The Analysis of Participation of Individual Proteins in the Protein Interactome Formation

It becomes increasingly clear that most proteins of living systems exist as components of various protein complexes rather than individual molecules. The use of various proteomic techniques significantly extended our knowledge not only about functioning of individual complexes but also formed a basis for systemic analysis of protein-protein interactions. In this study gel-filtration chromatography accompanied by mass spectrometry was used for the interactome analysis of human liver proteins. In six fractions (with average molecular masses of 45 kDa, 60 kDa, 85 kDa, 150 kDa, 250 kDa, and 440 kDa) 797 proteins were identified. In dependence of their distribution profiles in the fractions, these proteins could be subdivided into four groups: (1) single monomeric proteins that are not involved in formation of stable protein complexes; (2) proteins existing as homodimers or heterodimers with comparable partners; (3) proteins that are partially exist as monomers and partially as components of protein complexes; (4) proteins that do not exist in the monomolecular state, but also exist within protein complexes containing three or more subunits. Application of this approach to known isatin-binding proteins resulted in identification of proteins involved in formation of the homo- and heterodimers and mixed protein complexes.     

Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.     

The Mycobacteriophage D29 Gene 65 Encodes an Early-Expressed Protein That Functions as a Structure-Specific Nuclease

The genomes of mycobacteriophages of the L5 family, which includes the lytic phage D29, contain several genes putatively linked to DNA synthesis. One such gene is 65, which encodes a protein belonging to the RecA/DnaB helicase superfamily. In this study a recombinant version of the mycobacteriophage D29 gp65 was functionally characterized. The results indicated that it is not a helicase as predicted but an exonuclease that removes 3′ arms from forked structures in an ATP-dependent manner. The gp65 exonuclease acts progressively from the 3′ end, until the fork junction is reached. As it goes past, its progress is stalled over a stretch of seven to eight nucleotides immediately downstream of the junction. It efficiently acts on forked structures with single stranded arms. It also acts upon 5′ and 3′ flaps, though with somewhat relaxed specificity, but not on double-stranded forks. Sequence comparison revealed the presence of a KNRXG motif in the C-terminal half of the protein. This is a conserved element found in the RadA/Sms family of DNA repair proteins. A mutation (R203G) in this motif led to complete loss of nuclease activity. This indicated that KNRXG plays an important role in the nuclease function of not only gp65, but possibly other RadA/Sms family proteins as well. This is the first characterization of a bacteriophage-derived RadA/Sms class protein. Given its mode of action, it is very likely that gp65 is involved in processing branched replication intermediates formed during the replication of phage DNA.Fork structures are intricately associated with DNA replication. Such structures result due to unwinding of the DNA ahead of the replicating machinery. The unwound single strands are then used as templates for the synthesis of the new strands, either continuously (leading strand) or discontinuously (lagging strand). Repair of stalled forks involve complex mechanisms which may vary from one organism to another (5). However, in most cases the process requires nucleases that recognize stalled fork structures and cleave them specifically. Such nucleases are generally referred to as structure-specific nucleases (25). One such nuclease named FEN1 found in eukaryotes has been studied fairly extensively, and it is believed that this nuclease is involved in the removal of 5′ flaps from Okazaki fragments (11, 23). FEN1 belongs to a larger family of structure-specific nucleases, which includes human XPG (17), an endonuclease related to the disease xeroderma pigmentosa. Although the XPG family is associated with the removal of 5′ flaps the XPF type proteins are needed for removing the 3′ flaps (3). Similar proteins have been found in several Archaea (28). In Escherichia coli, the Holliday junction resolving enzyme system RuvABC is believed to be involved in resolving stalled forks by creating double-stranded breaks, which may be repaired through homologous recombination (29). Studies in E. coli have revealed that there are multiple redundant pathways that are capable of repairing stalled forks. One such pathway involves a protein named RadA/Sms, the absence of which results in partial increase in sensitivity to radiation in E. coli (2). Genes encoding RadA/Sms family proteins are present in many bacteria, including mycobacteria. Most of these members carry a conserved element KNRFG. It is believed (2) that RadA/Sms family of proteins may generate double-stranded breaks at fork junctions, although this has not been specifically demonstrated.Mycobacteriophages of the L5 family, which includes D29, BxB1, may be either temperate or potentially temperate (D29) (14, 15, 27). Despite their temperate character these phages share a strong resemblance with lytic phages. An important feature shared by lytic phages in general is their ability to synthesize DNA using phage-encoded DNA polymerases (13). They also possess many genes linked to nucleotide metabolism. It appears that as far as DNA replication is concerned, lytic phages prefer to be self-sufficient. This is apparently an important issue since lytic phages inactivate their host and therefore host-specific functions cannot be used to support phage growth.Following the availability of the genome sequence, many interesting aspects of mycobacteriophages have come to light. The central region of mycobacteriophage L5/D29 genome has been predicted to harbor several genes whose products may contribute directly or indirectly toward synthesis of new DNA strands. In a recent investigation from this laboratory it has been demonstrated (4) that at least some of the genes in this region are involved in the production of deoxyribonucleotide precursors which are probably needed at increased levels during phage replication. Apart from these genes there are several others which probably encode DNA polymerization related functions. One such gene that drew our interest was gene 65, which appears to encode a RecA/DnaB helicase superclass protein (22). The N-terminal region of this protein contains the Walker motifs A and B, which are characteristically present in the members of the RecA/DnaB superfamily. Walker motifs A and B (30) are found in proteins that hydrolyze ATP for executing their respective functions. To investigate the possible function of gp65, its gene was overexpressed in E. coli, and the recombinant protein was purified. Assays performed with the recombinant gp65 revealed that it is a structure-specific nuclease that acts exonucleolytically on fork structures, resulting in truncated forms lacking the 3′ arm. This function was demonstrated to require a particular motif KNRXG that is omnipresent in the RadA/Sms family of proteins (2). This characterization of D29 gp65 could give us better insight into how mycobacteriophages replicate their DNA within their hosts.     

Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein

KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein–protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.     

Yeast Protein Interactome topology provides framework for coordinated-functionality

The architecture of the network of protein–protein physical interactions in Saccharomyces cerevisiae is exposed through the combination of two complementary theoretical network measures, betweenness centrality and ‘Q-modularity’. The yeast interactome is characterized by well-defined topological modules connected via a small number of inter-module protein interactions. Should such topological inter-module connections turn out to constitute a form of functional coordination between the modules, we speculate that this coordination is occurring typically in a pairwise fashion, rather than by way of high-degree hub proteins responsible for coordinating multiple modules. The unique non-hub-centric hierarchical organization of the interactome is not reproduced by gene duplication-and-divergence stochastic growth models that disregard global selective pressures.     

Distinctive Network Topology of Phase-Separated Proteins in Human Interactome

Liquid-liquid phase separation (LLPS) is an important mechanism that mediates the formation of biomolecular condensates. Despite the immense interest in LLPS, phase-separated proteins verified by experiments are still limited, and identification of phase-separated proteins at proteome-scale is a challenging task. Multivalent interaction among macromolecules is the driving force of LLPS, which suggests that phase-separated proteins may harbor distinct biological characteristics in protein–protein interactions (PPIs). In this study, we constructed an integrated human PPI network (HPIN) and mapped phase-separated proteins into it. Analysis of the network parameters revealed differences of network topology between phase-separated proteins and others. The results further suggested the efficiency when applying topological similarities in distinguishing components of MLOs. Furthermore, we found that affinity purification mass spectrometry (AP-MS) detects PPIs more effectively than yeast-two hybrid system (Y2H) in phase separation-driven condensates. Our work provides the first global view of the distinct network topology of phase-separated proteins in human interactome, suggesting incorporation of PPI network for LLPS prediction in further studies.     

RNA结合蛋白与RNA互作鉴定技术

RNA结合蛋白（RNA binding proteins,RBPs）通过与RNA相互作用,广泛参与到RNA的剪切、转运、编辑、胞内定位及翻译调控等过程中。RNA领域尤其是非编码RNA（non-coding RNA,ncRNA）研究的快速发展,催生了多种RBPs RNAs相互作用鉴定技术。这些技术反之又推动了 RNA领域的研究进程。本文对紫外交联免疫沉淀（ultraviolet crosslinking and immunoprecipitation,CLIP）,CLIP cDNA文库高通量测序 (high-throughput sequencing of CLIP cDNA library,HITS-CLIP),光活化核苷增强的CLIP(photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation,PAR-CLIP),单核苷酸分离CLIP (individual nucleotide resolution CLIP,iCLIP),TRIBE (targets of RNA-binding protein identified by editing),RNA 标记,相互作用组捕获(interactome capture,IC) 和SerIC (serial RNA interactome capture)等RBPs-RNAs相互作用鉴定技术的基本原理和优缺点以及应用进行综述。     

Glycosaminoglycan–Protein Interactions: The First Draft of the Glycosaminoglycan Interactome

The six mammalian glycosaminoglycans (GAGs), chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate, are linear polysaccharides. Except for hyaluronan, they are sulfated to various extent, and covalently attached to proteins to form proteoglycans. GAGs interact with growth factors, morphogens, chemokines, extracellular matrix proteins and their bioactive fragments, receptors, lipoproteins, and pathogens. These interactions mediate their functions, from embryonic development to extracellular matrix assembly and regulation of cell signaling in various physiological and pathological contexts such as angiogenesis, cancer, neurodegenerative diseases, and infections. We give an overview of GAG–protein interactions (i.e., specificity and chemical features of GAG- and protein-binding sequences), and review the available GAG–protein interaction networks. We also provide the first comprehensive draft of the GAG interactome composed of 832 biomolecules (827 proteins and five GAGs) and 932 protein–GAG interactions. This network is a scaffold, which in the future should integrate structures of GAG–protein complexes, quantitative data of the abundance of GAGs in tissues to build tissue-specific interactomes, and GAG interactions with metal ions such as calcium, which plays a major role in the assembly of the extracellular matrix and its interactions with cells. This contextualized interactome will be useful to identify druggable GAG–protein interactions for therapeutic purpose:     

Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network

Mammalian phospholipase D (PLD) enzyme family consists of six members. Among them, PLD1/2/6 catalyzes phosphatidic acid (PA) production, while PLD3/4/5 has no catalytic activities. Deregulation of the PLD-PA lipid signaling has been associated with various human diseases including cancer. However, a comprehensive analysis of the regulators and effectors for this crucial lipid metabolic pathway has not been fully achieved. Using a proteomic approach, we defined the protein interaction network for the human PLD family of enzymes and PA and revealed diverse cellular signaling events involving them. Through it, we identified PJA2 as a novel E3 ubiquitin ligase for PLD1 involved in control of the PLD1-mediated mammalian target of rapamycin signaling. Additionally, we showed that PA interacted with and positively regulated sphingosine kinase 1. Taken together, our study not only generates a rich interactome resource for further characterizing the human PLD-PA lipid signaling but also connects this important metabolic pathway with numerous biological processes.     

PSIbase: a database of Protein Structural Interactome map (PSIMAP)

Protein Structural Interactome map (PSIMAP) is a global interaction map that describes domain-domain and protein-protein interaction information for known Protein Data Bank structures. It calculates the Euclidean distance to determine interactions between possible pairs of structural domains in proteins. PSIbase is a database and file server for protein structural interaction information calculated by the PSIMAP algorithm. PSIbase also provides an easy-to-use protein domain assignment module, interaction navigation and visual tools. Users can retrieve possible interaction partners of their proteins of interests if a significant homology assignment is made with their query sequences. AVAILABILITY: http://psimap.org and http://psibase.kaist.ac.kr/     

富含半胱氨酸分泌蛋白生物学功能的研究进展

富含半胱氨酸分泌蛋白(cysteine-rich secretory proteins,CRISPs)包含众多不同起源的蛋白质,其大部分成员功能未知。近年来研究发现,哺乳动物中的CRISP家族各成员主要存在于生殖道中,在精子的成熟、精卵融合以及免疫系统中发挥着非常重要的作用,并且其表达水平的改变与人类多种重大疾病密切相关,有望成为某些疾病理想的生物标记物和药物靶点;而非哺乳动物中的CRISP家族成员则主要存在于腺体的分泌液中,能够阻断Na+、K+、Ca2+及环核苷酸门控通道,并与炎症反应密切相关。近来,作者所在实验室从低等无颌类脊椎动物七鳃鳗的口腔腺中分离纯化出富含半胱氨酸分泌蛋白,其与CRISP家族成员具有较高的同源性。该文针对CRISP家族成员生物学功能的最新进展做了分析归纳,并指出了相关研究的发展趋势。