Special stretches of sequence with low complexity, highly rich in one certain residue, such as glutamine, asparagines, glutamic acid and histidine, to fulfill certain unique functions, are defined as single-residue-rich sequence (SRRs). Increasing SRRs containing proteins have recently been characterized and some of them have been indentified to be associated with immune system diseases or neuro-degenerative. A systematic and comprehensive analysis on the relationship between the occurrence of histidine-rich motifs (HRMs) and the functions of corresponding proteins have been overlooked. In this thesis, proteome sequences of 675 prokaryotes including 50 archeae proteome sequences and 625 bacteria were examined and analyzed for HRMs. The HRMs are shown to be extensively distributed in prokaryotic proteomes and the majority (62%) of them is identified to be involved in metal homeostasis. Intriguingly, HRMs are essentially absent from obligate intracellular pathogenic species such as Rickettsiales, Chlamydiae and Tenericutes but are frequently found in the proteomes of Rhizobiales and Burkholderiales, both of which habitat in soils, indicative of environmental habitat-related occurrence of HRMs. Based on the primary sequence to explore the histidine-rich proteins, the present approach could be extended to apply for searching other single-residue-rich proteins, which may shed lights on gaining a further understanding about relationship between the proteins’ sequences and their functions. A novel group of globally histidine-rich proteins was discovered, among which a histidine-rich protein, bacterioferritin-associated ferredoxin ((BFD)-like [2Fe-2S]) protein from Rhodopseudomonas Palustris BisB18 (termed as BFD shortly) was digged out. The BFD protein consists of a Fe-S cluster domain (FeSD) at the N-terminus and an extremely histidine-rich domain (HRD) at the C-terminus. The intact protein BFD as well as its histidine-rich domain (HRD) was over-expressed, purified and characterized and the effects of metal binding on BFD and HRD were examined in this work. The intact protein BFD presents as a 20 mer whereas the HRD protein exists as a monomer in solution. However, the CD spectrum of BFD showed the presence of both α-helix and β-sheet in the structure of BFD. The CD spectrum of HRD demonstrated that an extremely large portion of the structure of HRD was random coils, which indicated that the most of the α-helix and β-sheet predominately were located in the Fe-S cluster domain (FeSD) of BFD. It also indicated that HRD adopted a very flexible conformation, which was in good agreement with the results that obtained from the 2D 1H-15N HSQC spectrum of HRD. Isothermal titration calorimetry and equilibrium dialysis revealed that HRD possessed a large binding capacity to divalent metal ions (up to 9 Ni2+, 5 Zn2+ and 4 Co2+ respectively). The E. coli cells over-expressed with the HRD protein showed a significantly evaluated metal resistance to the toxic Ni and Co ions. The amounts of meals in these cells were determined to be approximate 3-5 fold higher than those in the control groups. These results of HRD taken together suggest the characteristics of common globally histidine-rich proteins. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

No description available.

Thesis (M.A.)--Humboldt State University, 2007. / Includes bibliographical references (leaves 84-101). Also available via Humboldt Digital Scholar.

Prokaryotes are single-cell microorganisms. These creatures can be further classified to bacteria and archaea. Their DNA genetic meterials are spread around the cytoplasm rather than residing in the nucleus. Unlike eukaryotes, a high percentage of prokaryotic genome is composed of genes. The evolution of prokaryotes is different from that of the eukaryotes. Prokaryotes are found almost everywhere including the harshest environments on Earth. Understanding the whole pictures of their genomes will benefit us a lot in terms of new enzyme discovery, decoding drug resistance, biofuel development, etc. 　High-throughput sequencing technology is becoming increasingly popular in various sequencing projects. With different platforms, scientists are able to achieve millions ~ billions of sequences within days. In the last two years, there are a lot of prokaryotic genomes being sequenced under these platforms. However, there are only 1,542 complete chromosomes available in NCBI GenBank (September 2011) since the first complete genome of Bacillus subtilis was published in 1997. The most difficult step in finishing a complete genome is closing all gaps among different contigs. In this thesis, a series of comprehensive simulation studies based on 1,542 complete chromosomes have been performed in search of a cost-effective way to achieve complete prokaryotic genomes. Solutions to both draft and complete genome sequencing were provided by computer simulation. Moreover, classification studies have been performed to identify special prokaryotic phyla/orders (if any) dissatisfying our proposed strategies. 　Our results indicate that: 1) low coverage (6x-10x) pyrosequencing with long reads (400 bp) is sufficient to produce highly continuous and complete assemblies, presenting a tiny proportion of false gene duplication/loss. High quality draft genomes could be generated by this strategy; 2) Long repeats to some extent influence the assembly quality, especially for the genome coverage and contig number. The number of contigs and genome coverage rate are significantly correlated with the total size of repeat regions; 3) With a combination of one run of single-end reads (10x, 400bp read length) and one run of paired end reads (10x, 8kb library, 400bp read length), ~90% of chromosome assemblies are less than 10 scaffolds and ~95% of chromosome assemblies are less than 150 contigs. Most of the chromosomes can be assembled into high quality draft chromosomes (<50 contigs, ~4 scaffolds, >370kb contig N50 size, >99.99% single base accuracy and <0.5% false gene duplication/loss rate in average); 4) Similar patterns found in both simulated and real reads imply that our simulation analysis is not overestimated; 5) Greater attention is needed regarding the orders Thiotrichales, Enterobacteriales and Nostocales, when applying the above strategies for complete genome sequencing; 6) For prokaryotic species with multiple chromosomes, Pulse Field Gel Electrophoresis is needed to separate all their chromosomes which will be individually collected by electroelution prior to draft/complete genome sequencing. A comprehensive computer simulation study based on 1,542 chromosomes (all availabe prokaryotic complete chromosomes, September 2011) has been performed in this thesis. The sequencing strategies for both prokaryotic draft and complete genome proposed by the simulation study could facilitate the ongoing prokaryotic complete genome sequencing projects. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2007. / Ph.D. in Marine Environmental Science. Includes bibliographical references (leaves 168-184). Also available in electronic version.

Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2007. / Ph.D. in Marine Environmental Science. Includes bibliographical references. Also available in electronic version.

Thesis (MSc)--University of Stellenbosch, 2005. / Bibliography. Also available via the Internet.

Ammonia/ammonium-oxidizing prokaryotes (AOPs) play a crucial role in nitrogen transformation in the natural ecosystems including mangrove wetlands. The objectives of the present study were to investigate the spatial and temporal distribution of AOPs in the mangrove wetland sediments in subtropical Hong Kong and their ecophysiology. When AOP communities and abundances in a natural coastal mangrove wetland and a constructed freshwater wetland were compared, the constructed freshwater wetland contained a broader range of phylotypes, higher diversity, more complex community structures, and more uneven abundances of AOPs than the mangrove wetland. Typha angustifolia affected the community structures of all AOPs and enhanced their abundances in the rhizosphere. Both Phragmites australis and Cyperus malaccensis showed some effects on the community structures of ammonia-oxidizing bacteria (AOB), but little effects on those of anaerobic ammonium oxidizing (anammox) bacteria or ammonia-oxidizing archaea (AOA). Kandelia obovata had no detectable effect on any group of the AOPs due to their smaller size. AOPs in oxic and anoxic sediments of a protected mangrove wetland were investigated in both winter and summer. Seasonality had little effect on community structure and abundance of anammox bacteria. AOA community structures were stable between the two seasons, but AOA abundance was significantly higher in winter than summer. The community structures of AOB were different between winter and summer, but the abundance in winter was apparently higher than that in summer. Sediment type had a noticeable influence on community structure and abundance of anammox bacteria. No apparent difference in AOA community structures between the different types of sediments in winter was observed, but the oxic sediments showed obviously different AOA community structures from anoxic sediments in summer. Sediment type had little effect on AOB community structures, but AOB abundance in oxic sediments was obviously lower than anoxic ones in both seasons. Addition of acetate or leaf litter into sediment inhibited the growth of anammox bacteria in laboratory incubation. The inhibition of anammox bacteria by acetate was more pronounced than by leaves. Acetate and leaf litter did not affect AOA community structures, but promoted their growth. Both acetate and leaf litter affected the AOB community structures and promoted their growth in the early phase of the incubation. The promoting effects by leaf litter were more obvious than by acetate. Allylthiourea effectively inhibited the growth of both AOA and AOB in laboratory incubation, but only slightly for anammox bacteria. Acidic condition altered AOB community structure, but affected anammox bacteria and AOA slightly. Alkaline condition strongly affected community structures of anammox bacteria and AOA, but slightly for AOB. Alkaline condition inhibited the growth of anammox bacteria, but promoted AOA and AOB slightly. Increase in salinity resulted in higher diversity of anammox bacteria, and AOA and AOB might have species specific preference for salinity. High salinity promoted anammox bacteria growth; inhibited AOA for 5-10 days, but promoted them afterward; and promoted AOB. Totally, this study revealed new and specific information on the spatial and temporal distribution of AOPs in mangrove wetland and factors affecting their ecophysiology. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

No description available.

Thesis (Ph. D.)--Lehigh University, 2000. / Includes vita. Includes bibliographical references (leaves 151-159).