| Relationship between microbes, environmental protection and human health isan important research subject. Microbes in nature can be divided into two classes:microbes related to pollution degradation (MRPDs) and microbes irrelevant topollution degradation (MIPDs). MRPDs can be directly used for contaminantdegradation. Some MIPDs such as Escherichia coli can be used for environmentalmonitoring, while some of other MIPDs such as Human Immunodeficiency VirusType1(HIV-1) and Hepatitis C virus (HCV) threaten human health. Studies onenzyme-mediated degradation mechanism of pollution, and organization rules ofmicrobial genomes or their small RNAs are helpful in understanding the microbialdegradation, microbial genome evolution and regulation. These studies are veryimportant for the increase of pollution degradation efficiency, identification ofmicrobes related to environmental monitoring, and treatment and control o f diseases.Lignin is a very complex biopolymer that is difficult to degrade. Itsaccumulation often causes serious environmental pollution problems. Microbes areable to degrade lignin by secreting ligninolytic enzymes. The degrading abilitygreatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolyticenzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganeseperoxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP andMnP were systematically determined, respectively. Robustness of these modes wasfurther verified by molecular dynamics (MD) simulations. Residues GLU460,PRO346and SER113in Lac, residues ARG43, ALA180and ASP183in LiP andresidues ARG42, HIS173and ARG177in MnP were most crucial in binding of lignin,respectively. Interactional analyses showed hydrophobic contacts were mostabundant, playing an important role in the determination of substrate specificity.This information has important contribution to the details of enzyme-catalyzedreactions in the process of lignin biodegradation, which can be used as references fordesigning enzyme mutants with a better lignin-degrading activity. E. coli cannot be directly used for environmental protection, but are helpful inenvironmental monitoring. E. coli acts as an indicator of water quality, containingdiverse strains. So far compound microsatellites have not been investigated in anyprokaryotic genomes. We have therefore, examined compound microsatellites in22complete genomes of E. coli which is one of the ideal model organisms to analyzethe nature and evolution of prokaryotic compound microsatellites. Compoundmicrosatellites consisting of two or more repeats in close proximity have been foundin eukaryotic genomes. Our results indicated about1.75–2.85%of allmicrosatellites could be accounted as compound microsatellites with very lowcomplexity, and most compound microsatellites were composed of very differentmotifs. Compound microsatellites were significantly overrepresented in all surveyedgenomes. These results were dramatically different from those in eukaryotes. Wediscussed the possible reasons for the observed divergence.HIV-1and HCV, two types of MIPDs, are associated with human diseases.HIV-1and HCV belong to RNA virus with high genetic diversity. Studies onmicrosatellites or compound microsatellites in HIV-1and HCV genomes are crucialfor understanding the instability of viral genomes. The present study analyzed81HIV-1genomes from34different countries or districts over6continents, andinvestigated54HCV genomes from six genotypes. In these surveyed HIV-1genomesequences, although relative abundance and relative density exhibited very highsimilarity, some of these sequences showed different preference for most commonmicrosatellites and longest microsatellites. Our results suggested proportion ofvarious repeat types might be related to genome stability. We identified andcharacterized238compound microsatellites in81completed HIV-1genomes. About0-24.24%of all microsatellites could be categorized as compound microsatellites.Compound microsatellite distribution was very different in two aspects betweendiverse HIV-1genomes. First, the number and motifs of compound microsatelliteswere variable between surveyed genomes. Second, the relative abundance andrelative density of compound microsatellites exhibit ed very significant differencesbetween these surveyed genomes, respectively. The relative abundance and relative density of compound microsatellites were weakly correlated with genome size andmicrosatellite density. We observed a more dynamic picture of compoundmicrosatellites than previously reported in eukaryotes. This might be attributed tothe lack of proofreading in HIV-1genomes, as it has been demonstrated that the lossof polymerase proofreading activity can greatly enhance the mutation rate ofmicrosatellites. Microsatellites were an important component of HCV genomes. Ourresults showed, in all analyzed HCV genomes, genome size and GC content had aweak influence on number, relative abundance and relative density of microsatellites,respectively. For each HCV genome, mono-, di-and trinucleotide repeats were verypredominant, whereas other types of repeats rarely occurred. Our results revealedthat the occurrence of microsatellites was significantly less than higher prokaryotesand eukaryotes and that all identified microsatellites were very short. The discoveryof microsatellites in HCV genomes may become useful for population genetic,evolutionary analysis and strain (isolate) identification. Viral pre-miRNAs maycontain microsatellites besides viral genomes. Pre-miRNAs are characteristicstem-loop sequences and are finally processed into~22nt functional miRNAscontributing to regulate several biological processes. In order to revealmicrosatellite distribution rule in pre-miRNAs in a great detail, the present study notonly analyzed microsatellite in viral pre-miRNAs, but also investigatedmicrosatellites in pre-miRNAs from all other species in miRBase12.0. In this study,we analyzed microsatellites in8619pre-miRNAs from87species, includingArthropoda, Nematoda, Platyhelminthes, Urochordata, Vertebrata, Mycetozoa,Protistae, Viridiplantae, and Viruses. We found that microsatellites widely existed inthe pre-miRNAs analyzed. Our analysis showed that mononucleotide repeats werethe most abundant repeats, followed by dinucleotide repeats, whereas tri-, tetra-,penta-, and hexanucleotide repeats rarely occurred in pre-miRNAs. The number ofmicrosatellites per pre-miRNA on average ranged from4.1for viruses to13.5forMycetozoa. Our results confirmed that the number of repeats correlated inversely tothe length of repeats. Generally, in each taxonomic group, the occurrence andrelative count of microsatellites decreased with the increase of repeat unit. Microsatellites did not exhibit obvious preference for special location inpre-miRNAs. The repeats in pre-miRNAs were complementary to repeats in codingor noncoding regions of genomes, and no significant difference was observedbetween these two classes with respect to the occurrence of repeats. These data onmicrosatellites might become a useful resource of pre-miRNAs, and their possiblefunctions were discussed. |
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