Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease

The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates.     

In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly

1. Download : Download high-res image (120KB)
2. Download : Download full-size image

Highlights

• •In-depth proteome underpins the gland ontogeny and age-specific activity of the HGs.
• •The well-developed acini in the HGs of NBs promote the RJ secretary activities.
• •The enhanced protein and energy metabolism in the HGs boost the stronger RJ secretion of RJBs.

     

Determinants of Affinity and Proteolytic Stability in Interactions of Kunitz Family Protease Inhibitors with Mesotrypsin

An important functional property of protein protease inhibitors is their stability to proteolysis. Mesotrypsin is a human trypsin that has been implicated in the proteolytic inactivation of several protein protease inhibitors. We have found that bovine pancreatic trypsin inhibitor (BPTI), a Kunitz protease inhibitor, inhibits mesotrypsin very weakly and is slowly proteolyzed, whereas, despite close sequence and structural homology, the Kunitz protease inhibitor domain of the amyloid precursor protein (APPI) binds to mesotrypsin 100 times more tightly and is cleaved 300 times more rapidly. To define features responsible for these differences, we have assessed the binding and cleavage by mesotrypsin of APPI and BPTI reciprocally mutated at two nonidentical residues that make direct contact with the enzyme. We find that Arg at P₁ (versus Lys) favors both tighter binding and more rapid cleavage, whereas Met (versus Arg) at P′₂ favors tighter binding but has minimal effect on cleavage. Surprisingly, we find that the APPI scaffold greatly enhances proteolytic cleavage rates, independently of the binding loop. We draw thermodynamic additivity cycles analyzing the interdependence of P₁ and P′₂ substitutions and scaffold differences, finding multiple instances in which the contributions of these features are nonadditive. We also report the crystal structure of the mesotrypsin·APPI complex, in which we find that the binding loop of APPI displays evidence of increased mobility compared with BPTI. Our data suggest that the enhanced vulnerability of APPI to mesotrypsin cleavage may derive from sequence differences in the scaffold that propagate increased flexibility and mobility to the binding loop.     

Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease

1. Download : Download high-res image (89KB)
2. Download : Download full-size image

Highlights

• •Quantitative global proteome, acetylome and succinylome of phytoplasma-infected Paulownia tomentosa seedlings.
• •Acetylation may be more important than succinylation in response to phytoplasma infection.
• •Acetylation modified the activities of POR and RuBisCO.
• •Possible model to elucidate the molecular mechanism responses to PaWB from proteome and PTMs.

     

Structure and Mechanism of Rhomboid Protease

Rhomboid protease was first discovered in Drosophila. Mutation of the fly gene interfered with growth factor signaling and produced a characteristic phenotype of a pointed head skeleton. The name rhomboid has since been widely used to describe a large family of related membrane proteins that have diverse biological functions but share a common catalytic core domain composed of six membrane-spanning segments. Most rhomboid proteases cleave membrane protein substrates near the N terminus of their transmembrane domains. How these proteases function within the confines of the membrane is not completely understood. Recent progress in crystallographic analysis of the Escherichia coli rhomboid protease GlpG in complex with inhibitors has provided new insights into the catalytic mechanism of the protease and its conformational change. Improved biochemical assays have also identified a substrate sequence motif that is specifically recognized by many rhomboid proteases.     

Conodipine-P1-3, the First Phospholipases A2 Characterized from Injected Cone Snail Venom*

1. Download : Download high-res image (110KB)
2. Download : Download full-size image

Highlights

• •Three novel Conodipines P1-3 in the injected venom of Conus purpurascens.
• •Conodipines P1-3 have consensus catalytic characteristics of sPLA₂.
• •We determined multiple modification sites in Conodipines P1-3.
• •Evaluated the activity of Conohyal-P1 by a MS-based method.

     

Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*

1. Download : Download high-res image (115KB)
2. Download : Download full-size image

Highlights

• •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
• •Label-free quantification determined 2843 phagosomal proteins.
• •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
• •Increased recruitment of antigen cross-presentation molecules to these phagosomes.

     

蛋白酶分泌菌对重金属胁迫的反应

本文研究了Pb、zn、cu和Cd对3种蛋白酶产生菌:碱性地衣芽孢杆菌2709(Bacilluslicheniformis 2709)、中性枯草杆菌1.398(Bacillus subtilis1.398)和酸性宇佐美曲霉537(Aspergillususamii 537)生长及其酶活性的影响,并采用生长抑制皿分析(GIPA)方法针对3种菌株在Pb、zn、Cu、Cd不同胁迫浓度下的生长量进行打分,分析其耐性与抗性指标(MTC与MIC).结果表明4种重金属在超过一定临界浓度后,对3种菌株的生长和蛋白酶活性均产生了较大的抑制作用.碱性蛋白酶对4种重金属均具有较大的适应性,其次是中性蛋白酶对Zn和Cd具有一定的适应性.而酸性蛋白酶对4种重金属均表现出被抑制状态.3种菌株对Pb和Zn耐性与抗性最高(2.0 mmol/L～6.0 mmol/L),其次是对Cd也具有一定的抗性(0.5 mmol/L～0.75 mmol/L).     

蛋白酶分泌菌对重金属胁迫的反应

本文研究了Pb、Zn、Cu和Cd对3种蛋白酶产生菌：碱性地衣芽孢杆菌2709(Bacillus licheniformis 2709)、中性枯草杆菌1.398(Bacillus subtilis1.398)和酸性宇佐美曲霉537(Aspergillus usamii 537)生长及其酶活性的影响, 并采用生长抑制皿分析(GIPA)方法针对3种菌株在Pb、Zn、Cu、Cd不同胁迫浓度下的生长量进行打分, 分析其耐性与抗性指标(MTC与MIC)。结果表明4种重金属在超过一定临界浓度后, 对3种菌株的生长和蛋白酶活性均产生了较大的抑制作用。碱性蛋白酶对4种重金属均具有较大的适应性, 其次是中性蛋白酶对Zn和Cd具有一定的适应性, 而酸性蛋白酶对4种重金属均表现出被抑制状态。3种菌株对Pb和Zn耐性与抗性最高(2.0 mmol/L~6.0 mmol/L), 其次是对Cd也具有一定的抗性(0.5 mmol/L~0.75 mmol/L)。     

The Protease Domain Increases the Translocation Stepping Efficiency of the Hepatitis C Virus NS3-4A Helicase

Hepatitis C virus (HCV) NS3 protein has two enzymatic activities of helicase and protease that are essential for viral replication. The helicase separates the strands of DNA and RNA duplexes using the energy from ATP hydrolysis. To understand how ATP hydrolysis is coupled to helicase movement, we measured the single turnover helicase translocation-dissociation kinetics and the pre-steady-state P_i release kinetics on single-stranded RNA and DNA substrates of different lengths. The parameters of stepping were determined from global fitting of the two types of kinetic measurements into a computational model that describes translocation as a sequence of coupled hydrolysis-stepping reactions. Our results show that the HCV helicase moves with a faster rate on single stranded RNA than on DNA. The HCV helicase steps on the RNA or DNA one nucleotide at a time, and due to imperfect coupling, not every ATP hydrolysis event produces a successful step. Comparison of the helicase domain (NS3h) with the protease-helicase (NS3-4A) shows that the most significant contribution of the protease domain is to improve the translocation stepping efficiency of the helicase. Whereas for NS3h, only 20% of the hydrolysis events result in translocation, the coupling for NS3-4A is near-perfect 93%. The presence of the protease domain also significantly reduces the stepping rate, but it doubles the processivity. These effects of the protease domain on the helicase can be explained by an improved allosteric cross-talk between the ATP- and nucleic acid-binding sites achieved by the overall stabilization of the helicase domain structure.     

蛋壳内膜分解菌的筛选、鉴定及其所产蛋白酶性质的初步研究

从土壤中分离筛选到具有分解利用蛋壳内膜能力的菌株Pes207,通过生理生化鉴定及16S rRNA序列分析,确定其为恶臭假单胞菌（Pseudomonas putida）。通过分离纯化及初步酶学性质研究发现,该菌株所产胞外蛋白酶分子量约为32 ku,最适反应温度为60℃,最适pH为8.0,Km值为2.89 mmol/L。Pes207具有很强的分解液化蛋壳内膜的能力,其所产蛋白酶在pH 5.5～9.0、温度30～70℃之间具有良好的分解活性,具有较好的应用前景。     

Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus

Papain-like protease (PLpro) of coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses. Avian infectious bronchitis virus (IBV), the causative agent of bronchitis in chicken that results in huge economic losses every year in the poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade Lys⁴⁸- and Lys⁶³-linked polyubiquitin chains to monoubiquitin but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15-Å resolution. The overall structure is reminiscent of the structure of severe acute respiratory syndrome CoV PLpro. However, unlike the severe acute respiratory syndrome CoV PLpro that lacks blocking loop (BL) 1 of deubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys¹⁰¹, His²⁶⁴, and Asp²⁷⁵ is regulated by the flexible BL2. A model of ubiquitin-bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 subsites as well as residues interacting with the β-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-7-amino-4-methylcoumarin and LRGG-7-amino-4-methylcoumarin with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.     

Substrate-induced Changes in Protease Active Site Conformation Impact on Subsequent Reactions with Substrates

Enzymatic catalysis of biochemical reactions is essential to all living systems. The “lock and key” and “induced fit” models were early contributions to our understanding of the mechanisms involved in the reaction between an enzyme and its substrate. However, whether a given substrate-induced conformation is rigid or remains flexible has not yet been determined. By measuring the enzyme activity and intrinsic fluorescence of a nonspecific Eisenia fetida protease-I with different chromogenic substrates, we show that in subsequent reactions of protease with substrates, both the “lock and key” and “induced fit” mechanisms are used depending on the degree of conformational change required. Chromozym-Th- or chromosym-Ch-induced protease conformations were unable to bind chromozym-U. The chromosym-U-induced protease conformation remained flexible and could be further induced by chromozym-Th and chromozym-Ch. When low concentrations of guanidine HCl were used to disturb the conformation of the enzyme, only small changes in intrinsic fluorescence of the chromozym-Th-induced protease were detected, in contrast to the native enzyme whose intrinsic fluorescence markedly increased. This indicates that the substrate-induced enzyme was relatively rigid compared with the native protease. Utilizing a lock and key mechanism for secondary substrate reactions may have adaptive value in that it facilitates high efficiency in enzymatic reactions.     

Integration of Two In-depth Quantitative Proteomics Approaches Determines the Kallikrein-related Peptidase 7 (KLK7) Degradome in Ovarian Cancer Cell Secretome

1. Download : Download high-res image (59KB)
2. Download : Download full-size image

Highlights

• •Kallikrein-related peptidase 7 is over expressed in ovarian cancer.
• •Quantitative PROTOMAP and TAILS approaches identified putative substrates of KLK7.
• •Pro-MMP10 is activated by KLK7.
• •KLK7 cleaves thrombospondin 1 and IGFBP6 in vitro.

     

Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis

1. Download : Download high-res image (98KB)
2. Download : Download full-size image

Highlights

• •First report on the quantitative proteomic profiling of Drosophila lymph glands.
• •Comparative proteomic analysis under conditions of perturbed blood cell homeostasis.
• •Resource for identifying new regulators of insect and vertebrate hematopoiesis.