1
|
Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Biochemistry 2018; 57:4717-4725. [PMID: 29920078 DOI: 10.1021/acs.biochem.8b00410] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.
Collapse
Affiliation(s)
- Karl W Barber
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Chad J Miller
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jay W Jun
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14850 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| |
Collapse
|
2
|
Kim SW, Jun JW, Giri SS, Chi C, Yun S, Kim HJ, Kim SG, Kang JW, Park SC. First report of carp oedema virus infection of koi (Cyprinus carpio haematopterus) in the Republic of Korea. Transbound Emerg Dis 2017; 65:315-320. [PMID: 29226602 DOI: 10.1111/tbed.12782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Indexed: 11/29/2022]
Abstract
Twenty-five koi (Cyprinus carpio haematopterus) bought from a wholesale fish market in Korea, showed lethargic behaviour and 100% mortality within 20 days. Carp oedema virus (CEV) was detected by PCR in all 25 koi. Results of detailed histopathological and clinical examinations of 17 koi indicated loss of body balance, severe infiltration of inflammatory cells into the inter-lamellar spaces of the gills and vacuolization and inclusion bodies in gill epithelial cells. Sequence analysis of PCR products of these koi showed up to 99% identity to the previously reported sequences, suggesting that the observed mass mortality resulted from koi sleepy disease (KSD) due to CEV infection. To the best of our knowledge, this study is the first report of KSD in the Republic of Korea. Partial sequences of 4a protein from the virus indicated that the present CEV detected in koi from Korea is more closely related to that from the UK and Poland than from Japan. The present findings indicate that the prevalence and spread of KSD must be closely monitored in both European and Asian countries to avoid potential economic losses to the global koi industry.
Collapse
Affiliation(s)
- S W Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - J W Jun
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - S S Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - C Chi
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - S Yun
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - H J Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - S G Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - J W Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - S C Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| |
Collapse
|
3
|
Abstract
Metabolic organs such as the liver and adipose tissue produce several peptide hormones that influence metabolic homeostasis. Fat bodies, the Drosophila counterpart of liver and adipose tissues, have been thought to analogously secrete several hormones that affect organismal physiology, but their identity and regulation remain poorly understood. Previous studies have indicated that microRNA miR-8, functions in the fat body to non-autonomously regulate organismal growth, suggesting that fat body-derived humoral factors are regulated by miR-8. Here, we found that several putative peptide hormones known to have mitogenic effects are regulated by miR-8 in the fat body. Most members of the imaginal disc growth factors and two members of the adenosine deaminase-related growth factors are up-regulated in the absence of miR-8. Drosophila insulin-like peptide 6 (Dilp6) and imaginal morphogenesis protein-late 2 (Imp-L2), a binding partner of Dilp, are also up-regulated in the fat body of miR-8 null mutant larvae. The fat body-specific reintroduction of miR-8 into the miR-8 null mutants revealed six peptides that showed fat-body organ-autonomous regulation by miR-8. Amongst them, only Imp-L2 was found to be regulated by U-shaped, the miR-8 target for body growth. However, a rescue experiment by knockdown of Imp-L2 indicated that Imp-L2 alone does not account for miR-8's control over the insect's growth. Our findings suggest that multiple peptide hormones regulated by miR-8 in the fat body may collectively contribute to Drosophila growth.
Collapse
Affiliation(s)
- G J Lee
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | | | | |
Collapse
|
4
|
Kim JH, Son JS, Choi YJ, Choresca CH, Shin SP, Han JE, Jun JW, Kang DH, Oh C, Heo SJ, Park SC. Isolation and characterization of a lytic Myoviridae bacteriophage PAS-1 with broad infectivity in Aeromonas salmonicida. Curr Microbiol 2012; 64:418-26. [PMID: 22314935 DOI: 10.1007/s00284-012-0091-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 01/18/2012] [Indexed: 10/14/2022]
Abstract
To search for candidate control agents against Aeromonas salmonicida subsp. salmonicida infections in aquaculture, one bacteriophage (phage), designated as PAS-1, was isolated from the sediment samples of the rainbow trout (Oncorhynchus mykiss) culture farm in Korea. The PAS-1 was morphologically classified as Myoviridae and possessed approximately 48 kb of double-strand genomic DNA. The phage showed broad host ranges to other subspecies of A. salmonicida as well as A. salmonicida subsp. salmonicida including antibiotic-resistant strains. Its latent period and burst size were estimated to be approximately 40 min and 116.7 PFU/cell, respectively. Furthermore, genomic and structural proteomic analysis of PAS-1 revealed that the phage was closely related to other Myoviridae phages infecting enterobacteria or Aeromonas species. The bacteriolytic activity of phage PAS-1 was evaluated using three subspecies of A. salmonicida strain at different doses of multiplicity of infection, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, PAS-1 could be considered as a novel Aeromonas phage and might have potentiality to reduce the impacts of A. salmonicida infections in aquaculture.
Collapse
Affiliation(s)
- J H Kim
- Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Kim JH, Kim HK, Nguyen VG, Park BK, Choresca CH, Shin SP, Han JE, Jun JW, Park SC. Genomic sequence of infectious hypodermal and hematopoietic necrosis virus (IHHNV) KLV-2010-01 originating from the first Korean outbreak in cultured Litopenaeus vannamei. Arch Virol 2011; 157:369-73. [PMID: 22038073 DOI: 10.1007/s00705-011-1155-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 10/17/2011] [Indexed: 11/25/2022]
Abstract
Due to the need to track and monitor genetic diversity, the genome of the infectious hypodermal and hematopoietic necrosis virus (IHHNV) strain KLV-2010-01 in cultured Litopenaeus vannamei shrimp that originated from the first Korean outbreak in 2010 was sequenced and analyzed. The genome, with a length of 3914 nucleotides, was sequenced from the Korean IHHNV. The genome encoded three large and overlapping open reading frames: ORF1 (NS-1) of 2001 bp, ORF2 (NS-2) of 1092 bp and ORF3 (capsid protein) of 990 bp. The overall organization, size and predicted amino acid sequence of the three ORFs in Korean IHHNV were highly similar to those of members of the infectious IHHNV group, and the most closely related strains were IHHNVs described from Ecuador and Hawaii. Additionally, phylogenetic analysis showed that the Korean IHHNV was clustered with lineage III in the infectious IHHNV group and was most similar to IHHNV isolates from Ecuador, China and Taiwan.
Collapse
Affiliation(s)
- J H Kim
- Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Han SY, Kang BK, Kang BJ, Shin SP, Soen BH, Kim JM, Kim JH, Choresca CH, Han JE, Jun JW, Park SC. Prevalence and different characteristics of two serotypes of Streptococcus parauberis isolated from the farmed olive flounder, Paralichthys olivaceus (Temminck and Schlegel), in Korea. J Fish Dis 2011; 34:731-739. [PMID: 21916898 DOI: 10.1111/j.1365-2761.2011.01289.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The prevalence of two serotypes of Streptococcus parauberis isolated from the olive flounder, Paralichthys olivaceus, was evaluated in a total of 29 isolates between 2003 and 2010 in Korea. Streptococcus parauberis isolates were divided into two serologically distinct types (serotype 1 and serotype 2), except for one strain (S1091), using an agglutination assay with rabbit antiserum, and serotype 1 was identified as the dominant type (24 of 29 isolates) in this study. To identify the characteristics of the two serotypes of S. parauberis, we conducted a biochemical test using the API 20 Strep kit, a transmission electron microscopy (TEM) assay, sequence analysis of 16S-23S rRNA intergenic spacer region (ISR) and a pathogenicity test. In TEM, both serotypes possessed polysaccharide capsule layers around the cell surface when bacterial cells were treated with a homologous serotype of rabbit antiserum. However, we were unable to discriminate serotype-specific biochemical characteristics and genetic characteristics of 16S-23S rRNA ISR between the two serotypes. In the pathogenicity test, the serotype 1 strains induced significantly higher mortality than the serotype 2 strains in olive flounder when experimentally inoculated via the intraperitoneal route.
Collapse
Affiliation(s)
- S Y Han
- Research Unit, Green Cross Veterinary Product, Yongin, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Convery ME, Taylor CC, Jun JW. Vacuum structure, zero modes, and the effective potential in light-cone quantization. Int J Clin Exp Med 1995; 51:4445-4450. [PMID: 10018918 DOI: 10.1103/physrevd.51.4445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
8
|
|
9
|
Brown RW, Jun JW, Shvartsman SM, Taylor CC. Role of zero modes in the canonical quantization of heavy-fermion QED in light-cone coordinates. Int J Clin Exp Med 1993; 48:5873-5882. [PMID: 10016253 DOI: 10.1103/physrevd.48.5873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
10
|
Jun JW, Kim JK. Evaluation of the conformal anomaly of N=1 superstring theory by the stochastic quantization method. Phys Rev D Part Fields 1988; 38:3819-3822. [PMID: 9959149 DOI: 10.1103/physrevd.38.3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
11
|
Jun JW, Kim JK. Evaluation of the conformal anomaly of Polyakov's string theory by the stochastic quantization method. Phys Rev D Part Fields 1988; 37:2238-2242. [PMID: 9958928 DOI: 10.1103/physrevd.37.2238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
|
12
|
Han CW, Han SK, Jun JW, Kim JK, Koh IG. Absence of leading divergence in the parity-odd one-loop amplitude of type-I SO(32) superstring theory. Int J Clin Exp Med 1986; 34:1219-1221. [PMID: 9957275 DOI: 10.1103/physrevd.34.1219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|