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Cellular Localization of Gold and Mechanisms of Gold Resistance in Rhodobacter sphaeroides  [PDF]
Hannah Johnson, Ram C. Kafle, Madhusudan Choudhary
Advances in Microbiology (AiM) , 2017, DOI: 10.4236/aim.2017.78047
Abstract: Heavy metal pollution is a worldwide problem with many associated health risks, including bone loss, kidney damage, and several forms of cancer. There is a great need of bioremediation of these toxic metals from the environment, as well as implementing a monitoring system to control the spreading pollution. This study focuses on the bioremediation potential of Rhodobacter sphaeroides in the presence of the toxic gold chloride (AuCl3). Growth characteristics of the bacterial cells exposed to a range of toxic gold concentrations were analyzed through the growth kinetics and the colony forming units under aerobic, photosynthetic, and anaerobic growth conditions. The localization of the gold particles within two cellular fractions, cytoplasm and the plasma membrane, are analyzed using Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Results of this study demonstrated the photosynthetic growth condition as best suited for the metal tolerance, compared to the aerobic and anaerobic growth conditions. Results also revealed the overall accumulation and localization of gold particles, while not different between the membrane and the cytoplasmic fractions increased at different concentrations of the gold contamination. The results of the localization under photosynthetic growth condition revealed the accumulation reached the highest very quickly, and an overall shift in localization of the gold particles from an equal distribution to an increase within the membrane fraction at the highest concentrations of gold contamination. The localization of the gold particles was validated by Transmission Electron Microscopy (TEM) where the results confirmed the increase in accumulation within the membrane, and photosynthetic membranes, of R. sphaeroides.
Bacterial Heavy Metal Resistance Genes and Bioremediation Potential  [PDF]
Hannah Johnson, Hyuk Cho, Madhusudan Choudhary
Computational Molecular Bioscience (CMB) , 2019, DOI: 10.4236/cmb.2019.91001
Abstract: There is a worldwide distribution of heavy metal pollution that can be managed with a bioremediation approach using microorganisms. Several bacterial species belonging to the Proteobacteria have been shown to tolerate heavy metal stress, including toxic salts of noblemetals. Rhodobacter sphaeroides, a model bacterium has previously been utilized for bioremediation studies. A bioinformatics approach was employed here to identify the distribution of genes associated with heavy metal tolerance among the sequenced bacterial genomes currently available on the NCBI database. The distribution of these genes among different groups of bacteria and the Cluster of Orthologous Groups (COGs) were further characterized. A total of 170,000 heavy metal related genes were identified across all bacterial species, with a majority of the genes found in Proteobacteria (46%) and Terrabacteria (39%). Analysis of COGs revealed that the majority of heavy metal related genes belong to metabolism (COG 3), including ionic transport, amino acid biosynthesis, and energy production.
CtrA Is Nonessential for Cell Cycle Regulation in Rhodobacter sphaeroides  [PDF]
Lin Lin, Abha Choudhary, Anish Bavishi, Madhusudan Choudhary
Advances in Microbiology (AiM) , 2018, DOI: 10.4236/aim.2018.87037
Abstract: The bacterial cell cycle consists of a series of genetically coordinated biochemical and biophysical events. In Caulobacter crescentus, CtrA is an essential cell cycle regulator that modulates many cell cycle processes. In the present study, the role of the CtrA was investigated in Rhodobacter sphaeroides 2.4.1 by employing genetic, molecular, and bioinformatic approaches. Examination of the ctrA-null mutant revealed that the loss of CtrA did not affect growth characteristics and cell morphology in R. sphaeroides when grown under aerobic or photosynthetic growth conditions but slower growth was noticed in the anaerobic-dark-DMSO condition. Phylogenetic analyses demonstrated that CtrA has diversified its role in major lineages of α-Proteobacteria and has possibly been involved in adaptation to variable lifestyles. Analysis of the CtrA binding sites in the R. sphaeroides genome suggests that CtrA may regulate 127 genes involving different cellular processes. Protein homology searches revealed that only a small number of ctrA-regulated genes are homologous across C. crescentus, R. capsulatus, and R. sphaeroides. Comparison of the functions of putative ctrA-regulated genes in C. crescentus, R. capsulatus, and R. sphaeroides revealed that all three species possessed broad pathway control across a variety of cluster of orthologous gene functions (COGs). However, interestingly, it seems that the essentiality of CtrA in C. crescentus may depend more on the selective control that it exerts on a few critical cell cycle genes and pathways that are not controlled by CtrA in a similar fashion in R. capsulatus and R. sphaeroides.
Evolution of PE35 and PPE68 Gene Families in Mycobacterium: Roles of Horizontal Gene Transfer and Evolutionary Constraints  [PDF]
Ashay Bavishi, Lin Lin, Madhusudan Choudhary, Todd P. Primm
Journal of Tuberculosis Research (JTR) , 2014, DOI: 10.4236/jtr.2014.24023
Abstract: Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.
Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1
Anne E Peters, Anish Bavishi, Hyuk Cho, Madhusudan Choudhary
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-192
Abstract: The results revealed that most gene-pairs in in-paralogs are maintained under negative selection (ω?≤?0.3), but the strength of selection differed among in-paralog gene-pairs. Although in-paralogs located on different replicons are maintained under purifying selection, the duplicated genes distributed between the primary chromosome (CI) and the second chromosome (CII) are relatively less selectively constrained than the gene-pairs located within each chromosome. The mRNA expression patterns of duplicate gene-pairs were examined through microarray analysis of this organism grown under seven different growth conditions. Results revealed that ~62% of paralogs have similar expression patterns (cosine ≥ 0.90) over all of these growth conditions, while only ~7% of paralogs are very different in their expression patterns (cosine?<?0.50).The overall findings of the study suggest that only a small proportion of paralogs contribute to the metabolic diversity and the evolution of novel metabolic functions in R. sphaeroides. In addition, the lack of relationships between structural constraints and gene-pair expression suggests that patterns of gene-pair expression are likely associated with conservation or divergence of gene-pair promoter regions and other coregulation mechanisms.Rhodobacter sphaeroides is a well-studied photosynthetic eubacterium that belongs to the α-3 subgroup of the Proteobacteria[1,2]. R. sphaeroides 2.4.1 is a model strain for this organism and is noteworthy since its genome consists of two chromosomes, chromosome I (CI; ~3.2 Mb) and chromosome II (CII; ~0.9 Mb), and five endogenous plasmids [3-6]. It possesses significant metabolic diversity [7-14] and is capable of growing under aerobic, semiaerobic, and photosynthetic growth conditions, while utilizing a wide variety of carbon and nitrogen nutrient sources [15,16]. Therefore, R. sphaeroides is an ideal model for the examination and study of gene duplications and their roles in both the evolution of gen
The Effects of Different Carbon Sources on the Growth of Rhodobacter sphaeroides  [PDF]
Noah Zavala, Lorenzo Baeza, Santos Gonzalez, Madhusudan Choudhary
Advances in Microbiology (AiM) , 2019, DOI: 10.4236/aim.2019.98045
Abstract: Rhodobacter sphaeroides is a purple non-sulfur bacterium that belongs to the α-3 subdivision of Proteobacteria. R. sphaeroides is a model bacterial species because of its complex genome structure and expanded metabolic capabilities. The genome of R. sphaeroides consists of two circular chromosomes and five endogenous plasmids. It has the ability to grow under a wide variety of environmental conditions. It grows aerobically (~20% O2), semi-aerobically (~2% O2), and photosynthetically (under anaerobic condition plus light). It has been previously shown that many bacterial species utilize a number of alternate carbon sources for their optimal growth under a variety of growth conditions. We hypothesize that different or an additional carbon source in the minimal medium differentially affects the bacterial growth under dark-aerobic conditions. The bacterial growth kinetics and the number of cells in the bacterial culture were analyzed by measuring the optical density (OD at 600 nm) and the colony forming units (CFUs) at regular intervals of bacterial cultures. Results reveal that sodium succinate is the preferred sole carbon source for the optimal growth of R. sphaeroides. The results of growth kinetics and CFUs together concluded that from the tested carbon sources, sodium succinate is the best single carbon source in the minimal media for the optimal growth of R. sphaeroides. Interestingly, cell culture grown in SIS supplemented with sodium acetate exhibits a prolonged lag phase with the lowest ODs and CFUs that later switches to the growth-burst phase support previously discovered similar phenomenon of the growth-rate switch in the presence of acetate metabolism. Future work will utilize the aerobically grown R. sphaeroides’ cells as a biocatalyst to deplete the oxygen levels from natural gas streams and industrial gas pipelines.
Multiple Chromosomes in Bacteria: Low Level of Evolutionary Constraint Drives the Rapid Genetic Divergence of Chromosome II  [PDF]
Cheramie Trahan, Ravi S. Pandey, Utkarsh Singh, Anushka Choudhary, Hyuk Cho, Rajeev K. Azad, Madhusudan Choudhary
Advances in Microbiology (AiM) , 2019, DOI: 10.4236/aim.2019.97041
Abstract: Multiple chromosomes in bacteria are designated as a larger primary chromosome (CI) and smaller accessory chromosomes (CII and CIII). Although previous studies examined multiple chromosomes in several bacterial species, the evolutionary mechanisms for the origin of CIIs still remain unclear. In this study, the four following hypotheses were tested. 1) CIIs exhibit lower sequence conservation and sequence divergence compared to their corresponding CIs across species of Proteobacteria. 2) The differential sequence divergence of CI and CII depends on pathogenic and non-pathogenic lifestyles. 3) CIIs harbor a higher level of horizontal gene transfers (HGTs) than CIs. 4) Orthologs located on CIIs experience less purifying selection than their corresponding orthologs on CIs. Results reveal a higher level of sequence conservation of CIs than the sequence conservation of CIIs. There is no significant difference in HGT estimates between CIs and CIIs. A majority of orthologous genes of CIs and CIIs experience purifying selection; however, genes on CIIs were significantly less constrained than the corresponding ones on CIs. This finding is true for both pathogenic and non-pathogenic bacteria, but the selective constraints for non-pathogenic bacteria are relatively less constrained. It was concluded that the differential selective constraint is a potent driving force for the rapid evolution of CII. Therefore, gene expression analysis at the transcriptome and proteome levels may shed light on the gene regulation mechanisms that might affect the sequence divergence between CI and CII.
The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1
Anish Bavishi, Lin Lin, Kristen Schroeder, Anne Peters, Hyuk Cho, Madhusudan Choudhary
BMC Microbiology , 2010, DOI: 10.1186/1471-2180-10-331
Abstract: A protein similarity search (BLASTP) identified 1247 orfs (~29.4% of the total protein coding orfs) that are present in 2 or more copies, 37.5% (234 gene-pairs) of which exist in duplicate copies. The distribution of the duplicate gene-pairs in all Clusters of Orthologous Groups (COGs) differed significantly when compared to the COG distribution across the whole genome. Location plots revealed clusters of gene duplications that possessed the same COG classification. Phylogenetic analyses were performed to determine a tree topology predicting either a Type-A or Type-B phylogenetic relationship. A Type-A phylogenetic relationship shows that a copy of the protein-pair matches more with an ortholog from a species closely related to R. sphaeroides while a Type-B relationship predicts the highest match between both copies of the R. sphaeroides protein-pair. The results revealed that ~77% of the proteins exhibited a Type-A phylogenetic relationship demonstrating the ancient origin of these gene duplications. Additional analyses on three other strains of R. sphaeroides revealed varying levels of gene loss and retention in these strains. Also, analyses on common gene pairs among the four strains revealed that these genes experience similar functional constraints and undergo purifying selection.Although the results suggest that the level of gene duplication in organisms with complex genome structuring (more than one chromosome) seems to be not markedly different from that in organisms with only a single chromosome, these duplications may have aided in genome reorganization in this group of eubacteria prior to the formation of R. sphaeroides as gene duplications involved in specialized functions might have contributed to complex genomic development.Rhodobacter sphaeroides 2.4.1, a purple nonsulfur photosynthetic eubacterium, belongs to the α-3 subgroup of Proteobacteria [1,2], members of which display an array of metabolic capabilities in the assembly and regulation of metabol
Madhusudan Karmakar
Tourismos : an International Multidisciplinary Journal of Tourism , 2011,
Abstract: Ecotourism, the nature based travel with emphasis on education, management, development of sustainable tourism product and activity and wellbeing of the local people is not simply a marginal activity to finance protection of the environment but it has proved to be an engine of growth in many economies of the world. Eco tourism has been recognized as the backbone of economies of many countries. North Bengal being the northern territory of West Bengal of India is fortunate for its rich ecotourism destinations. The present paper will explore the ecotourism landscape of this tract of India. It will also reflect an overview of its impact on the regional economy with six case studies. The paper will be concluded with some problems and management strategies of ecotourism activity of the area.
Aromatic Plant Trade and Livelihood Strategies in Rural Nepal: A Case of Wintergreen in Dolakha District
Madhusudan Subedi
Occasional Papers in Sociology and Anthropology , 2009, DOI: 10.3126/opsa.v11i0.3032
Abstract: The objective of this paper is to assess opportunities for Wintergreen, a natural product's intervention on poverty reduction, strengthening local governance, and improving resource management. DOI: 10.3126/opsa.v11i0.3032 Occasional Papers in Sociology and Anthropology Vol.11 2009 84-103
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