1
|
Ujaoney AK, Anaganti N, Padwal MK, Basu B. Deinococcus lineage and Rad52 family-related protein DR0041 is involved in DNA protection and compaction. Int J Biol Macromol 2023; 248:125885. [PMID: 37473881 DOI: 10.1016/j.ijbiomac.2023.125885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
DR0041 ORF encodes an uncharacterized Deinococcus lineage protein. We earlier reported presence of DR0041 protein in DNA repair complexes of Ssb and RecA in Deinococcus radiodurans. Here, we systematically examined the role of DR0041 in DNA metabolism using various experimental methodologies including electrophoretic mobility assays, nuclease assays, strand exchange assays and transmission electron microscopy. Interaction between DR0041 and the C-terminal acidic tail of Ssb was assessed through co-expression and in vivo cross-linking studies. A knockout mutant was constructed to understand importance of DR0041 ORF for various physiological processes. Results highlight binding of DR0041 protein to single-stranded and double-stranded DNA, interaction with Ssb-coated single-stranded DNA without interference with RecA-mediated strand exchange, protection of DNA from exonucleases, and compaction of high molecular weight DNA molecules into tightly condensed forms. Bridging and compaction of sheared DNA by DR0041 protein might have implications in the preservation of damaged DNA templates to maintain genome integrity upon exposure to gamma irradiation. Our results suggest that DR0041 protein is dispensable for growth under standard growth conditions and following gamma irradiation but contributes to protection of DNA during transformation. We discuss the role of DR0041 protein from the perspective of protection of broken DNA templates and functional redundancy.
Collapse
Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
| |
Collapse
|
2
|
Basu B. The radiophiles of Deinococcaceae family: Resourceful microbes for innovative biotechnological applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100153. [PMID: 35909625 PMCID: PMC9325910 DOI: 10.1016/j.crmicr.2022.100153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/24/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
- Corresponding author.
| |
Collapse
|
3
|
Joshi S, Ujaoney AK, Ghosh P, Deobagkar DD, Basu B. N6-methyladenine and epigenetic immunity of Deinococcus radiodurans. Res Microbiol 2020; 172:103789. [PMID: 33188877 DOI: 10.1016/j.resmic.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
DNA methylation is ubiquitously found in all three domains of life. This epigenetic modification on adenine or cytosine residues serves to regulate gene expression or to defend against invading DNA in bacteria. Here, we report the significance of N6-methyladenine (6mA) to epigenetic immunity in Deinococcus radiodurans. Putative protein encoded by DR_2267 ORF (Dam2DR) contributed 35% of genomic 6mA in D. radiodurans but did not influence gene expression or radiation resistance. Dam2DR was characterized to be a functional S-adenosyl methionine (SAM)-dependent N6-adenine DNA methyltransferase (MTase) but with no endonuclease activity. Adenine methylation from Dam2DR or Dam1DR (N6-adenine MTase encoded by DR_0643) improved DNA uptake during natural transformation. To the contrary, methylation from Escherichia coli N6-adenine MTase (DamEC that methylates adenine in GATC sequence) on donor plasmid drastically reduced DNA uptake in D. radiodurans, even in presence of Dam2DR or Dam1DR methylated adenines. With these results, we conclude that self-type N6-adenine methylation on donor DNA had a protective effect in absence of additional foreign methylation, a separate methylation-dependent Restriction Modification (R-M) system effectively identifies and limits uptake of G6mATC sequence containing donor DNA. This is the first report demonstrating presence of epigenetic immunity in D. radiodurans.
Collapse
Affiliation(s)
- Suraj Joshi
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Molecular Biology Research Laboratory, Department of Zoology, SPPU, Pune 411007, India; Bioinformatics Centre, SPPU, Pune 411007, India.
| | - Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Payel Ghosh
- Bioinformatics Centre, SPPU, Pune 411007, India.
| | - Deepti D Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, SPPU, Pune 411007, India.
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
| |
Collapse
|
4
|
Nageswara S, Guntuku G, Yakkali BL. Purification, characterization, and structural elucidation of serralysin-like alkaline metalloprotease from a novel source. J Genet Eng Biotechnol 2019; 17:1. [PMID: 31659553 PMCID: PMC6821148 DOI: 10.1186/s43141-019-0002-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/15/2022]
Abstract
Background Serratiopeptidase is an alkaline metalloendopeptidase, which acquired wide significance because of its therapeutic applications. The present study was undertaken for purification, characterization, and structural elucidation of serratiopeptidase produced from Streptomyces hydrogenans var. MGS13. Result The crude enzyme was purified by precipitating with ammonium sulfate, dialysis, and Sephadex gel filtration, resulting in 34% recovery with a 12% purification fold. The purified enzyme S.AMP13 was spotted as a single clear hydrolytic band on casein zymogram and whose molecular weight was found to be 32 kDa by SDS-PAGE. The inhibitor and stability studies revealed that this enzyme is metalloprotease, thermostable, and alkaline in nature. The maximum serratiopeptidase activity was observed at 37 °C and pH 9.0. The partial amino acid sequence of the purified enzyme S.AMP13 by LC-MS/MS analysis shows the closest sequence similarities with previously reported alkaline metalloendopeptidases. The amino acid sequence alignment of S.AMP13 shared a conserved C-terminus region with peptidase-M10 serralysin superfamily at amino acid positions 128–147, i.e., ANLSTRATDTVYGFNSTAGR revealed that this enzyme is a serralysin-like protease. The kinetic studies of the purified enzyme revealed a Km of 1 mg/mL for its substrate casein and Vmax of 319 U/mL/min. The 3D structure of the purified enzyme was modeled by using SWISS-MODEL, and the quality of the structure was authenticated by assessing the Ramachandran plot using PROCHECK server, which suggested that the enzyme was stable with good quality. Conclusion Inhibitor, stability, electrophoretic, and bioinformatic studies suggested that the purified enzyme obtained from S. hydrogenans var. MGS13 is a serralysin-like protease. Electronic supplementary material The online version of this article (10.1186/s43141-019-0002-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Swathi Nageswara
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India. .,, Srikakulam, India.
| | - Girijasankar Guntuku
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| | - Bhagya Lakshmi Yakkali
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| |
Collapse
|
5
|
Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
Collapse
Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| |
Collapse
|
6
|
Anaganti N, Padwal MK, Dani P, Basu B. Pleiotropic effects of a cold shock protein homolog PprM on the proteome of Deinococcus radiodurans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:98-106. [PMID: 30389625 DOI: 10.1016/j.bbapap.2018.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
An extremophile D. radiodurans encodes a non-cold shock inducible cold shock protein homolog DR_0907 (also known as PprM). The DR_0907 ORF was deleted by knockout mutagenesis and the resultant deletion mutant (ΔpprM D. radiodurans) displayed growth defect as well as gamma-radiation sensitivity (D10 values = ΔpprM D. radiodurans: 12.1 kGy versus wild type (WT) D. radiodurans: 14 kGy). 2D gel based comparative proteomics revealed a comparable induction of DNA repair proteins in ΔpprM D. radiodurans and WT D. radiodurans recovering from 5 kGy gamma irradiation (60Co gamma source, dose rate: 2 kGy/h), suggesting that pprM does not cause radiation sensitivity through modulation of DdrO-regulated DNA repair genes. However, deletion of pprM did result in repression of several proteins that belonged to vital housekeeping pathways such as metabolism and protein homeostasis that might contribute to slow growth phenotype. These deficiencies intrinsic to ΔpprM D. radiodurans might also contribute to its radiation sensitivity.
Collapse
Affiliation(s)
- Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Pratiksha Dani
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
| |
Collapse
|
7
|
Ravindran A, Saenkham P, Levy J, Tamborindeguy C, Lin H, Gross DC, Pierson E. Characterization of the Serralysin-Like Gene of 'Candidatus Liberibacter solanacearum' Associated with Potato Zebra Chip Disease. PHYTOPATHOLOGY 2018; 108:327-335. [PMID: 29106346 DOI: 10.1094/phyto-02-17-0064-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The nonculturable bacterium 'Candidatus Liberibacter solanacearum' is the causative agent of zebra chip disease in potato. Computational analysis of the 'Ca. L. solanacearum' genome revealed a serralysin-like gene based on conserved domains characteristic of genes encoding metalloprotease enzymes similar to serralysin. Serralysin and other serralysin family metalloprotease are typically characterized as virulence factors and are secreted by the type I secretion system (T1SS). The 'Ca. L. solanacearum' serralysin-like gene is located next to and divergently transcribed from genes encoding a T1SS. Based on its relationship to the T1SS and the role of other serralysin family proteases in circumventing host antimicrobial defenses, it was speculated that a functional 'Ca. L. solanacearum' serralysin-like protease could be a potent virulence factor. Gene expression analysis showed that, from weeks 2 to 6, the expression of the 'Ca. L. solanacearum' serralysin-like gene was at least twofold higher than week 1, indicating that gene expression stays high as the disease progresses. A previously constructed serralysin-deficient mutant of Serratia liquefaciens FK01, an endophyte associated with insects, as well as an Escherichia coli lacking serralysin production were used as surrogates for expression analysis of the 'Ca. L. solanacearum' serralysin-like gene. The LsoA and LsoB proteins were expressed as both intact proteins and chimeric S. liquefaciens-'Ca. L. solanacearum' serralysin-like proteins to facilitate secretion in the S. liquefaciens surrogate and as intact proteins or as a truncated LsoB protein containing just the putative catalytic domains in the E. coli surrogate. None of the 'Ca. L. solanacearum' protein constructs expressed in either surrogate demonstrated proteolytic activity in skim milk or zymogram assays, or in colorimetric assays using purified protein, suggesting that the 'Ca. L. solanacearum' serralysin-like gene does not encode a functional protease, or at least not in our surrogate systems.
Collapse
Affiliation(s)
- Aravind Ravindran
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Panatda Saenkham
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Julien Levy
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Cecilia Tamborindeguy
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Hong Lin
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Dennis C Gross
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Elizabeth Pierson
- First and sixth authors: Department of Plant Pathology and Microbiology, second, third, and seventh authors: Department of Horticultural Sciences, and fourth author: Department of Entomology, Texas A&M University, College Station 77843; and fifth author: Department of Agriculture-Agricultural Research Service, CDPG, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| |
Collapse
|
8
|
Dani P, Ujaoney AK, Apte SK, Basu B. Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans. PLoS One 2017; 12:e0188998. [PMID: 29206865 PMCID: PMC5716572 DOI: 10.1371/journal.pone.0188998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022] Open
Abstract
The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.
Collapse
Affiliation(s)
- Pratiksha Dani
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Shree Kumar Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
- * E-mail:
| |
Collapse
|
9
|
Production, purification and characterization of fibrinolytic enzyme from Serratia sp. KG-2-1 using optimized media. 3 Biotech 2017; 7:184. [PMID: 28664371 DOI: 10.1007/s13205-017-0808-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022] Open
Abstract
Intravascular thrombosis is one of the major causes of variety of cardiovascular disorders leading to high mortality worldwide. Fibrinolytic enzymes from microbial sources possess ability to dissolve these clots and help to circumvent these problems in more efficient and safer way. In the present study, fibrinolytic protease with higher fibrinolytic activity than plasmin was obtained from Serratia sp. KG-2-1 isolated from garbage dump soil. Response surface methodology was used to study the interactive effect of concentration of maltose, yeast extract + peptone (1:1), incubation time, and pH on enzyme production and biomass. Maximum enzyme production was achieved at 33 °C after 24 h at neutral pH in media containing 1.5% Maltose, 4.0% yeast extract + peptone and other trace elements resulting in 1.82 folds increased production. The enzyme was purified from crude extract using ammonium sulfate precipitation and DEAE-Sephadex chromatography resulting in 12.9 fold purification with 14.9% yield. The purified enzyme belongs to metalloprotease class and had optimal activity in conditions similar to physiological environment with temperature optima of 40 °C and pH optima of 8. The enzyme was found to be stable in various solvents and its activity was enhanced in presence of Na+, K+, Ba2+, Cu2+, Mn2+, Hg2+ but inhibited by Ca2+ and Fe3+. Hence, the obtained enzyme may be used as potential therapeutic agent in combating various thrombolytic disorders.
Collapse
|
10
|
Li S, Wang L, Lin S, Yang J, Ma Z, Wang Y, Liu J, Hao J, Sun M. Rapid and efficient one-step purification of a serralysin family protease by using a p-aminobenzamidine-modified affinity medium. J Sep Sci 2017; 40:1960-1965. [PMID: 28304138 DOI: 10.1002/jssc.201601375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022]
Abstract
The metalloproteinase MP belongs to the serralysin family, which is involved in important functions such as nutrient acquisition and infection pathogenesis. Serralysin proteases in highly purified form are commonly used at the industrial level with several purposes. In this study, we set up an efficient and rapid purification protocol for MP using a p-aminobenzamidine-modified affinity chromatography. The affinity medium was synthesized by using p-aminobenzamidine as affinity ligand immobilized via cyanuric chloride spacer to Sepharose 6B sorbent carrier. According to the adsorption analysis, the dissociation constant Kd and theoretical maximum adsorption Qmax of this medium were 24.2 μg/mL and 24.1 mg/g wet sorbent, respectively. The purity of MP was assessed by a high-performance liquid chromatography on a TSK3000SW column and sodium dodecyl sulfate polyacrylamide gel electrophoresis, revealing values of 98.7 and ∼98%, respectively. The specific activity of purified MP was 95.6 U/mg, which is similar to values obtained through traditional purification protocols. In conclusion, our protocol could be easily employed for the rapid isolation of MP with high purity, and could be implemented for other serralysin family proteases.
Collapse
Affiliation(s)
- Shangyong Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Linna Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Shengxiang Lin
- Laboratory of Oncology and Molecular Endocrinology, CHUL Research Center (CHUQ) and Laval University, Quebec, Canada
| | - Juan Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Zibin Ma
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Yuejun Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Junzhong Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China
| | - Jianhua Hao
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R China
| | - Mi Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, P. R China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R China
| |
Collapse
|
11
|
Anaganti N, Basu B, Apte SK. In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans. J Biosci 2017; 41:193-203. [PMID: 27240980 DOI: 10.1007/s12038-016-9608-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A third generation promoter probe shuttle vector pKG was constructed, using the green fluorescent protein as a reporter, for in situ evaluation of Deinococcal promoter activity in Escherichia coli or Deinococcus radiodurans. The construct yielded zero background fluorescence in both the organisms, in the absence of promoter sequences. Fifteen Deinococcal promoters, either harbouring Radiation and Desiccation Response Motif (RDRM) or not, were cloned in vector pKG. Only the RDRM-promoter constructs displayed (i) gamma radiation inducible GFP expression in D. radiodurans, following gamma irradiation, (ii) DdrO-mediated repression of GFP expression in heterologous E. coli, or (iii) abolition in GFP induction following gamma irradiation, in pprI mutant of D. radiodurans. Utility of pKG vector for real-time in situ assessment of Deinococcal promoter function was, thus, successfully demonstrated.
Collapse
Affiliation(s)
- Narasimha Anaganti
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | | | | |
Collapse
|
12
|
Patil NA, Basu B, Deobagkar DD, Apte SK, Deobagkar DN. Putative DNA modification methylase DR_C0020 of Deinococcus radiodurans is an atypical SAM dependent C-5 cytosine DNA methylase. Biochim Biophys Acta Gen Subj 2016; 1861:593-602. [PMID: 28038990 DOI: 10.1016/j.bbagen.2016.12.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/17/2016] [Accepted: 12/24/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Control of cellular processes by epigenetic modification of cytosine in DNA is widespread among living organisms, but, is hitherto unknown in the extremely radioresistant microbe D. radiodurans. METHODS C-5 methyl cytosines (m5C) were detected by immuno-blotting with m5C-specific antibody. Site of cytosine methylation by DR_C0020 encoded protein was investigated by bisulfite sequencing. The DR_C0020 knockout mutant (Δdcm), constructed by site directed mutagenesis, was assessed for effect on growth, radiation resistance and proteome. Proteins were identified by mass spectrometry. RESULTS Methylated cytosines were detected in the D. radiodurans genome. The DR_C0020 encoded protein (Dcm, NCBI accession: WP_034351354.1), whose amino acid sequence resembles m4C methylases, was shown to be the lone SAM-dependent C-5 cytosine methyltransferase. Purified Dcm protein was found to methylate CpN sequence with a preference for methylation of two consecutive cytosines. The Δdcm strain completely lost m5C modification from its genome, had no effect on growth but became radiation sensitive. The Δdcm cells exhibited minor alterations in the abundance of several proteins involved primarily in protein homeostasis, oxidative stress defense, metabolism, etc. CONCLUSION DR_C0020 encoded SAM-dependent methyltransferase Dcm is solely responsible for C-5cytosine methylation at CpN sites in the genome of D. radiodurans and regulates protein homeostasis under normal growth conditions. The protein is an unusual case of an amino methyltransferase that has evolved to producing m5C. GENERAL SIGNIFICANCE Although, dispensable under optimal growth conditions, the presence of m5C may be important for recognition of parent strand and, thus, could contribute to the extraordinary DNA repair in D. radiodurans.
Collapse
Affiliation(s)
- Nayana A Patil
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India; Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Deepti D Deobagkar
- Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India
| | - Shree K Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
| | - Dileep N Deobagkar
- Department of Zoology, Centre for Advanced Studies, Savitribai Phule Pune University, Pune 411007, India.
| |
Collapse
|
13
|
Abstract
The extremophile Deinococcus radiodurans wild type R1 produces peptidases (metallo- and serine-) in TGY medium and in the media supplemented with human hair (HMY) and chicken feathers (FMY). Enzymatic screening on agar plates revealed peptidase activity. In TGY medium metallopeptidases were detected corresponding to a molecular mass range of 300-85 kDa (gelatinases); 280-130 (caseinases) and a 300 and a 170 kDa (keratinases); and a gelatinolytic serine peptidase (75 kDa). In HMY medium after 144 h, D. radiodurans produced keratinase (290 U/ml), gelatinase (619 U/ml) and sulfite (26 µg/ml). TGY medium produced higher proteolytic activity: 950 U/ml of gelatinolytic (24 h); 470 U/ml of keratinolytic (24 h) and 110 U/ml of caseinolytic (72 h). In the FMY medium, we found gelatinolytic (317 U/ml), keratinolytic (43 U/ml) and caseinolytic (85 U/ml) activities. The sulfite had a maximum release at 48 h (8.1 µg/ml). Enzymography analysis revealed that the keratinases degraded keratin after 24 h of reaction. The addition of sodium sulfite (1.0 %) improved the keratin degradation. Environmental Scanning Electron microscopy revealed alterations such as damage and holes in the hair fiber cuticle after D. radiodurans growth. This work presents for the first time D. radiodurans as a new keratinolytic microorganism.
Collapse
|
14
|
Wang N, Trivedi P. Citrus huanglongbing: a newly relevant disease presents unprecedented challenges. PHYTOPATHOLOGY 2013; 103:652-65. [PMID: 23441969 DOI: 10.1094/phyto-12-12-0331-rvw] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Citrus huanglongbing (HLB) is one of the oldest citrus diseases and has been known for over a century. HLB is caused by 'Candidatus Liberibacter' spp. that are phloem-limited, fastidious α-proteobacteria and infect hosts in different Kingdoms (i.e., Animalia and Plantae). When compared with well-characterized, cultivatable plant-pathogenic Gram-negative bacteria, the interactions of uncultured insect-vectored plant-pathogenic bacteria, including 'Ca. Liberibacter' spp., with their hosts remain poorly understood. 'Ca. Liberibacter' spp. have been known to cause HLB, which has been rapidly spreading worldwide, resulting in dramatic economic losses. HLB presents an unprecedented challenge to citrus production. In this review, we focus on the most recent research on citrus, 'Candidatus Liberibacter asiaticus', and psyllid interactions, specifically considering the following topics: evolutionary relationships among 'Ca. Liberibacter' spp., genetic diversity, host range, genome analysis, transmission, virulence mechanisms, and the ecological importance of HLB. Currently, no efficient management strategy is available to control HLB, although some promising progress has been made. Further studies are needed to understand citrus, 'Ca. L. asiaticus', and psyllid interactions to design innovative management strategies. Although HLB has been problematic for over a century, we can only win the battle against HLB with a coordinated and deliberate effort by the citrus industry, citrus growers, researchers, legislatures, and governments.
Collapse
Affiliation(s)
- Nian Wang
- Cirtrus Research Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred 33850, USA.
| | | |
Collapse
|
15
|
Yan Q, Sreedharan A, Wei S, Wang J, Pelz-Stelinski K, Folimonova S, Wang N. Global gene expression changes in Candidatus Liberibacter asiaticus during the transmission in distinct hosts between plant and insect. MOLECULAR PLANT PATHOLOGY 2013; 14:391-404. [PMID: 23336388 PMCID: PMC6638839 DOI: 10.1111/mpp.12015] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Huanglongbing (HLB) or citrus greening disease is a destructive disease of citrus worldwide, which is associated with Candidatus Liberibacter asiaticus. This phloem-limited fastidious pathogen is transmitted by the Asian citrus psyllid, Diaphorina citri, and appears to be an intracellular pathogen that maintains an intimate association with the psyllid or the plant throughout its life cycle. The molecular basis of the interaction of this pathogen with its hosts is not well understood. We hypothesized that, during infection, Ca. L. asiaticus differentially expresses the genes critical for its survival and/or pathogenicity in either host. To test this hypothesis, quantitative reverse transcription-polymerase chain reaction was performed to compare the gene expression of Ca. L. asiaticus in planta and in psyllid. Overall, 381 genes were analysed for their gene expression in planta and in psyllid. Among them, 182 genes were up-regulated in planta compared with in psyllid (P < 0.05), 16 genes were up-regulated in psyllid (P < 0.05) and 183 genes showed no statistically significant difference (P ≥ 0.05) in expression between in planta and in psyllid. Our study indicates that the expression of the Ca. L. asiaticus genes involved in transcriptional regulation, transport system, secretion system, flagella assembly, metabolic pathway and stress resistance are changed significantly in a host-specific manner to adapt to the distinct environments of plant and insect. To our knowledge, this is the first large-scale study to evaluate the differential expression of Ca. L. asiaticus genes in a plant host and its insect vector.
Collapse
Affiliation(s)
- Qing Yan
- Department of Microbiology and Cell Science, Citrus Research and Education Center, IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Shanks RMQ, Stella NA, Arena KE, Fender JE. Mutation of crp mediates Serratia marcescens serralysin and global secreted protein production. Res Microbiol 2012; 164:38-45. [PMID: 23072819 DOI: 10.1016/j.resmic.2012.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/27/2012] [Indexed: 12/13/2022]
Abstract
The bacterial species Serratia marcescens secretes both beneficial and cytotoxic proteins. Here we report that a crp mutant exhibited elevated secreted protease activity. A genetic screen revealed that the gene coding for the metalloprotease serralysin was necessary for the elevated proteolysis, and this was confirmed by western blot analysis. Proteomic analysis of secreted proteins corroborated increased secretion of serralysin protease by crp mutants compared to the wild type. The crp-mutant-secreted fractions also contained less chitinase and chitin binding protein. These data support the hypothesis that cAMP-CRP is an upstream indirect regulator of serralysin production and they provide novel insight into the S. marcescens secretome.
Collapse
Affiliation(s)
- Robert M Q Shanks
- The Charles T. Campbell Laboratory, UPMC Eye Center, Ophthalmology and Visual Sciences Research Center, Eye and Ear Institute, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15208, USA.
| | | | | | | |
Collapse
|
17
|
Characterization of the role of DR0171 in transcriptional response to radiation in the extremely radioresistant bacterium Deinococcus radiodurans. Arch Microbiol 2011; 193:741-50. [DOI: 10.1007/s00203-011-0712-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 04/12/2011] [Accepted: 04/18/2011] [Indexed: 01/28/2023]
|