Annual Review of Biochemistry
Vol. 61:1175-1212 (Volume publication date July 1992)
https://doi.org/10.1146/annurev.bi.61.070192.005523
Haifeng Wang, Marie La Russa, Lei S. Qi
Vol. 85, 2016
The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-...Read More
Figure 1: CRISPR-associated protein 9 (Cas9)-mediated sequence-specific genomic editing. (a) Comparison of programmable sequence-specific genome editing nucleases. (Top) Zinc-finger nucleases (ZFNs) a...
Figure 2: Nuclease-deactivated Cas9 (dCas9)-mediated sequence-specific gene regulation. (a) CRISPR interference (CRISPRi) strategies. Repression can occur with dCas9 alone in bacteria, which stericall...
Figure 3: Applications of CRISPR-associated protein 9 (Cas9) in gene editing, gene regulation, epigenome editing, and genomic imaging. (a) Cas9-mediated site-specific genome editing has a variety of a...
Roger Y. Tsien
Vol. 67, 1998
In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a ...Read More
Figure 1: GFP sequences. (Line 1) The wild-type (WT) gfp10 gene as originally cloned and sequenced by Prasher et al (10). (Line 2) A popular humanized version (EGFP, Clontech Laboratories, Palo Alto,...
Figure 2: Mechanism proposed by Cubitt et al (22) for the intramolecular biosynthesis of the GFP chromophore, with rate constants estimated for the Ser65 → Thr mutant by Reid & Flynn (23) and Heim et...
Figure 3: Stereoview of the three-dimensional structure of GFP (30), showing 11 β-strands forming a hollow cylinder through which is threaded a helix bearing the chromophore, shown in ball-and-stick ...
Figure 4: Amino acid side chains, main chain carbonyls and amides, and solvent waters in the immediate vicinity of the chromophore of S65T GFP (30). Side chains are labeled with the one-letter code f...
Figure 5: Fluorescence excitation and emission spectra (solid and dashed lines, respectively) for typical members of the six major classes of GFP mutants, together with the chromophore structures bel...
Figure 6: Location on the GFP crystal structure (30) of the most important sites that improve folding at 37°C. The amino acids shown in space-filling representation are the wild-type residues that ar...
Nils Wiedemann and Nikolaus Pfanner
Vol. 86, 2017
Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport ...Read More
Figure 1: Overview of the five major protein import pathways of mitochondria. Presequence-carrying preproteins are imported by the translocase of the outer mitochondrial membrane (TOM) and the presequ...
Figure 2: The presequence pathway into the mitochondrial inner membrane (IM) and matrix. The translocase of the outer membrane (TOM) consists of three receptor proteins, the channel-forming protein To...
Figure 3: Role of the oxidase assembly (OXA) translocase in protein sorting. Proteins synthesized by mitochondrial ribosomes are exported into the inner membrane (IM) by the OXA translocase; the ribos...
Figure 4: Carrier pathway into the inner membrane. The precursors of the hydrophobic metabolite carriers are synthesized without a cleavable presequence. The precursors are bound to cytosolic chaperon...
Figure 5: Mitochondrial intermembrane space import and assembly (MIA) machinery. Many intermembrane space (IMS) proteins contain characteristic cysteine motifs. The precursors are kept in a reduced an...
Figure 6: Biogenesis of β-barrel proteins of the outer mitochondrial membrane. The precursors of β-barrel proteins are initially imported by the translocase of the outer membrane (TOM), bind to small ...
Figure 7: The dual role of mitochondrial distribution and morphology protein 10 (Mdm10) in protein assembly and organelle contact sites. Mdm10 associates with the sorting and assembly machinery (SAM) ...
Figure 8: Multiple import pathways for integral α-helical proteins of the mitochondrial outer membrane. The precursors of proteins with an N-terminal signal anchor sequence are typically inserted into...
Figure 9: The mitochondrial contact site and cristae organizing system (MICOS) interacts with protein translocases. MICOS consists of two core subunits, Mic10 and Mic60. Mic10 forms large oligomers th...
Helmut Sies, Carsten Berndt, Dean P. Jones
Vol. 86, 2017
Oxidative stress is two sided: Whereas excessive oxidant challenge causes damage to biomolecules, maintenance of a physiological level of oxidant challenge, termed oxidative eustress, is essential for governing life processes through redox signaling. ...Read More
Figure 1: Redox processes have fundamental implications in biology. Oxidative stress, either as reversible oxidative eustress in redox regulation or as a cause of damage to biomolecules (oxidative dis...
Figure 2: Timeline showing the concepts of stress and adaptive stress responses. Mithridates VI (see 210) and Paracelsus (see 211) had early insights. Bernard's concept of milieu intérieur (see 212) r...
Figure 3: (a) Nicotinamide adenine dinucleotide (NADH) and reduced nicotinamide adenine dinucleotide phosphate (NADPH) redox potentials in the cytosol and the mitochondrial matrix. The major redox ind...
Figure 4: Role of H2O2 and NO in redox signaling (oxidative eustress) and in oxidative damage (oxidative distress). Major endogenous H2O2 sources via superoxide radical formation include NADPH oxidase...
Figure 5: Role of aquaporins as peroxiporins in growth factor receptor signaling. NOX enzymes are activated upon ligand–receptor interaction, and extracellular SOD3 captures the superoxide, providing ...
Figure 6: Mitochondrial H2O2 sources. The mitochondrial inner membrane complexes I, II, and III as well as a number of flavin-dependent enzymes, membrane bound or in the matrix space, produce superoxi...
Figure 7: Thioredoxin reductase and glutathione reductase maintain complex stability of NF-κB/IκB and Nrf2/Keap1. Cytosolic H2O2 leads to dissociation of the complexes, allowing for transport of NF-κB...
Figure 8: Singlet molecular oxygen and physical quenching by carotenoids. Photoexcitation or chemiexcitation of a sensitizer molecule leads to electronically excited states. The triplet sensitizer rea...
Figure 9: Oxidized microRNA (miR) can change mRNA specificity. Native miR-184 does not bind to the 3′-UTRs of Bcl-xL and Bcl-w, allowing their translation, which leads to blocked apoptosis (a). A guan...
Figure 10: (a) H2O2 production in the ER is coupled to generation of disulfide bonds. Each insertion of a disulfide bond via PDI leads to generation of one H2O2 molecule. This H2O2 is reduced by GPx8,...
Figure 11: Clinical relevance of biomarkers of oxidative stress. Protein (green), lipid (blue), and DNA (red) biomarkers were analyzed in various diseases listed across the top. Color coding on top il...
Figure 12: Synoptic view of oxidative stress and its relation to nutrition and redox medicine. Cofactors include micronutrients and metal ions. Redoxins are the thioredoxin, glutaredoxin, and peroxire...
Christian R. H. Raetz and Chris Whitfield
Vol. 71, 2002
▪ Abstract Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain known as lipid A (or endotoxin), a nonrepeating “core” oligosaccharide, and a distal polysaccharide (or O-antigen). Recent genomic data have facilitated study of LPS ...Read More
Figure 1: Model of the inner and outer membranes of E. coli K-12. Only the Kdo and lipid A regions of LPS are required for the growth of E. coli and most other Gram-negative bacteria (2). Exceptions ...
Figure 2: Structure and biosynthesis of Kdo2-lipid A in E. coli K-12. The symbols indicate the relevant structural genes encoding each of the enzymes (2, 48). A single enzyme catalyzes each reaction....
Figure 3: Detection of lipid A by the TLR4 innate immunity receptor of animal cells. The paradigm is based mainly on studies of the human, mouse, and hamster immune cells and macrophage lines (12, 13...
Figure 4: Regulated modifications of lipid A in E. coli and S. typhimurium and unusual lipid A structures in other bacteria. Partial covalent modifications are indicated with the dashed bonds. Panel ...
Figure 5: Pathway for L-Ara4N biosynthesis and mechanism of polymyxin resistance in E. coli and S. typhimurium. In accordance with the proposal of Reeves et al. (9), we have renamed the genes of the ...
Figure 6: Structure of the E. coli MsbA dimer at 4.5 Å resolution. This backbone tracing was made from protein data bank file 1JSQ (120). Trans-membrane helices 1–6 are colored purple, blue, yellow, ...
Figure 7: Model for MsbA-mediated lipid export in E. coli. Following the MsbA-mediated transport at the inner membrane, additional proteins are likely to be involved in steps 2 and 3, but these have ...
Figure 8: Structures of the known lipopolysaccharide core oligosaccharides from E. coli and Salmonella. The outer cores are shown, together with one heptose residue of the inner core. The ligation si...
Figure 9: Structures of the core oligosaccharides from K. pneumoniae O1 and P. aeruginosa O5. The β-galacturonic acid residues on the K. pneumoniae core are nonstoichiometric, and details of the stru...
Figure 10: Structure of lipooligosaccharides from N. meningitidis. The structures and immunotypes have been reviewed elsewhere (168, 246). The structure of the single α-chain in each LOS varies, and ...
Figure 11: Structure and biosynthesis of the E. coli R1 core. Organization of the waa locus is shown. Each gene has been mutated with a nonpolar insertion, and the structures of LPSs from the resulti...
Figure 12: Biosynthesis pathway for ADP-L-glycero-D-manno-heptose in E. coli. The figure is adapted from recent studies that necessitate revision of the previously proposed pathway (215).
Figure 13: Biosynthesis and assembly of O polysaccharides in a Wzy-dependent pathway. Panel A shows the sequence of reactions involved in the formation of the undecaprenyl-linked repeat units and the...
Figure 14: Biosynthesis and assembly of O polysaccharides in an ABC-transporter-dependent pathway. Panel A shows the predicted structures of undecaprenyl-linked intermediates in the biosynthesis of t...
Figure 15: Biosynthesis and assembly of O polysaccharides in a synthase-dependent pathway. The only current example is the plasmid-encoded O:54 antigen of S. enterica serovar Borreze. Panel A shows t...
