Projects

RECENT PROJECTS

Dynamic comparative secretome analysis of Bacillus subtilis

The members of the genus Bacillus produce a wide variety of secondary metabolites with antimetabolic and pharmacological activities. Bacilysin, being produced and excreted by certain strains of Bacillus subtilis, is a dipeptide antibiotic composed of L-alanine and L-anticapsin. Bacilysin blocked mutant strain OGU1 was constructed in our laboratory and were extensively studied in terms of cytoplasmic proteome. In the present study aims at the identification of secreted and differentially expressed proteins of the standard (B. subtilis PY79) and bacilysin nonproducer mutant (B. subtilis OGU1) in a time dependent manner.

Tübitak- KBAG- Bacillus Subtilis Standart Suş (PY79) ile Basilisinin Bloke Edildiği Suşun (OGU1) Karşılaştırmalı Dinamik Sekretom Analizi (2017-Devam ediyor)


Acellular vaccine strategies against pertussis

A worldwide mass vaccination against pertussis was started in the 1940s and a number of whole cell and acellular vaccine compositions have been developed thus far. However, these current vaccines still show inadequacies in providing sustainable immunity and avoiding the subclinical disease. In present study, selected proteins from B. pertussis immunoproteme studies in our laboratory are assessed for their potential immune protective capacities.

Tübitak- TBAG- Bordetella Pertussis'e Ait Rekombinant Fimbrial Protein X (Fimx), Putatif Peptidil Prolil Sis-Trans İzomeraz (Pppiase) Glutamin Bağlayıcı Periplasmik Protein (Glnbp), Putatif Peptidoglikan Bağlayıcı Protein Ve Şaperonin 10 (Hsp 10) Proteinlerinin Immün Koruyucu Kapasitelerinin Değerlendirilmesi (2013-2015)


PROTEOMICS

Immunoproteomics of Bordetella pertussis and Bordetella parapertussis 

Whooping cough is a worldwide acute respiratory disease that predominantly involves infants with characteristic violent, spasmodic and recurrent cough. While Bordetella pertussis is the causative agents of the disease, its close relative B. parapertussis causes a pertussis-like syndrome which is generally asymptomatic. The study in our laboratory aims at analysis of surface proteome and secretome of B. pertussis and B. parapertussis with the intention of identifiying candidate antigens of B. pertussis and B. parapertussis for vaccine development.


Heavy metal response proteome of  
Phanerocheate chrysosporium

The white rot fungus Phanerochaete chrysosporium has a high resistance and accumulating capacity for toxic heavy metals. By employing the 2-DE based proteomic technologies our laboratory aims to identify heavy metal stress related proteins of P. chrysosporium and the related resistant mechanisms.

BIOTECHNOLOGY

Cephamycin C production by recombinant S.clavuligerus

Streptomyces clavuligerus is a well-known actinomycete for its ability to produce beta-lactam antibiotics such as cephamycin C and clavulanic acid. The primary pathway for cephamycin C synthesis is the aspartate pathway branching into two paths, one ending up with the production of methionine and threonine and the other with cephamycin C. By blocking the path leading to amino acid production and as such favoring the cephamycin C production, one recombinant strain of S.clavuligerus was obtained previously in our laboratory. Currently we are trying to determine the effect of medium components on the growth and cephamycin C production of both the recombinant and the wild type strain of S.clavuligerus aiming to develop an optimum medium for the maximal cephamycin C production.


Transcriptional and Translational analysis of the effect of ccaR regulatory gene in Cephamycin C biosynthesis by Streptomyces clavuligerus

Streptomyces clavuligerus is a Gram-positive filamentous actinomycete producing a medically important β-Lactam antibiotic, Cephamycin C and a potent β-Lactamase inhibitor, clavulanic acid as a secondary metabolite. The genes of cephamycin pathway are lat, pcbAB, pcbC, cefD, cefE, cefF, cmcH, cmcI, cmcJ, cmcT, pbpA, bla, blp and pcbR, and the regulatory gene is ccaR. The sequences of these genes were reported previously and there are many studies trying to identify their functions via mRNA and protein levels (Perez-Llarena et al., 1997; Alexander and Jensen, 1998). However, the data describing the expression profile of all genes in cephamycin C metabolic pathway were obtained by using the molecular techniques of 10 years ago. The presence of new molecular techniques such as transcriptome and proteome makes it possible to obtain more accurate results both qualitatively and quantitatively about the molecular mechanisms during cephamycin C biosynthesis in the cell and the function of ccaR regulatory gene in cephamycin C gene cluster. In this study, the possible effect of ccaR gene will be examined in detail by quantitatively (Q-PCR) on transcriptional level and translational level via proteome in ccaR- disrupted mutant and ccaR++ super mutant.

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