An environmental signature for 323 microbial genomes based on codon adaptation indices

Background

Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias.

Results

The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism, and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria, and that this translational codon usage bias may be used for prediction of highly expressed genes. By analyzing more than 300 bacterial genomes, as well as five fungal genomes, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for instance soil bacteria and soil symbionts, spore formers, enteric bacteria, aquatic bacteria, and intercellular and extracellular pathogens.

Conclusion

The results and the approach described here may be used to acquire new knowledge regarding species lifestyle and to elucidate relationships between organisms that are far apart evolutionarily.     

An array of diverse microbial genomes

Methods for comparing gene frequencies across large, epidemiologically defined bacterial collections are limited. A novel microarray technology has been developed called 'library on a slide'. In this technology, hundreds of entire microbial genomes are arrayed, rather than sequences of a single genome or sets of genes. These slides can then be probed for the presence of specific genes allowing researchers to draw inferences regarding important differences between related strains that differ in their pathogenic potential.     

Environmental shaping of codon usage and functional adaptation across microbial communities

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species’ boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a ‘functional metagenomics’ platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.     

High-throughput screening of microbial adaptation to environmental stress

We developed a microwell plate, high-throughput, screening method aimed at quantitating the tolerance of a panel of Gram-positive and Gram-negative bacteria to metals (Frankia sp., Escherichia coli, Cupriavidus metallidurans, Rhizobium leguminosarum, and Streptomyces scabies). Microbial viability was quantified using MTS; a tetrazolium salt converted to a water-soluble formazan through microbial reduction. In this paper, we present the stepwise development of the method, highlighting the main elements underlying its reliability, and compare results obtained with literature. We conclude the method is well suited to efficiently screen bacteria, including those that are filamentous and slow-growing, without the need for large amounts of inoculum which may not always be available. The method allows testing of compound gradients with sufficient replicates to generate statistically robust results, and is transposable to other types of cell proliferation assays such as those for antimicrobial susceptibility, and chemoresistance.     

Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages

Seven GC-rich (group I) and three AT-rich (group II) microbial genomes are analyzed in this paper. The seven microbes in group I belong to different phylogenetic lineages, even different domains of life. The common feature is that they are highly GC-rich organisms, with more than 60% genomic GC content. Group II includes three bacteria, which belong to the same subdivision as Pseudomonas aeruginosa in group I. The genomic GC content of the three bacteria is in the range of 26-50%. It is shown that although the phylogenetic lineages of the organisms in group I are remote, the common feature of highly genomic GC content forces them to adopt similar codon usage patterns, which constitutes the basis of an algorithm using a set of universal parameters to recognize known genes in the seven genomes. The common codon usage pattern of function known genes in the seven genomes is GGS type, where G, G, and S are the bases of G, non-G, and G/C, respectively. On the contrary, although the phylogenetic lineages of the three bacteria in group II are quite close, the codon usage patterns of function known genes in these genomes are obviously distinct. There are no universal parameters to identify known genes in the three genomes in group II. It can be deduced that the genomic GC content is more important than phylogenetic lineage in gene recognition programs. We hope that the work might be useful for understanding the common characteristics in the organization of microbial genomes.     

Regression analysis for general adaptation in pearl millet using different environmental indices

Summary Regression analyses on grain yield of 20 hybrid and 13 composite varieties of pearl millet (Pennisetum typhoides (Burm. S. & H.)) evaluated at 19 sites in India were performed to assess their relative stability and to compare different measures of environmental values. A large portion of the significant genotype X environment interactions was attributed to the non-linear component and deviations mean squares (S_di ²) were a very important parameter for selection of stable varieties. The mean grain yield was positively associated with regression coefficients and deviations mean squares. The hybrids MH 31, MH 35, MH 36 and MH 62 and composite populations MP 16, MP 31 and MP 36 possessed general adaptability. The use of dependent, independent and near-independent measures of environmental values has been found to have little influence on the general interpretation of regression analysis in pearl millet.     

Positive selection for unpreferred codon usage in eukaryotic genomes

Background  

Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency) in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (K_p/K_u).     

An automated comparative analysis of 17 complete microbial genomes

MOTIVATION: As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality; identification of enzymes, putative operons and metabolic pathways; and to derive phylogenetic classification of microbes. RESULTS: This paper extends an automated pair-wise genome comparison technique (Bansal et al., Math. Model. Sci. Comput., 9, 1-23, 1998, Bansal and Bork, in First International Workshop of Declarative Languages, Springer, pp. 275-289, 1999) used to identify orthologs and gene groups to derive orthologous genes in a group of genomes and to identify genes with conserved functionality. Seventeen microbial genomes archived at ftp://ncbi.nlm.nih.gov/genbank/genomes have been compared using the automated technique. Data related to orthologs, gene groups, gene duplication, gene fusion, orthologs with conserved functionality, and genes specifically orthologous to Escherichia coli and pathogens has been presented and analyzed. AVAILABILITY: A prototype database is available at ftp://www.mcs.kent.edu/arvind/intellibio / orthos.html. The software is free for academic research under an academic license. The detailed database for every microbial genome in NCBI is commercially available through intellibio software and consultancy corporation (Web site: http://www.mcs.kent.edu/?rvind/intellibio . html). CONTACT: arvind@mcs.kent.edu.     

An integrative method for identifying the over-annotated protein-coding genes in microbial genomes

The falsely annotated protein-coding genes have been deemed one of the major causes accounting for the annotating errors in public databases. Although many filtering approaches have been designed for the over-annotated protein-coding genes, some are questionable due to the resultant increase in false negative. Furthermore, there is no webserver or software specifically devised for the problem of over-annotation. In this study, we propose an integrative algorithm for detecting the over-annotated protein-coding genes in microorganisms. Overall, an average accuracy of 99.94% is achieved over 61 microbial genomes. The extremely high accuracy indicates that the presented algorithm is efficient to differentiate the protein-coding genes from the non-coding open reading frames. Abundant analyses show that the predicting results are reliable and the integrative algorithm is robust and convenient. Our analysis also indicates that the over-annotated protein-coding genes can cause the false positive of horizontal gene transfers detection. The webserver of the proposed algorithm can be freely accessible from www.cbi.seu.edu.cn/RPGM.     

Searching for drug targets in microbial genomes

Comparative analysis of the complete genome sequences of 10 bacterial pathogens available in the public databases offers the first insights into the drug discovery approaches of the near future. Genes that are conserved in different genomes often turn out to be essential, which makes them attractive targets for new broad-spectrum antibiotics. Subtractive genome analysis reveals the genes that are conserved in all or most of the pathogenic bacteria but not in eukaryotes; these are the most obvious candidates for drug targets. Species-specific genes, on the other hand, may offer the possibility to design drugs against a particular, narrow group of pathogens.     

Constraint on di-nucleotides by codon usage bias in bacterial genomes

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes.     

A combination dimensionality reduction approach to codon position patterns of eubacteria based on their complete genomes

Graphical techniques have become powerful tools for the visualization and analysis of complicated biological systems. However, we cannot give such a graphical representation in a 2D/3D space when the dimensions of the represented data are more than three dimensions. The proposed method, a combination dimensionality reduction approach (CDR), consists of two parts: (i) principal component analysis (PCA) with a newly defined parameter ρ and (ii) locally linear embedding (LLE) with a proposed graphical selection for its optional parameter k. The CDR approach with ρ and k not only avoids loss of principal information, but also sufficiently well preserves the global high-dimensional structures in low-dimensional space such as 2D or 3D. The applications of the CDR on characteristic analysis at different codon positions in genome show that the method is a useful tool by which biologists could find useful biological knowledge.     

A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content,protein functional domains and bacterial phenotypes

Multiple synonymous codons code for the same amino acid, resulting in the degeneracy of the genetic code and in the preferred used of some codons called codon bias usage (CBU). We performed a large-scale analysis of codon usage bias analysing the distribution of the codon adaptation index (CAI) and the codon relative adaptiveness index (RA) in 4868 bacterial genomes. We found that CAI values differ significantly between protein functional domains and part of the protein outside domains and show how CAI, GC content and preferred usage of polymerase III alpha subunits are related. Additionally, we give evidence of the association between CAI and bacterial phenotypes.     

An experimental evaluation of diversity indices as environmental discriminators

Seven diversity indices were calculated for each of fifty-eight microcosm communities. All fifty-eight communities were initiated from equal density inoculations of fourteen algal species. Each microcosm developed in one of six controlled experimental environments; the environments differing only in their temporal patterns of disturbance. Five linear discriminating techniques were used to evaluate the diversity index most useful for discriminating between these environments. The Shannon-Wiener index was best according to two of the discriminating methodologies and second best using the other techniques. Evenness was best when the Shannon-Wiener index was second best and vice versa.     

高原湖泊湿地以植被指示为主的环评指标初探

分析探讨高原湖泊湿地的环境评价中,如何应用一套由植被为主指示要素构成的环评指标,并以云南石林长湖湖泊湿地为实例。按植被及其植物区系组成、动物区系和生境方面所表现特征的现况,共设置以植被特征为主的10个评定指示要素。使用此类指标评价的前提是:所评的各个高原湖泊湿地,均在上述10个所规定的指示要素方面,已取得调查研究的定量和定性数据资料。所以本方案的使用,反而促成各高原湖泊湿地在以植被特征为主各评价要素的进一步考察和研究,以作为参评的依据。     

No evidence for tissue-specific adaptation of synonymous codon usage in humans

It has been proposed that the synonymous codon usage of human tissue-specific genes was under selective pressure to modulate the expression of proteins by codon-mediated translational control (Plotkin, J. B., H. Robins, and A. J. Levine. 2004. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA 101:12588-12591.) To test this model, we analyzed by internal correspondence analysis the codon usage of 2,126 human tissue-specific genes expressed in 18 different tissues. We confirm that synonymous codon usage differs significantly between the tissues. However, the effect is very weak: the variability of synonymous codon usage between tissues represents only 2.3% of the total codon usage variability. Moreover, this variability is directly linked to isochore-scale (>100 kb) variability of GC-content that affect both coding and introns or intergenic regions. This demonstrates that variations of synonymous codon usage between tissue-specific genes expressed in different tissues are due to regional variations of substitution patterns and not to translational selection.     

Stationary phase mutagenesis: mechanisms that accelerate adaptation of microbial populations under environmental stress

Microorganisms are exposed to constantly changing environmental conditions. In a growth-restricting environment (e.g. during starvation), mutants arise that are able to take over the population by a process known as stationary phase mutation. Genetic adaptation of a microbial population under environmental stress involves mechanisms that lead to an elevated mutation rate. Under stressful conditions, DNA synthesis may become more erroneous because of the induction of error-prone DNA polymerases, resulting in a situation in which DNA repair systems are unable to cope with increasing amounts of DNA lesions. Transposition may also increase genetic variation. One may ask whether the rate of mutation under stressful conditions is elevated as a result of malfunctioning of systems responsible for accuracy or are there specific mechanisms that regulate the rate of mutations under stress. Evidence for the presence of mutagenic pathways that have probably been evolved to control the mutation rate in a cell will be discussed.