058 Basel SWITZERLAND
| | - Nicola Nuti
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Biosystems Science and Engineering SWITZERLAND
| | - Philipp Rottmann
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Biosystems Science and Engineering SWITZERLAND
| | - Ariane Stucki
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Biosystems Science and Engineering SWITZERLAND
| | - Philipp Koch
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Biosystems Science and Engineering SWITZERLAND
| | - Sven Panke
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Biosysystems Science and Engineering SWITZERLAND
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20
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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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21
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Fijalkowski I, Peeters MKR, Van Damme P. Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides. Front Genet 2021; 12:713400. [PMID: 34721520 PMCID: PMC8554064 DOI: 10.3389/fgene.2021.713400] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
With the rapid growth in the number of sequenced genomes, genome annotation efforts became almost exclusively reliant on automated pipelines. Despite their unquestionable utility, these methods have been shown to underestimate the true complexity of the studied genomes, with small open reading frames (sORFs; ORFs typically considered shorter than 300 nucleotides) and, in consequence, their protein products (sORF encoded polypeptides or SEPs) being the primary example of a poorly annotated and highly underexplored class of genomic elements. With the advent of advanced translatomics such as ribosome profiling, reannotation efforts have progressed a great deal in providing translation evidence for numerous, previously unannotated sORFs. However, proteomics validation of these riboproteogenomics discoveries remains challenging due to their short length and often highly variable physiochemical properties. In this work we evaluate and compare tailored, yet easily adaptable, protein extraction methodologies for their efficacy in the extraction and concomitantly proteomics detection of SEPs expressed in the prokaryotic model pathogen Salmonella typhimurium (S. typhimurium). Further, an optimized protocol for the enrichment and efficient detection of SEPs making use of the of amphipathic polymer amphipol A8-35 and relying on differential peptide vs. protein solubility was developed and compared with global extraction methods making use of chaotropic agents. Given the versatile biological functions SEPs have been shown to exert, this work provides an accessible protocol for proteomics exploration of this fascinating class of small proteins.
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Affiliation(s)
- Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Marlies K. R. Peeters
- BioBix, Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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22
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Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases. Biomolecules 2021; 11:biom11101524. [PMID: 34680156 PMCID: PMC8534201 DOI: 10.3390/biom11101524] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
Two-component signal transduction systems (TCSs) are widely conserved in bacteria to respond to and adapt to the changing environment. Since TCSs are also involved in controlling the expression of virulence, biofilm formation, quorum sensing, and antimicrobial resistance in pathogens, they serve as candidates for novel drug targets. TCSs consist of a sensor histidine kinase (HK) and its cognate response regulator (RR). Upon perception of a signal, HKs autophosphorylate their conserved histidine residues, followed by phosphotransfer to their partner RRs. The phosphorylated RRs mostly function as transcriptional regulators and control the expression of genes necessary for stress response. HKs sense their specific signals not only in their extracytoplasmic sensor domain but also in their cytoplasmic and transmembrane domains. The signals are sensed either directly or indirectly via cofactors and accessory proteins. Accumulating evidence shows that a single HK can sense and respond to multiple signals in different domains. The underlying molecular mechanisms of how HK activity is controlled by these signals have been extensively studied both biochemically and structurally. In this article, we introduce the wide diversity of signal perception in different domains of HKs, together with their recently clarified structures and molecular mechanisms.
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23
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An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium. Proc Natl Acad Sci U S A 2021; 118:2103579118. [PMID: 34131082 PMCID: PMC8237595 DOI: 10.1073/pnas.2103579118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. However, little is known about the bacterium's transcriptome architecture and mechanisms of posttranscriptional control. Here, we have applied transcription start site and termination mapping to generate a single-nucleotide-resolution RNA map of C. difficile 5' and 3' untranslated regions, operon structures, and noncoding regulators, including 42 sRNAs. Our results indicate functionality of many conserved riboswitches and predict cis-regulatory RNA elements upstream of multidrug resistance (MDR)-type ATP-binding cassette (ABC) transporters and transcriptional regulators. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, the functions of Hfq-based posttranscriptional regulatory networks in gram-positive pathogens remain controversial. Using Hfq immunoprecipitation followed by sequencing of bound RNA species (RIP-seq), we identify a large cohort of transcripts bound by Hfq and show that absence of Hfq affects transcript stabilities and steady-state levels. We demonstrate sRNA expression during intestinal colonization by C. difficile and identify infection-related signals impacting its expression. As a proof of concept, we show that the utilization of the abundant intestinal metabolite ethanolamine is regulated by the Hfq-dependent sRNA CDIF630nc_085. Overall, our study lays the foundation for understanding clostridial riboregulation with implications for the infection process and provides evidence for a global role of Hfq in posttranscriptional regulation in a gram-positive bacterium.
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24
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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25
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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: 54] [Impact Index Per Article: 18.0] [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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26
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The Small Toxic Salmonella Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR. mBio 2020; 11:mBio.01659-20. [PMID: 33172998 PMCID: PMC7667032 DOI: 10.1128/mbio.01659-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has enabled the revelation of a vast number of genomes from organisms spanning all domains of life. To reduce complexity when new genome sequences are annotated, open reading frames (ORFs) shorter than 50 codons in length are generally omitted. However, it has recently become evident that this procedure sorts away ORFs encoding small proteins of high biological significance. For instance, tailored small protein identification approaches have shown that bacteria encode numerous small proteins with important physiological functions. As the number of predicted small ORFs increase, it becomes important to characterize the corresponding proteins. In this study, we discovered a conserved but previously overlooked small enterobacterial protein. We show that this protein, which we dubbed TimP, is a potent toxin that inhibits bacterial growth by targeting the cell membrane. Toxicity is relieved by a small regulatory RNA, which binds the toxin mRNA to inhibit toxin synthesis. Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has escaped identification as a small protein coding gene for nearly 2 decades. Since its identification in 2001, ryfA has been thought to encode a noncoding RNA and has been implicated in biofilm formation in Escherichia coli and pathogenesis in Shigella dysenteriae. Although a recent ribosome profiling study suggested ryfA to be translated, the corresponding protein product was not detected. In this study, we provide evidence that ryfA encodes a small toxic inner membrane protein, TimP, overexpression of which causes cytoplasmic membrane leakage. TimP carries an N-terminal signal sequence, indicating that its membrane localization is Sec-dependent. Expression of TimP is repressed by the small RNA (sRNA) TimR, which base pairs with the timP mRNA to inhibit its translation. In contrast to overexpression, endogenous expression of TimP upon timR deletion permits cell growth, possibly indicating a toxicity-independent function in the bacterial membrane.
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