4.4 Review

Small Proteins; Big Questions

Related references

Note: Only part of the references are listed.
Review Microbiology

Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer

Srujana S. Yadavalli et al.

Summary: Small membrane proteins are a class of recently discovered small proteins that play a role in regulating bacterial adaptation to environmental stressors. They have been found to interact with membrane proteins and impact their functions. There have been advancements in studying the functions of small membrane proteins using innovative tools. These proteins regulate various cellular processes and have potential clinical applications.

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Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

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Summary: Small open reading frames (sORFs) are often missed by annotation engines and are difficult to characterize. Ribosome profiling can improve genome annotations and has revealed new sORFs in bacterial model organisms. Antibiotics that trap ribosomes have played a key role in this development. This article describes new methods and provides important considerations for adapting ribosome profiling to different prokaryotic species.

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Small Proteins in Archaea, a Mainly Unexplored World

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Summary: This review summarizes the current state of research on small archaeal proteins and proposes systematic strategies for their global identification.

JOURNAL OF BACTERIOLOGY (2022)

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How Pathogens Feel and Overcome Magnesium Limitation When in Host Tissues

Anne-Beatrice Blanc-Potard et al.

Summary: Host organisms use nutritional immunity to restrict the availability of essential nutrients to invading pathogens, with magnesium deprivation playing a significant role in limiting the growth of Salmonella enterica serovar Typhimurium in host tissues. Pathogens' responses to factors promoting nutritional immunity may be more reflective of their internal cytoplasmic environment rather than the nutrient concentration in host cell compartments.

TRENDS IN MICROBIOLOGY (2021)

Article Genetics & Heredity

A novel type of colistin resistance genes selected from random sequence space

Michael Knopp et al.

Summary: Random sequences can generate novel antibiotic resistance determinants de novo, which act via specific peptide-protein interactions in the transmembrane domain. These peptides may potentially evolve as bona fide resistance determinants in natura.

PLOS GENETICS (2021)

Article Biochemistry & Molecular Biology

High complexity of Glutamine synthetase regulation in Methanosarcina mazei: Small protein 26 interacts and enhances glutamine synthetase activity

Miriam Gutt et al.

Summary: sORF-encoded small proteins have been overlooked for a long time, but the discovery of a small protein (sP26) in Methanosarcina mazei sheds light on its potential cellular function. The small protein interacts with glutamine synthetase (GlnA(1)) and PII-like protein GlnK(1) with high affinity, suggesting a role in enhancing GlnA(1) activity under nitrogen limitation.

FEBS JOURNAL (2021)

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Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure

Hendrik Melior et al.

Summary: Trans-acting regulatory RNAs, such as rnTrpL in Sinorhizobium meliloti, have the ability to pair with multiple mRNAs and may adjust their target specificity based on metabolic or environmental conditions. Tetracycline exposure can alter the target specificity of rnTrpL towards ribosomal protein-encoding mRNA, indicating the potential for sRNA target prioritization to shift in response to changing environmental cues.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover

Julian Gruetzner et al.

Summary: The DUF1127 domain, present in a wide range of bacterial proteins, mediates RNA binding and affects stability, thereby modulating the bacterial transcriptome and influencing different physiological processes.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria

Vanessa Krauspe et al.

Summary: The protein NblD plays a crucial role in the degradation of phycobilisomes in cyanobacteria under nitrogen-limited conditions. Studies have shown that NblD is essential for maintaining normal growth of cyanobacterial cells during nitrogen limitation.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Structural Basis of the Pore-Forming Toxin/Membrane Interaction

Yajuan Li et al.

Summary: Pore-forming toxins (PFTs) are a major virulence factor of many pathogenic bacteria, with well-characterized structural basis and interactions with host cell membranes. Understanding the mechanisms of PFTs can contribute to the development of novel therapeutic strategies and combat bacterial antibiotic resistance.

TOXINS (2021)

Article Microbiology

The Novel PII-Interacting Protein PirA Controls Flux into the Cyanobacterial Ornithine-Ammonia Cycle

Paul Bolay et al.

Summary: Cyanobacteria have unique regulatory mechanisms to control metabolic processes, exemplified by small proteins like PirA regulating nitrogen flux. The interaction between PirA and P-II impacts arginine synthesis, suggesting potential applications in metabolic engineering for biotechnological purposes.
Article Plant Sciences

Structural insights into photosystem II assembly

Jure Zabret et al.

Summary: Auxiliary proteins play a crucial role in assisting the assembly of photosystems, as shown by the structure of a PSII assembly intermediate resolved by cryo-electron microscopy. This structure reveals mechanisms that protect against photodamage during vulnerable stages of biogenesis and prepare the active site for the unique water-splitting reaction catalyzed by the Mn4CaO5 cluster.

NATURE PLANTS (2021)

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Alternative ORFs and small ORFs: shedding light on the dark proteome

Mona Wu Orr et al.

NUCLEIC ACIDS RESEARCH (2020)

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De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

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RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria

Ana P. Quendera et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2020)

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Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter

Jinki Yeom et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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MetaRibo-Seq measures translation in microbiomes

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Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle

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PLOS BIOLOGY (2020)

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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

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Unraveling the hidden universe of small proteins in bacterial genomes

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Regulation of Bacterial Gene Expression by Transcription Attenuation

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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

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A 2-dimensional ratchet model describes assembly initiation of a specialized bacterial cell surface

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Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

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Dual-Function RNAs

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SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci

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Communication between viruses guides lysis-lysogeny decisions

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Crystal structure of the potassium-importing KdpFABC membrane complex

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Increasing intracellular magnesium levels with the 31-amino acid MgtS protein

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The Complete Structure of the Mycobacterium smegmatis 70S Ribosome

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Dash-and-Recruit Mechanism Drives Membrane Curvature Recognition by the Small Bacterial Protein SpoVM

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Mechanisms of bacterial persistence during stress and antibiotic exposure

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Structural basis for the geometry-driven localization of a small protein

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Identification and characterization of sORF-encoded polypeptides

Qian Chu et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2015)

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Emerging evidence for functional peptides encoded by short open reading frames

Shea J. Andrews et al.

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The automatic annotation of bacterial genomes

Emily J. Richardson et al.

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Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

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NCBI GEO: archive for functional genomics data sets-update

Tanya Barrett et al.

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Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance

Errett C. Hobbs et al.

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Membrane Localization of Small Proteins in Escherichia coli

Fanette Fontaine et al.

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Geometric Cue for Protein Localization in a Bacterium

Kumaran S. Ramamurthi et al.

SCIENCE (2009)

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Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide

Andrew M. Lippa et al.

PLOS GENETICS (2009)

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Peptide-assisted degradation of the Salmonella MgtC virulence factor

Eric Alix et al.

EMBO JOURNAL (2008)

Review Microbiology

Small Toxic Proteins and the Antisense RNAs That Repress Them

Elizabeth M. Fozo et al.

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