-
The Journal of Biological Chemistry Apr 2018Circadian rhythms enable cells and organisms to coordinate their physiology with the cyclic environmental changes that come as a result of Earth's light/dark cycles.... (Review)
Review
Circadian rhythms enable cells and organisms to coordinate their physiology with the cyclic environmental changes that come as a result of Earth's light/dark cycles. Cyanobacteria make use of a post-translational oscillator to maintain circadian rhythms, and this elegant system has become an important model for circadian timekeeping mechanisms. Composed of three proteins, the KaiABC system undergoes an oscillatory biochemical cycle that provides timing cues to achieve a 24-h molecular clock. Together with the input/output proteins SasA, CikA, and RpaA, these six gene products account for the timekeeping, entrainment, and output signaling functions in cyanobacterial circadian rhythms. This Minireview summarizes the current structural, functional and mechanistic insights into the cyanobacterial circadian clock.
Topics: Bacterial Proteins; Circadian Clocks; Circadian Rhythm Signaling Peptides and Proteins; Cyanobacteria; Gene Expression Regulation, Bacterial; Models, Molecular; Photoperiod; Protein Conformation; Protein Kinases; Signal Transduction
PubMed: 29440392
DOI: 10.1074/jbc.TM117.001433 -
FEMS Microbiology Letters Jun 2018The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG. Many newly synthesized proteins... (Review)
Review
The bacterial membrane protein SecDF enhances protein translocation across the membrane driven by the complex of SecA ATPase and SecYEG. Many newly synthesized proteins in the cytoplasm are programmed to be translocated to the periplasm via the narrow channel that is formed in the center of SecYEG. During the protein-translocation process, SecDF is proposed to undergo repeated conformational transitions to pull out the precursor protein from the SecYEG channel into the periplasm. Once SecDF captures the precursor protein on the periplasmic surface, SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion, implying that SecDF is a protein-translocation motor that works independent of SecA. Structural and functional analyses of SecDF in 2011 suggested that SecDF utilizes the proton gradient and interacts with precursor protein in the flexible periplasmic region. The crystal structures of SecDF in different states at more than 3Å resolution were reported in 2017 and 2018, which further improved our understanding of the dynamic molecular mechanisms of SecDF. This review summarizes recent structural studies of SecDF.
Topics: Amino Acid Sequence; Bacteria; Bacterial Proteins; Crystallization; Crystallography, X-Ray; Membrane Proteins; Membrane Transport Proteins; Protein Transport; Protons
PubMed: 29718185
DOI: 10.1093/femsle/fny112 -
Toxins May 2017n/a.
n/a.
Topics: Animals; Antitoxins; Bacterial Proteins; Bacterial Toxins; Humans
PubMed: 28492500
DOI: 10.3390/toxins9050160 -
Molecular Microbiology Apr 2004Protein secretion systems in prokaryotes are increasingly shifting from being considered as experimental models for 'more complex' processes (i.e. eukaryotes) to being a... (Review)
Review
Protein secretion systems in prokaryotes are increasingly shifting from being considered as experimental models for 'more complex' processes (i.e. eukaryotes) to being a major source of key biological questions in their own right. The pathways by which proteins move between compartments or insert into membranes in prokaryotic cells are certainly less numerous than in eukaryotes (though not dramatically so). However, the quality and complexity of bacterial protein targeting systems indicate that virtually all mechanistic problems associated with protein traffic were solved very efficiently well before eukaryotes appeared on the Earth crust. Indeed, recent studies have both increased the number of known prokaryotic protein traffic systems and indicated new layers of complexity for those that were already well characterized. This report describes some recent developments in bacterial protein traffic that were presented at two meetings in the autumn of 2003.
Topics: Archaea; Archaeal Proteins; Bacteria; Bacterial Proteins; Models, Molecular; Protein Transport
PubMed: 15049806
DOI: 10.1111/j.1365-2958.2003.03966.x -
International Journal of Molecular... Jan 2018Protein glycosylation is emerging as an important feature in bacteria. Protein glycosylation systems have been reported and studied in many pathogenic bacteria,... (Review)
Review
Protein glycosylation is emerging as an important feature in bacteria. Protein glycosylation systems have been reported and studied in many pathogenic bacteria, revealing an important diversity of glycan structures and pathways within and between bacterial species. These systems play key roles in virulence and pathogenicity. More recently, a large number of bacterial proteins have been found to be glycosylated in gut commensal bacteria. We present an overview of bacterial protein glycosylation systems (- and -glycosylation) in bacteria, with a focus on glycoproteins from gut commensal bacteria, particularly Lactobacilli. These emerging studies underscore the importance of bacterial protein glycosylation in the interaction of the gut microbiota with the host.
Topics: Bacterial Proteins; Gastrointestinal Microbiome; Glycoproteins; Glycosylation; Lactobacillus; Models, Biological
PubMed: 29301365
DOI: 10.3390/ijms19010136 -
Molecular Microbiology Jan 2000The Tat (twin-arginine translocation) system is a bacterial protein export pathway with the remarkable ability to transport folded proteins across the cytoplasmic... (Review)
Review
The Tat (twin-arginine translocation) system is a bacterial protein export pathway with the remarkable ability to transport folded proteins across the cytoplasmic membrane. Preproteins are directed to the Tat pathway by signal peptides that bear a characteristic sequence motif, which includes consecutive arginine residues. Here, we review recent progress on the characterization of the Tat system and critically discuss the structure and operation of this major new bacterial protein export pathway.
Topics: Amino Acid Sequence; Bacterial Proteins; Biological Transport; Cell Membrane; Gram-Negative Bacteria; Molecular Sequence Data; Protein Folding; Protein Sorting Signals
PubMed: 10652088
DOI: 10.1046/j.1365-2958.2000.01719.x -
PloS One 2021Ultra-low temperature (ULT) storage of microbial biomass is routinely practiced in biological laboratories. However, there is very little insight regarding the effects...
Ultra-low temperature (ULT) storage of microbial biomass is routinely practiced in biological laboratories. However, there is very little insight regarding the effects of biomass storage at ULT and the structure of the cell envelope, on cell viability. Eventually, these aspects influence bacterial cell lysis which is one of the critical steps for biomolecular extraction, especially protein extraction. Therefore, we studied the effects of ULT-storage (-80°C) on three different bacterial platforms: Escherichia coli, Bacillus subtilis and the cyanobacterium Synechocystis sp. PCC 6803. By using a propidium iodide assay and a modified MTT assay we determined the impact of ULT storage on cellular viability. Subsequently, the protein extraction efficiency was determined by analyzing the amount of protein released following the storage. The results successfully established that longer the ULT-storage time lower is the cell viability and larger is the protein extraction efficiency. Interestingly, E. coli and B. subtilis exhibited significant reduction in cell viability over Synechocystis 6803. This indicates that the cell membrane structure and composition may play a major role on cell viability in ULT storage. Interestingly, E. coli exhibited concomitant increase in cell lysis efficiency resulting in a 4.5-fold increase (from 109 μg/ml of protein on day 0 to 464 μg/ml of protein on day 2) in the extracted protein titer following ULT storage. Furthermore, our investigations confirmed that the protein function, tested through the extraction of fluorescent proteins from cells stored at ULT, remained unaltered. These results established the plausibility of using ULT storage to improve protein extraction efficiency. Towards this, the impact of shorter ULT storage time was investigated to make the strategy more time efficient to be adopted into protocols. Interestingly, E. coli transformants expressing mCherry yielded 2.7-fold increase (93 μg/mL to 254 μg/mL) after 10 mins, while 4-fold increase (380 μg/mL) after 120 mins of ULT storage in the extracted soluble protein. We thereby substantiate that: (1) the storage time of bacterial cells in -80°C affect cell viability and can alter protein extraction efficiency; and (2) exercising a simple ULT-storage prior to bacterial cell lysis can improve the desired protein yield without impacting its function.
Topics: Bacteria; Bacterial Proteins; Cold Temperature; Microbial Viability
PubMed: 33999956
DOI: 10.1371/journal.pone.0251640 -
BioMed Research International 2021is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through...
is a thermophilic bacterium that produces a multitude of proteins within its genome. Bioinformatics strategies can facilitate comprehending this organism through functional and structural interpretation assessments. This study is aimed at allocating the structure and function through an approach required for bacterial protein biosynthesis. This viewpoint provides copious properties, including the physicochemical properties, subcellular location, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein (WP_012256288.1). The STRING program is utilized for the explication of protein-protein interactions. The investigation documented the protein's hydrophilic nature with predominantly alpha () helices in its secondary structure. The tertiary-structure model of the protein has been shown to exhibit reasonably high consistency based on various quality assessment methods. The functional interpretation suggested that the protein can act as a translation initiation factor, a protein required for translation and protein biosynthesis. Protein-protein interactions also demonstrated high credence that the protein interconnected with 30S ribosomal subunit involved in protein synthesis. This study bioinformatically examined that the protein (WP_012256288.1) is affiliated in protein biosynthesis as a translation initiation factor IF-3 of .
Topics: Amino Acid Sequence; Bacterial Proteins; Catalytic Domain; Chloroflexus; Computer Simulation; Models, Molecular; Molecular Sequence Annotation; Protein Biosynthesis; Protein Interaction Maps; Protein Structure, Secondary; Protein Structure, Tertiary; Structure-Activity Relationship; Subcellular Fractions
PubMed: 34307671
DOI: 10.1155/2021/9050026 -
Biochemistry Feb 2014Prokaryote-specific sugars, including N,N'-diacetylbacillosamine (diNAcBac) and pseudaminic acid, have experienced a renaissance in the past decade because of their... (Review)
Review
Prokaryote-specific sugars, including N,N'-diacetylbacillosamine (diNAcBac) and pseudaminic acid, have experienced a renaissance in the past decade because of their discovery in glycans related to microbial pathogenicity. DiNAcBac is found at the reducing end of oligosaccharides of N- and O-linked bacterial protein glycosylation pathways of Gram-negative pathogens, including Campylobacter jejuni and Neisseria gonorrhoeae. Further derivatization of diNAcBac results in the nonulosonic acid known as legionaminic acid, which was first characterized in the O-antigen of the lipopolysaccharide (LPS) in Legionella pneumophila. Pseudaminic acid, an isomer of legionaminic acid, is also important in pathogenic bacteria such as Helicobacter pylori because of its occurrence in O-linked glycosylation of flagellin proteins, which plays an important role in flagellar assembly and motility. Here, we present recent advances in the characterization of the biosynthetic pathways leading to these highly modified sugars and investigation of the roles that each plays in bacterial fitness and pathogenicity.
Topics: Acetylglucosamine; Acyltransferases; Bacteria; Bacterial Proteins; Glycoproteins; Glycosylation; Hydro-Lyases; Protein Conformation; Sugar Acids; Transaminases; Virulence Factors
PubMed: 24383882
DOI: 10.1021/bi401546r -
Physiology (Bethesda, Md.) Oct 2008Considering the biological abundance and importance of Mg2+, there is a surprising lack of information regarding the proteins that transport Mg2+, the mechanisms by... (Review)
Review
Considering the biological abundance and importance of Mg2+, there is a surprising lack of information regarding the proteins that transport Mg2+, the mechanisms by which they do so, and their physiological roles within the cell. The best characterized Mg2+ channel to date is the bacterial protein CorA, present in a wide range of bacterial species. The CorA homolog Mrs2 forms the mitochondrial Mg2+ channel in all eukaryotes. Physiologically, CorA is involved in bacterial pathogenesis, and the Mrs2 eukaryotic homolog is essential for cell survival. A second Mg2+ channel widespread in bacteria is MgtE. Its eukaryotic homologs are the SLC41 family of carriers. Physiological roles for MgtE and its homologs have not been established. Recently, the crystal structures for the bacterial CorA and MgtE Mg2+ channels were solved, the first structures of any divalent cation channel. As befits the unique biological chemistry of Mg2+, both structures are unique, unlike that of any other channel or transporter. Although structurally quite different, both CorA and MgtE appear to be gated in a similar manner through multiple Mg2+ binding sites in the cytosolic domain of the channels. These sites essentially serve as Mg2+ "sensors" of cytosolic Mg2+ concentration. Many questions about these channels remain, however, including the molecular basis of Mg2+ selectivity and the physiological role(s) of their eukaryotic homologs.
Topics: Animals; Antiporters; Bacterial Proteins; Carrier Proteins; Humans; Ion Channels; Magnesium
PubMed: 18927203
DOI: 10.1152/physiol.00019.2008