Publications by authors named "Nazia Mojib"

16 Publications

  • Page 1 of 1

Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium .

Mar Drugs 2020 03 18;18(3). Epub 2020 Mar 18.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

A new cyclic peptide, kakeromamide B (), and previously described cytotoxic cyanobacterial natural products ulongamide A (), lyngbyabellin A (), 18-lyngbyaloside C (), and lyngbyaloside () were identified from an antimalarial extract of the Fijian marine cyanobacterium . Compounds and exhibited moderate activity against blood-stages with EC values of 0.89 and 0.99 µM, respectively, whereas was more potent with an EC value of 0.15 nM, respectively. Compounds , , and displayed moderate liver-stage antimalarial activity against liver schizonts with EC values of 1.1, 0.71, and 0.45 µM, respectively. The threading-based computational method FINDSITE predicted the binding of and to potentially druggable proteins of , prompting formulation of hypotheses about possible mechanisms of action. Kakeromamide B () was predicted to bind to several actin-like proteins and a sortilin protein suggesting possible interference with parasite invasion of host cells. When 1 was tested in a mammalian actin polymerization assay, it stimulated actin polymerization in a dose-dependent manner, suggesting that 1 does, in fact, interact with actin.
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http://dx.doi.org/10.3390/md18030167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142784PMC
March 2020

Peyssonnosides A-B, Unusual Diterpene Glycosides with a Sterically Encumbered Cyclopropane Motif: Structure Elucidation Using an Integrated Spectroscopic and Computational Workflow.

J Org Chem 2019 07 18;84(13):8531-8541. Epub 2019 Jun 18.

Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

Two sulfated diterpene glycosides featuring a highly substituted and sterically encumbered cyclopropane ring have been isolated from the marine red alga Peyssonnelia sp. Combination of a wide array of 2D NMR spectroscopic experiments, in a systematic structure elucidation workflow, revealed that peyssonnosides A-B (1-2) represent a new class of diterpene glycosides with a tetracyclo [7.5.0.0.0] tetradecane architecture. A salient feature of this workflow is the unique application of quantitative interproton distances obtained from the rotating frame Overhauser effect spectroscopy (ROESY) NMR experiment, wherein the β-d-glucose moiety of 1 was used as an internal probe to unequivocally determine the absolute configuration, which was also supported by optical rotatory dispersion (ORD). Peyssonnoside A (1) exhibited promising activity against liver stage Plasmodium berghei and moderate antimethicillin-resistant Staphylococcus aureus (MRSA) activity, with no cytotoxicity against human keratinocytes. Additionally, 1 showed strong growth inhibition of the marine fungus Dendryphiella salina indicating an antifungal ecological role in its natural environment. The high natural abundance and novel carbon skeleton of 1 suggests a rare terpene cyclase machinery, exemplifying the chemical diversity in this phylogenetically distinct marine red alga.
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http://dx.doi.org/10.1021/acs.joc.9b00884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614789PMC
July 2019

Antibacterial Oligomeric Polyphenols from the Green Alga Cladophora socialis.

J Org Chem 2019 05 3;84(9):5035-5045. Epub 2019 Apr 3.

Aquatic Chemical Ecology Center , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.

A series of oligomeric phenols including the known natural product 3,4,3',4'-tetrahydroxy-1,1'-biphenyl (3), the previously synthesized 2,3,8,9-tetrahydroxybenzo[ c]chromen-6-one (4), and eight new related natural products, cladophorols B-I (5-12), were isolated from the Fijian green alga Cladophora socialis and identified by a combination of NMR spectroscopy, mass spectrometric analysis, and computational modeling using DFT calculations. J-resolved spectroscopy and line width reduction by picric acid addition aided in resolving the heavily overlapped aromatic signals. A panel of Gram-positive and Gram-negative pathogens used to evaluate pharmacological potential led to the determination that cladophorol C (6) exhibits potent antibiotic activity selective toward methicillin-resistant Staphylococcus aureus (MRSA) with an MIC of 1.4 μg/mL. Cladophorols B (5) and D-H (7-11) had more modest but also selective antibiotic potency. Activities of cladophorols A-I (4-12) were also assessed against the asexual blood stages of Plasmodium falciparum and revealed cladophorols A (4) and B (5) to have modest activity with EC values of 0.7 and 1.9 μg/mL, respectively.
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http://dx.doi.org/10.1021/acs.joc.8b03218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503470PMC
May 2019

RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions.

Database (Oxford) 2017 01;2017

School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA 30332, USA.

Database Url: http://rampdb.biology.gatech.edu.
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http://dx.doi.org/10.1093/database/bax067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737055PMC
January 2017

Zebrafish aversive taste co-receptor is expressed in both chemo- and mechanosensory cells and plays a role in lateral line development.

Sci Rep 2017 10 18;7(1):13475. Epub 2017 Oct 18.

School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

Fishes rely on both chemical and tactile senses to orient themselves to avoid predators, and to detect and taste food. This is likely achieved by highly coordinated reception of signals by mechano- and chemosensory receptors in fish. A small co-receptor from zebrafish, receptor activity modifying protein (RAMP)-like triterpene glycoside receptor (RL-TGR), was previously found to be involved in recognition of triterpene glycosides, a family of naturally occurring compounds that act as chemical defenses in various prey species. However, its localization, function, and how it impacts sensory organ development in vivo is not known. Here we show that RL-TGR is expressed in zebrafish in both i) apical microvilli of the chemosensory cells of taste buds including the epithelium of lips and olfactory epithelium, and ii) mechanosensory cells of neuromasts belonging to the lateral line system. Loss-of-function analyses of RL-TGR resulted in significantly decreased number of neuromasts in the posterior lateral line system and decreased body length, suggesting that RL-TGR is involved in deposition and migration of the neuromasts. Collectively, these results provide the first in vivo genetic evidence of sensory cell-specific expression of this unusual co-receptor and reveal its additional role in the lateral line development in zebrafish.
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http://dx.doi.org/10.1038/s41598-017-14042-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647393PMC
October 2017

Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica.

Front Microbiol 2017 4;8:1347. Epub 2017 Aug 4.

Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States.

In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically sp., sp., and sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.
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http://dx.doi.org/10.3389/fmicb.2017.01347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543034PMC
August 2017

Chemical ecology of marine plankton.

Nat Prod Rep 2016 Jul 19;33(7):843-60. Epub 2016 Apr 19.

School of Biology, Aquatic Chemical Ecology Center, Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.

Covering: January 2013 to online publication December 2014This review summarizes recent research in the chemical ecology of marine pelagic ecosystems, and aims to provide a comprehensive overview of advances in the field in the time period covered. In order to highlight the role of chemical cues and toxins in plankton ecology this review has been organized by ecological interaction types starting with intraspecific interactions, then interspecific interactions (including facilitation and mutualism, host-parasite, allelopathy, and predator-prey), and finally community and ecosystem-wide interactions.
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http://dx.doi.org/10.1039/c6np00015kDOI Listing
July 2016

Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252).

3 Biotech 2015 Aug 10;5(4):379-392. Epub 2014 Jul 10.

Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., CH464, Birmingham, AL, 35294-1170, USA.

In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3-V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of  the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.
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http://dx.doi.org/10.1007/s13205-014-0233-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522729PMC
August 2015

Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).

Antonie Van Leeuwenhoek 2014 Nov 10;106(5):993-1009. Epub 2014 Sep 10.

Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35204, USA.

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.
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http://dx.doi.org/10.1007/s10482-014-0268-3DOI Listing
November 2014

Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia.

Mol Ecol 2014 Jun;23(11):2740-56

Red Sea Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.

The tropical oligotrophic oceanic areas are characterized by high water transparency and annual solar radiation. Under these conditions, a large number of phylogenetically diverse mesozooplankton species living in the surface waters (neuston) are found to be blue pigmented. In the present study, we focused on understanding the metabolic and genetic basis of the observed blue phenotype functional equivalence between the blue-pigmented organisms from the phylum Arthropoda, subclass Copepoda (Acartia fossae) and the phylum Chordata, class Appendicularia (Oikopleura dioica) in the Red Sea. Previous studies have shown that carotenoid-protein complexes are responsible for blue coloration in crustaceans. Therefore, we performed carotenoid metabolic profiling using both targeted and nontargeted (high-resolution mass spectrometry) approaches in four different blue-pigmented genera of copepods and one blue-pigmented species of appendicularia. Astaxanthin was found to be the principal carotenoid in all the species. The pathway analysis showed that all the species can synthesize astaxanthin from β-carotene, ingested from dietary sources, via 3-hydroxyechinenone, canthaxanthin, zeaxanthin, adonirubin or adonixanthin. Further, using de novo assembled transcriptome of blue A. fossae (subclass Copepoda), we identified highly expressed homologous β-carotene hydroxylase enzymes and putative carotenoid-binding proteins responsible for astaxanthin formation and the blue phenotype. In blue O. dioica (class Appendicularia), corresponding putative genes were identified from the reference genome. Collectively, our data provide molecular evidences for the bioconversion and accumulation of blue astaxanthin-protein complexes underpinning the observed ecological functional equivalence and adaptive convergence among neustonic mesozooplankton.
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http://dx.doi.org/10.1111/mec.12781DOI Listing
June 2014

UV and cold tolerance of a pigment-producing Antarctic Janthinobacterium sp. Ant5-2.

Extremophiles 2013 May 20;17(3):367-78. Epub 2013 Mar 20.

Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., CH464, Birmingham, AL 35294-1170, USA.

In this paper, we describe the UV and cold tolerance of a purple violet pigment (PVP)-producing Antarctic bacterium, Janthinobacterium sp. Ant5-2 (PVP(+)) and compared its physiological adaptations with a pigmentless mutant strain (PVP(-)). A spontaneous deletion of vioA that codes for tryptophan monooxygenase, the first gene involved in the biosynthesis of PVP was found in PVP(-) strain. The PVP(-) culture exhibited significantly reduced survival during exponential and stationary growth phase following exposure to UVB (320 nm) and UVC (254 nm) (dose range: 0-300 J/m²) when compared to wild-type (PVP(+)) cultures. In addition, upon biochemical inhibition of pigment synthesis by 2(5H)-furanone, wild-type PVP(+) cultures exhibited approximately 50-fold growth reduction at a higher dose (300 J/m²) of UV. Increased resistance to UV was observed upon inducing starvation state in both PVP(+) and PVP(-) cultures. There was 80% (SD = ±8) reduction in extrapolymeric substance (EPS) production in the PVP(-) cultures along with a compromised survival to freeze-thaw cycles when compared to the PVP(+) cultures. Perhaps synthesis of PVP and EPS are among the key adaptive features that define the survival of this bacterium in Antarctic extreme conditions, especially during austral summer months.
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http://dx.doi.org/10.1007/s00792-013-0525-9DOI Listing
May 2013

The antiproliferative function of violacein-like purple violet pigment (PVP) from an Antarctic Janthinobacterium sp. Ant5-2 in UV-induced 2237 fibrosarcoma.

Int J Dermatol 2011 Oct 26;50(10):1223-33. Epub 2011 Jul 26.

Department of Biology, University of Alabama at Birmingham, AL 35294-1170, USA.

Background: In this study, we have investigated the chemotherapeutic potential of a purple violet pigment (PVP), which was isolated from a previously undescribed Antarctic Janthinobacterium sp. (Ant5-2), against murine UV-induced 2237 fibrosarcoma and B16F10 melanoma cells.

Methods: The 2237, B16F10, C50, and NIH3T3 cells were treated with PVP at different doses and for different times, and their proliferation and viability were detected by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay. Cell cycle arrest induced by PVP in 2237 fibrosarcoma cells was assessed by flow cytometry and expression analysis of cell cycle regulatory proteins were done by Western blot. Apoptosis induced by PVP in 2237 cells was observed by annexin-V/propidium iodide double staining flow cytometry assay and fluorescence microscopy. To further determine the molecular mechanism of apoptosis induced by PVP, the changes in expression of Bcl-2, Bax and cytochrome c were detected by Western blot. The loss of mitochondrial membrane potential in PVP treated 2237 cells was assessed by staining with JC-1 dye following flow cytometry. Caspase-3, Caspase-9 and PARP cleavage were analyzed by Western blot and Caspase-3 and -9 activities were measured by colorimetric assays.

Results: In vitro treatment of murine 2237 cells with the PVP resulted in decreased cell viability (13-79%) in a time (24-72 h) and dose (0.1-1 μM)-dependent manner. The PVP-induced growth inhibition in 2237 cells was associated with both G0/G1 and G2/M phase arrest accompanied with decrease in the expression of cyclin dependent kinases (Cdks) and simultaneous increase in the expression of cyclin dependent kinase inhibitors (Cdki) - Cip1/p21 and Kip1/p27. Further, we observed a significant increase in the apoptosis of the 2237 fibrosarcoma cells which was associated with an increased expression of pro-apoptotic protein Bax, decreased expression of anti-apoptotic proteins Bcl-2, disruption of mitochondrial membrane potential, cytochrome c release, activation of caspase-3, caspase-9 and poly-ADP-ribose-polymerase (PARP) cleavage.

Conclusions: We describe the anti-cancer mechanism of the PVP for the first time from an Antarctic bacterium and suggest that the PVP could be used as a potent chemotherapeutic agent against nonmelanoma skin cancers.
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http://dx.doi.org/10.1111/j.1365-4632.2010.04825.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760711PMC
October 2011

Structure and function of a cold shock domain fold protein, CspD, in Janthinobacterium sp. Ant5-2 from East Antarctica.

FEMS Microbiol Lett 2011 Jun 18;319(2):106-14. Epub 2011 Apr 18.

Department of Biology, University of Alabama at Birmingham, AL 35294-1170, USA.

A cold shock domain (CSD)-containing protein, CspD, of molecular mass ~7.28 kDa in a psychrotolerant Antarctic Janthinobacterium sp. Ant5-2 (ATCC BAA-2154) exhibited constitutive expression at 37, 22, 15, 4 and -1°C. The cspD gene encoding the CspD protein of Ant5-2 was cloned, sequenced and analyzed. The deduced protein sequence was highly similar to the conserved domains of the cold shock proteins (Csps) from bacteria belonging to the class Betaproteobacteria. Its expression was both time- and growth phase-dependent and increased when exposed to 37°C and UV radiation (UVC, dose: 1.8 and 2.8 mJ cm(-2)). The results from the electrophoretic mobility shift and subcellular localization study confirmed its single-stranded DNA-binding property. In silico analysis of the deduced tertiary structure of CspD from Ant5-2 showed a highly stable domain-swapped dimer, forming two similar monomeric Csp folds. This study established an overall framework of the structure, function and phylogenetic analysis of CspD from an Antarctic Janthinobacterium sp. Ant5-2, which may facilitate and stimulate the study of CSD fold proteins in the class Betaproteobacteria.
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http://dx.doi.org/10.1111/j.1574-6968.2011.02269.xDOI Listing
June 2011

Antimycobacterial activity in vitro of pigments isolated from Antarctic bacteria.

Antonie Van Leeuwenhoek 2010 Nov 17;98(4):531-40. Epub 2010 Jun 17.

Department of Biology, University of Alabama at Birmingham, 35294-1170, USA.

In this study, we describe the antimycobacterial activity of two pigments, violacein, a purple violet pigment from Janthinobacterium sp. Ant5-2 (J-PVP), and flexirubin, a yellow-orange pigment from Flavobacterium sp. Ant342 (F-YOP). These pigments were isolated from bacterial strains found in the land-locked freshwater lakes of Schirmacher Oasis, East Antarctica. The minimum inhibitory concentrations (MICs) of these pigments for avirulent and virulent mycobacteria were determined by the microplate Alamar Blue Assay (MABA) and Nitrate Reductase Assay (NRA). Results indicated that the MICs of J-PVP and F-YOP were 8.6 and 3.6 μg/ml for avirulent Mycobacterium smegmatis mc²155; 5 and 2.6 μg/ml for avirulent Mycobacterium tuberculosis mc²6230; and 34.4 and 10.8 μg/ml for virulent M. tuberculosis H₃₇Rv, respectively. J-PVP exhibited a ~15 times lower MIC for Mycobacterium sp. than previously reported for violacein pigment from Chromobacterium violaceum, while the antimycobacterial effect of F-YOP remains undocumented. Our results indicate these pigments isolated from Antarctic bacteria might be valuable lead compounds for new antimycobacterial drugs used for chemotherapy of tuberculosis.
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http://dx.doi.org/10.1007/s10482-010-9470-0DOI Listing
November 2010

Occurrence and distribution of capB in Antarctic microorganisms and study of its structure and regulation in the Antarctic biodegradative Pseudomonas sp. 30/3.

Extremophiles 2010 Mar 20;14(2):171-83. Epub 2009 Dec 20.

Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, CH103, Birmingham, AL, 34294-1170, USA.

The analysis of the cold-shock domain (CSD)-encoding genes, capB and cspA, by PCR amplification showed presence of capB in all 18 Antarctic Pseudomonas isolates, but the absence of cspA. Nucleotide sequence analysis of capB ORF from a biodegradative Pseudomonas 30/3 and its regulatory sequences including the promoter and 5'-UTR was determined and compared with the other CSD-encoding genes. Expression analysis using translational gene fusion of the putative capB promoter and its flanking sequence from Pseudomonas sp. 30/3 with lacZ' exhibited a significant increase in beta-galactosidase activity at 15 and 6 degrees C. Unlike the expression of E. coli CspA, Pseudomonas sp. 30/3 showed a slow but steady increase of the CapB expression at 6 degrees C. Subcellular localization of CapB at 6 degrees C showed accumulation in and around the nucleoid whereas at 22 or 30 degrees C, it was identified around the nucleoid as well as in the cytosol. Our study attempts to elucidate the detailed structure of capB from Pseudomonas 30/3 and the role of 5'UTR in the transcriptional regulation along with the possible role of CapB in transcription and translation suited for the cold adaptation of this bacterium in Antarctic environment.
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http://dx.doi.org/10.1007/s00792-009-0296-5DOI Listing
March 2010

Detection, expression and quantitation of the biodegradative genes in Antarctic microorganisms using PCR.

Antonie Van Leeuwenhoek 2010 Mar 31;97(3):275-87. Epub 2009 Dec 31.

Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA.

In this study, 28 hydrocarbon-degrading bacterial isolates from oil-contaminated Antarctic soils were screened for the presence of biodegradative genes such as alkane hydroxylase (alks), the ISPalpha subunit of naphthalene dioxygenase (ndoB), catechol 2,3-dioxygenase (C23DO) and toluene/biphenyl dioxygenase (todC1/bphA1) by using polymerase chain reaction (PCR) methods. All naphthalene degrading bacterial isolates exhibited the presence of a 648 bp amplicon that shared 97% identity to a known ndoB sequence from Pseudomonas putida. Twenty-two out of the twenty-eight isolates screened were positive for one, two or all three different regions of the C23DO gene. For alkane hydroxylase, all 6 Rhodococcus isolates were PCR-positive for a 194 bp and a 552 bp segment of the alkB gene, but exhibited variable results with primers located at different segments of this gene. Three Pseudomonas spp. 4/101, 19/1, 30/3 amplified 552 bp segment of alkB. Only two Pseudomonas sp. 7/156 and 4/101 amplified a segment of alkB exhibiting 89-94% nucleotide sequence identity with the existing sequence of alkB in the GenBank sequence database. Transcripts of three genes, alkB2, C23DO and ndoB, that were amplified by DNA-PCR in three different bacterial isolates also exhibited positive amplification by reverse transcriptase PCR (RT-PCR) method confirming that these genes are functional. A competitive PCR (cPCR) method was developed for a quantitative estimation of ndoB from pure cultures of the naphthalene-degrading Pseudomonas sp. 30/2. A minimum of 1 x 10(7) copies of the ndoB gene was detected based on the comparison of the intensities of the competitor and target DNA bands. It is expected that the identification and characterization of the biodegradative genes will provide a better understanding of the catabolic pathways in Antarctic psychrotolerant bacteria, and thereby help support bioremediation strategies for oil-contaminated Antarctic soils.
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http://dx.doi.org/10.1007/s10482-009-9408-6DOI Listing
March 2010
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