Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism

Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications

The conversion of lignocellulosic waste to energy offers a cost-effective biofuel. The current study discusses the utilization of cellulose in rice husks by lichen-associated Streptomyces sp. MS2A via carbohydrate metabolism. Out of 39 actinobacteria, one actinobacterial strain MS2A, showed CMCase, FPase, and cellobiohydrolase activity. The whole genome analysis of Streptomyces sp. MS2A showed maximum similarity with Streptomyces sp. CCM_MD2014. The genome analysis confirmed the presence of cellulose-degrading genes along with xylan-degrading genes that code for GH3, GH6, GH9, GH11, GH43, GH51, and 15 other GH families with glycosyl transferase, carbohydrate-binding modules, and energy metabolism groups. Protein family analysis corroborates the enzyme family. Among the 19,402 genes of Streptomyces sp. MS2A, approximately 70 GH family codes for lignocellulose degradation enzymes. The structure of cellulase was modeled and validated. Scanning electron microscopy and gas chromatography-mass spectrometry (GCMS) was performed to analyze the lignocellulosic degradation of rice husk and the end product bioethanol.

Codon Usage Analysis of Pro-Apoptotic Bim Gene Isoforms

Background: Bim is a Bcl-2 homology 3 (BH3)-only proteins, a group of pro-apoptotic proteins involved in physiological and pathological conditions. Both the overexpression and under-expression of Bim protein are associated with the diseased condition, and various isoforms of Bim protein are present with differential apoptotic potential. Objective: The present study attempted to envisage the association of various molecular signatures with the codon choices of Bim isoforms. Methods: Molecular signatures like composition, codon usage, nucleotide skews, the free energy of mRNA transcript, physical properties of proteins, codon adaptation index, relative synonymous codon usage, and dinucleotide odds ratio were determined and analyzed for their associations with codon choices of Bim gene. Results: Skew analysis of the Bim gene indicated the preference of C nucleotide over G, A, and T and preference of G over T and A nucleotides was observed. An increase in C content at the first and third codon position increased gene expression while it decreased at the second codon position. Compositional constraints on nucleotide C at all three codon positions affected gene expression. The analysis revealed an exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim. We correlated it with the requirement of rapid demethylation machinery to fine-tune the Bimgene expression. Also, mutational pressure played a dominant role in shaping codon usage bias in Bim isoforms. Conclusion: An exceptionally high usage of CpC dinucleotide in all the envisaged 31 isoforms of Bim indicates a high order selectional force to fine tune Bim gene expression.

The bacterial phylum Planctomycetes as novel source for bioactive small molecules

Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.

The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria

Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.

ChimeraUGEM: unsupervised gene expression modeling in any given organism

MOTIVATION

Regulation of the amount of protein that is synthesized from genes has proved to be a serious challenge in terms of analysis and prediction, and in terms of engineering and optimization, due to the large diversity in expression machinery across species.

RESULTS

To address this challenge, we developed a methodology and a software tool (ChimeraUGEM) for predicting gene expression as well as adapting the coding sequence of a target gene to any host organism. We demonstrate these methods by predicting protein levels in seven organisms, in seven human tissues, and by increasing in vivo the expression of a synthetic gene up to 26-fold in the single-cell green alga Chlamydomonas reinhardtii. The underlying model is designed to capture sequence patterns and regulatory signals with minimal prior knowledge on the host organism and can be applied to a multitude of species and applications.

AVAILABILITY AND IMPLEMENTATION

Source code (MATLAB, C) and binaries are freely available for download for non-commercial use at http://www.cs.tau.ac.il/~tamirtul/ChimeraUGEM/, and supported on macOS, Linux and Windows.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium

BACKGROUND

Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce.

RESULTS

Here, we identified a 5,436,472 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated.

CONCLUSIONS

The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.

Identification of potential therapeutic targets in Neisseria gonorrhoeae by an in-silico approach

Neisseria gonorrhoeae is a gram negative diplococcus bacterium and the causative agent of the sexually transmitted disease Gonorrhea. It has been recently given the status of "superbug" by World Health Organization because of the increasing antibiotic resistance and unavailability of a viable vaccine candidate. Over recent years, there have been increasing reports about the use of subtractive genomics to identify potential drug and vaccine targets. Our study utilizes codon biasing, a tool to identify the essential genes, in N. gonorrhoeae that could be utilized as novel therapeutic targets for drug or vaccine development. Through the screening of 2350 total genes, we present a list of 29 such drug candidate genes based on codon adaptation. Through the data-mining with BLAST2GO and InterProScan databases, we could predict the function of these 29 genes. These genes are involved in pivotal cellular functions like DNA replication, energy synthesis and metabolites production. This study also shortlists the essential genes of N. gonorrhoeae that could be used to target Neisseria. We identified a molecule/drug which can be used to target essential protein DapD (succinyltransferase).

Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the Genus Acidithiobacillus

Members of the genus Acidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. The results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in Acidithiobacillus spp. were acquired by early HGT events from species that shared habitats with Acidithiobacillus spp., such as Acidihalobacter, Thiobacillus, Acidiferrobacter, and Thiomonas species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing Acidithiobacillus ferridurans, Acidithiobacillus ferrivorans, and Acidithiobacillus ferrooxidans and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of Acidithiobacillus spp. to adapt to harsh environments. Altogether, the results suggested that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in Acidithiobacillus spp.IMPORTANCE Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in Acidithiobacillus species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in Acidithiobacillus are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of Acidithiobacillus spp.

Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis

Acinetobacter baumannii, the gram-negative bacteria emerged as an extremely critical pathogen causing nosocomial and different kinds of infections. A. baumannii exhibit resistivity towards various classes of antibiotics that shows that there is a dire need to search more drug targets by exploiting the full genome of the bacteria. In doing so, a strategy is made with the combination of computational biology, pathogen informatics and cheminformatics. Comparative genomics analysis, modeling and docking studies have been performed for the prediction of non-host essential genes and novel drug candidates against A. baumannii. Among 37 unique and 82 common metabolic pathways, 92 genes were predicted as non-host genes. Similarly, using homology search between A. baumannii genome and essential genes of different bacteria, 293 genes were predicted as essential genes of A. baumannii. Among these predicted non-host and essential genes, 86 genes were predicted as non-host essential genes which could serve as potential novel drug and vaccine targets. Additional drug-target like physicochemical properties were estimated such as the molecular weight, subcellular localization and druggability potential. On the structural part, the crystal structures of all the non-host essential genes of A. baumannii were found except the three genes. Out of these three, a homology model of Undecaprenyl-diphosphatase was built using a PDB template by MODELLER [version 9.18]. The quality of the model was assessed by the ProSA and RAMPAGE. The built model was subjected as a receptor for the molecular docking with Adenosine diphosphate (ADP) as a ligand. The molecular docking was performed by AutoDock4 and the best conformation with lowest binding energy (-4.39 kcal/mol) was obtained. The LigPlot was used to identify the close interactions between the ligand the receptor's residues. This study will further aid for the selection of putative inhibitors against a novel drug target identified against A. baumannii and hence could lead to the better therapeutics.

Could human coronavirus OC43 have co-evolved with early humans?

This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.

Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex

Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.

Biosynthetic energy cost of potentially highly expressed proteins vary with niche in selected actinobacteria

Amino acid and protein biosynthesis requires a number of high energy phosphate bonds and includes a dual energy cost for the synthesis of chemical intermediates during the fueling reactions and the conversion of precursor molecules to final products. One popular hypothesis is that the proteins encoded by putative highly expressed genes (hence called PHXPs) generally utilize low energy consuming amino acids to reduce the biosynthetic cost of the essential proteins. In our study, we found that this idea was not supported in the case of actinobacteria. With the actinobacteria, the energy costs of PHXPs varied in relation to their niche. Free-living, including aquatic, soil and extremophilic, and plant-associated actinobacteria were found to use energetically expensive amino acids in their PHXPs. An exception occurred with some animal-host-associated actinobacteria that used energy efficient amino acids. One explanation for these results may be due to the diverse metabolic patterns exhibited by actinobacteria under varied niches influenced by nutritional availability and physical environment.

An Improved Implementation of Codon Adaptation Index

Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular. Current computational implementations have a number of problems leading to various systematic biases. I illustrate these problems and provide a better computer implementation to solve these problems. The improved CAI can predict protein production better than CAI from other commonly used implementations.

Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification

Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.

Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump

Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV). The current study demonstrates that the adaptation to specific tissue and host codon bias affected CPV-2 evolution. Remarkably, FPV and CPV-2 showed a higher closeness toward the codon bias of the tissues they display the higher tropism for. Moreover, after the host jump, a clear and significant trend was evidenced toward a reduction in the distance between CPV-2 and the dog codon bias over time. This evidence was not confirmed for FPV, suggesting that an equilibrium has been reached during the prolonged virus-host co-evolution. Additionally, the presence of an intermediate pattern displayed by some strains infecting wild species suggests that these could have facilitated the host switch also by acting on codon bias.

Enrichment of apoplastic fluid with therapeutic recombinant protein for efficient biofarming

OBJECTIVE

For efficient biofarming we attempted to enrich plant interstitial fluid (IF)/apoplastic fluid with targeted recombinant therapeutic protein. We employed a synthetic human Glucocerebrosidase (GCB), a model biopharmaceutical protein gene in this study.

RESULTS

Twenty one Nicotiana varieties, species and hybrids were initially screened for individual IF recovery and based on the findings, we selected Nicotiana tabacum NN (S-9-6), Nicotiana tabacum nn (S-9-7) and Nicotiana benthamiana (S-6-6) as model plants for raising transgenic expressing GCB via Agrobacterium mediated transformation under the control of M24 promoter; GCB specific activity in each transgenic lines were analyzed and we observed higher concentration of recombinant GCB in IF of these transgenic lines (S-9-6, S-9-7, and S-6-6) in comparison to their concentration in crude leaf extracts.

CONCLUSION

Recovery of valuable therapeutics in plant IF as shown in the present study holds great promise for promoting plant based biofarming. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:726-736, 2017.

Evolutionary changes in transcription factor coding sequence quantitatively alter sensory organ development and function

Animals are characterized by a set of highly conserved developmental regulators. Changes in the cis-regulatory elements of these regulators are thought to constitute the major driver of morphological evolution. However, the role of coding sequence evolution remains unresolved. To address this question, we used the Atonal family of proneural transcription factors as a model. Drosophila atonal coding sequence was endogenously replaced with that of atonal homologues (ATHs) at key phylogenetic positions, non-ATH proneural genes, and the closest homologue to ancestral proneural genes. ATHs and the ancestral-like coding sequences rescued sensory organ fate in atonal mutants, in contrast to non-ATHs. Surprisingly, different ATH factors displayed different levels of proneural activity as reflected by the number and functionality of sense organs. This proneural potency gradient correlated directly with ATH protein stability, including in response to Notch signaling, independently of mRNA levels or codon usage. This establishes a distinct and ancient function for ATHs and demonstrates that coding sequence evolution can underlie quantitative variation in sensory development and function.

DOI:http://dx.doi.org/10.7554/eLife.26402.001

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

The Potential of Streptomyces as Biocontrol Agents against the Rice Blast Fungus, Magnaporthe oryzae (Pyricularia oryzae)

Rice is a staple food source for more than three billion people worldwide. However, rice is vulnerable to diseases, the most destructive among them being rice blast, which is caused by the fungus Magnaporthe oryzae (anamorph Pyricularia oryzae). This fungus attacks rice plants at all stages of development, causing annual losses of approximately 10-30% in various rice producing regions. Synthetic fungicides are often able to effectively control plant diseases, but some fungicides result in serious environmental and health problems. Therefore, there is growing interest in discovering and developing new, improved fungicides based on natural products as well as introducing alternative measures such as biocontrol agents to manage plant diseases. Streptomyces bacteria appear to be promising biocontrol agents against a wide range of phytopathogenic fungi, which is not surprising given their ability to produce various bioactive compounds. This review provides insight into the biocontrol potential of Streptomyces against the rice blast fungus, M. oryzae. The ability of various Streptomyces spp. to act as biocontrol agents of rice blast disease has been studied by researchers under both laboratory and greenhouse/growth chamber conditions. Laboratory studies have shown that Streptomyces exhibit inhibitory activity against M. oryzae. In greenhouse studies, infected rice seedlings treated with Streptomyces resulted in up to 88.3% disease reduction of rice blast. Studies clearly show that Streptomyces spp. have the potential to be used as highly effective biocontrol agents against rice blast disease; however, the efficacy of any biocontrol agent may be affected by several factors including environmental conditions and methods of application. In order to fully exploit their potential, further studies on the isolation, formulation and application methods of Streptomyces along with field experiments are required to establish them as effective biocontrol agents.

Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending

As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom on gymnosperms. Based on RNA-Seq data of the G. biloba transcriptome, amount to 17,579 unigenes longer than 300 bp were selected and analyzed from 68,547 candidates. The codon usage pattern tended towards more frequently use of A/U-ending codons, which showed an obvious gradient progressing from gymnosperms to dicots to monocots. Meanwhile, analysis of high/low-expression unigenes revealed that high-expression unigenes tended to use G/C-ending codons together with more codon usage bias. Variation of unigenes with different functions suggested that unigenes involving in environment adaptation use G/C-ending codons more frequently with more usage bias, and these results were consistent with the conclusion that the formation of G. biloba codon usage bias was dominated by natural selection.

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC₃ (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins.

CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences

Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often "optimized" as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in Escherichia coli, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education.

Analysis of synonymous codon usage patterns in sixty-four different bivalve species

Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates.

Breathing air to save energy--new insights into the ecophysiological role of high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis

The Streptomyces avermitilis genome encodes a putative high‐affinity [NiFe]‐hydrogenase conferring the ability to oxidize tropospheric H₂ in mature spores. Here, we used a combination of transcriptomic and mutagenesis approaches to shed light on the potential ecophysiological role of the enzyme. First, S. avermitilis was either exposed to low or hydrogenase‐saturating levels of H₂ to investigate the impact of H₂ on spore transcriptome. In total, 1293 genes were differentially expressed, with 1127 and 166 showing lower and higher expression under elevated H₂ concentration, respectively. High H₂ exposure lowered the expression of the Sec protein secretion pathway and ATP‐binding cassette‐transporters, with increased expression of genes encoding proteins directing carbon metabolism toward sugar anabolism and lower expression of NADH dehydrogenase in the respiratory chain. Overall, the expression of relA responsible for the synthesis of the pleiotropic alarmone ppGpp decreased upon elevated H₂ exposure, which likely explained the reduced expression of antibiotic synthesis and stress response genes. Finally, deletion of hhySL genes resulted in a loss of H₂ uptake activity and a dramatic loss of viability in spores. We propose that H₂ is restricted to support the seed bank of Streptomyces under a unique survival–mixotrophic energy mode and discuss important ecological implications of this finding.

Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria

Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (k_cat/K_M), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular environment of the host organism.

Horizontal gene transfer (HGT) is central to bacterial evolution. The outcome of an HGT event (fixation in a population, elimination, or separation as a subdominant clone) depends not only on the availability of a new gene but crucially on the fitness cost or benefit of the genomic incorporation of the foreign gene and its expression in recipient bacteria. Here we studied the fitness landscape for inter-species chromosomal replacement of an essential protein, dihydrofolate reductase (DHFR) encoded by the folA gene, by its orthologs from other mesophilic bacteria. We purified and biochemically characterized 33 out of 35 orthologous DHFRs and found that most of them are stable and more catalytically active than E. coli DHFR. However, the inter-species replacement of DHFR caused significant fitness loss for most transgenic strains due to low abundance of orthologous DHFRs in E. coli cytoplasm. Laboratory evolution resulted in an increase in orthologous DHFR abundance leading to a dramatic fitness improvement. Genomic and proteomic analyses of “naive” and evolved strains suggest a new function of protein homeostasis to discriminate between “self” and “non-self” proteins, thus creating fitness barriers to HGT.

Functional analysis of the molecular interactions of TATA box-containing genes and essential genes

Genes can be divided into TATA-containing genes and TATA-less genes according to the presence of TATA box elements at promoter regions. TATA-containing genes tend to be stress-responsive, whereas many TATA-less genes are known to be related to cell growth or “housekeeping” functions. In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation. Extending this research in yeast, we identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways that are statistically enriched in TATA-containing or TATA-less genes and evaluated the possibility that the enriched pathways are related to stress or growth as reflected by the individual functions of the genes involved. According to their enrichment for either of these two gene sets, we sorted KEGG pathways into TATA-containing-gene-enriched pathways (TEPs) and essential-gene-enriched pathways (EEPs). As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival. Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

Characterization of pseudogenes in members of the order Frankineae

Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.

Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation

Background

Selection pressure governs the relative mutability and the conservedness of a protein across the protein family. Biomolecules (DNA, RNA and proteins) continuously evolve under the effect of evolutionary pressure that arises as a consequence of the host parasite interaction. IPCS (Inositol phosphorylceramide synthase), SPL (Sphingosine-1-P lyase) and SPT (Serine palmitoyl transferase) represent three important enzymes involved in the sphingolipid metabolism of Leishmania. These enzymes are responsible for maintaining the viability and infectivity of the parasite and have been classified as druggable targets in the parasite metabolome.

Results

The present work relates to the role of selection pressure deciding functional conservedness and divergence of the drug targets. IPCS and SPL protein families appear to diverge from the SPT family. The three protein families were largely under the influence of purifying selection and were moderately conserved baring two residues in the IPCS protein which were under the influence of positive selection. To further explore the selection pressure at the codon level, codon usage bias indices were calculated to analyze genes for their synonymous codon usage pattern. IPCS gene exhibited slightly lower codon bias as compared to SPL and SPT protein families.

Conclusion

Evolutionary tracing of the proposed drug targets has been done with a viewpoint that the amino-acids lining the drug binding pocket should have a lower evolvability. Sites under positive selection (HIS20 and CYS30 of IPCS) should be avoided during devising strategies for inhibitor design.

Widespread predatory abilities in the genus Streptomyces

The natural role of antibiotics in the ecology of Streptomyces is debated and still largely unknown. The predatory myxobacteria and many other genera of prokaryotic epibiotic and wolfpack predators across different taxa possess secondary metabolites with antimicrobial action, and these compounds have a role in predation. If all epibiotic predators are antibiotic producers, it is worth testing whether all antibiotic producers are predators too. We show here that Streptomyces are non-obligate epibiotic predators of other microorganisms and that predatory abilities are widespread in this genus. We developed a test for predatory activity which revealed that a large proportion of traditionally isolated Streptomyces strains and all oligophilic Streptomyces isolates show predatory activity. Those that did not show predatory ability on first challenge could do so after many generations of selection or acclimation. Using time-lapse photomicrography, we demonstrate that the growth of the tips of Streptomyces hyphae is accompanied by disappearance of cells of other bacteria in the vicinity presumably due to lysis. Predatory activity is restricted to surface growth and is not obligately associated with antibiotic production in conventional culture. However, some of the genes crucial to the regulation of secondary metabolite pathways are differentially expressed during predatory growth on different prey species as compared to saprophytic growth. Our findings strengthen the association between epibiotic predation and antibiotic production.

Mutational pressure dictates synonymous codon usage in freshwater unicellular α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301

Background

Comparative study of synonymous codon usage variations and factors influencing its diversification in α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301 has not been reported so far. In the present study, we investigated various factors associated with synonymous codon usage in the genomes of P. chromatophora and S. elongatus PCC6301 and findings were discussed.

Results

Mutational pressure was identified as the major force behind codon usage variation in both genomes. However, correspondence analysis revealed that intensity of mutational pressure was higher in S. elongatus than in P. chromatophora. Living habitats were also found to determine synonymous codon usage variations across the genomes of P. chromatophora and S. elongatus.

Conclusions

Whole genome sequencing of α-cyanobacteria in the cyanobium clade would certainly facilitate the understanding of synonymous codon usage patterns and factors contributing its diversification in presumed ancestors of photosynthetic endosymbionts of P. chromatophora.

A database for Mycobacterium secretome analysis: 'MycoSec' to accelerate global health research

Abstract Members of the genus Mycobacterium are notorious for their pathogenesis. Investigations from various perspectives have identified the pathogenic strategies employed by these lethal pathogens. Secretomes are believed to play crucial roles in host cell recognition and cross-talks, in cellular attachment, and in triggering other functions related to host pathogen interactions. However, a proper idea of the mycobacterial secretomes and their mechanism of functionality still remains elusive. In the present study, we have developed a comprehensive database of potential mycobacterial secretomes (MycoSec) using pre-existing algorithms for secretome prediction for researchers interested in this particular field. The database provides a platform for retrieval and analysis of identified secretomes in all finished genomes of the family Mycobacteriaceae. The database contains valuable information regarding secretory signal peptides (Sec type), lipoprotein signal peptides (Lipo type), and Twin arginine (RR/KR) signal peptides (TAT type), prevalent in mycobacteria. Information pertaining to COG analysis, codon usage, and gene expression of the predicted secretomes has also been incorporated in the database. MycoSec promises to be a useful repertoire providing a plethora of information regarding mycobacterial secretomes and may well be a platform to speed global health research. MycoSec is freely accessible at http://www.bicnbu.in/mycosec .

Comparative proteomic analysis of Streptomyces lividans Wild-Type and ppk mutant strains reveals the importance of storage lipids for antibiotic biosynthesis

Streptomyces lividans TK24 is a strain that naturally produces antibiotics at low levels, but dramatic overproduction of antibiotics occurs upon interruption of the ppk gene. However, the role of the Ppk enzyme in relation to the regulation of antibiotic biosynthesis remains poorly understood. In order to gain a better understanding of the phenotype of the ppk mutant, the proteomes of the wild-type (wt) and ppk mutant strains, grown for 96 h on R2YE medium limited in phosphate, were analyzed. Intracellular proteins were separated on two-dimensional (2D) gels, spots were quantified, and those showing a 3-fold variation or more were identified by mass spectrometry. The expression of 12 proteins increased and that of 29 decreased in the ppk mutant strain. Our results suggested that storage lipid degradation rather than hexose catabolism was taking place in the mutant. In order to validate this hypothesis, the triacylglycerol contents of the wt and ppk mutant strains of S. lividans as well as that of Streptomyces coelicolor M145, a strain that produces antibiotics at high levels and is closely related to S. lividans, were assessed using electron microscopy and thin-layer chromatography. These studies highlighted the large difference in triacylglycerol contents of the three strains and confirmed the hypothetical link between storage lipid metabolism and antibiotic biosynthesis in Streptomyces.

Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

BACKGROUND

Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available.

RESULTS

It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation index (CAI), a predictor of the expression rate, in all the genes belonging to the core genome as well as the core secretory protein genes. The genomes of pathogenic Mycobacterium and Streptomyces also had reduced secretomes relative to saprophytes, as well as in general significant pairwise Ka/Ks ratios in their secretomes.

CONCLUSION

In marginally free-living facultative symbionts or pathogenic organisms under consideration, secretory protein genes as a whole evolve at a faster rate than the rest and this process may be an adaptive life-strategy to counter the host selection pressure. The higher evolutionary rate of signal peptide part compared to mature protein provides an indication that signal peptide parts may be under relaxed purifying selection, indicative of the signal peptides not being secreted into host cells. Codon usage analysis suggests that in actinobacterial strains under host selection pressure such as symbiotic Frankia, ACN, FD and the pathogenic Mycobacterium, codon usage bias was negatively correlated to the selective pressure exerted on the secretory protein genes.

Control of total GFP expression by alterations to the 3' region nucleotide sequence

Background

Previously, we distinguished the Escherichia coli type II cytoplasmic membrane translocation pathways of Tat, Yid, and Sec for unfolded and folded soluble target proteins. The translocation of folded protein to the periplasm for soluble expression via the Tat pathway was controlled by an N-terminal hydrophilic leader sequence. In this study, we investigated the effect of the hydrophilic C-terminal end and its nucleotide sequence on total and soluble protein expression.

Results

The native hydrophilic C-terminal end of GFP was obtained by deleting the C-terminal peptide LeuGlu-6×His, derived from pET22b(+). The corresponding clones induced total and soluble GFP expression that was either slightly increased or dramatically reduced, apparently through reconstruction of the nucleotide sequence around the stop codon in the 3′ region. In the expression-induced clones, the hydrophilic C-terminus showed increased Tat pathway specificity for soluble expression. However, in the expression-reduced clone, after analyzing the role of the 5′ poly(A) coding sequence with a substituted synonymous codon, we proved that the longer 5′ poly(A) coding sequence interacted with the reconstructed 3′ region nucleotide sequence to create a new mRNA tertiary structure between the 5′ and 3′ regions, which resulted in reduced total GFP expression. Further, to recover the reduced expression by changing the 3′ nucleotide sequence, after replacing selected C-terminal 5′ codons and the stop codon in the ORF with synonymous codons, total GFP expression in most of the clones was recovered to the undeleted control level. The insertion of trinucleotides after the stop codon in the 3′-UTR recovered or reduced total GFP expression. RT-PCR revealed that the level of total protein expression was controlled by changes in translational or transcriptional regulation, which were induced or reduced by the substitution or insertion of 3′ region nucleotides.

Conclusions

We found that the hydrophilic C-terminal end of GFP increased Tat pathway specificity and that the 3′ nucleotide sequence played an important role in total protein expression through translational and transcriptional regulation. These findings may be useful for efficiently producing recombinant proteins as well as for potentially controlling the expression level of specific genes in the body for therapeutic purposes.

Systems insight into the spore germination of Streptomyces coelicolor

An example of bacterium, which undergoes a complex development, is the genus of Streptomyces whose importance lies in their wide capacity to produce secondary metabolites, including antibiotics. In this work, a proteomic approach was applied to the systems study of germination as a transition from dormancy to the metabolically active stage. The protein expression levels were examined throughout the germination time course, the kinetics of the accumulated and newly synthesized proteins were clustered, and proteins detected in each group were identified. Altogether, 104 2DE gel images at 13 time points, from dormant state until 5.5 h of growth, were analyzed. The mass spectrometry identified proteins were separated into functional groups and their potential roles during germination were further assessed. The results showed that the full competence of spores to effectively undergo active metabolism is derived from the sporulation step, which facilitates the rapid initiation of global protein expression during the first 10 min of cultivation. Within the first hour, the majority of proteins were synthesized. From this stage, the full capability of regulatory mechanisms to respond to environmental cues is presumed. The obtained results might also provide a data source for further investigations of the process of germination.

Synonymous codon usage in chloroplast genome of Coffea arabica

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A(3), T(3), G(3), C(3), GC(3)) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC(3) plot grouped majority of the analyzed genes on or just below the left side of the expected GC(3) curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.

Deletion of TerD-domain-encoding genes: effect on Streptomyces coelicolor development

TerD-domain-encoding genes (tdd genes) are highly represented in the Streptomyces coelicolor genome. One of these, the tdd8 gene, was recently shown to have a crucial influence on growth, differentiation, and spore development of this filamentous bacterium. The investigation of the potential role of tdd genes has been extended here to tdd7 (SCO2367) and tdd13 (SCO4277). Both genes are highly expressed in bacteria grown in liquid-rich medium (tryptic soy broth). However, the deletion of these genes in S. coelicolor showed contrasting effects regarding developmental patterns, sporulation, and antibiotic production. Deletion of the tdd7 gene induced a reduction of growth in liquid medium, wrinkling of the mycelium on solid medium, and poor spore and actinorhodin production. On the other hand, deletion of the tdd13 gene did not significantly affect growth in liquid medium but induced a small colony phenotype on solid medium with abundant sporulation and overproduction of undecylprodigiosin. Although their exact functions remain undefined, the present data suggest a major involvement of TerD proteins in the proper development of S. coelicolor.

A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1

A total proteome map of the Pseudomonas aeruginosa PAO1 proteome is presented, generated by a combination of two-dimensional gel electrophoresis and protein identification by mass spectrometry. In total, 1128 spots were visualized, and 181 protein spots were characterized, corresponding to 159 different protein entries. In particular, protein chaperones and enzymes important in energy conversion and amino acid biosynthesis were identified. Spot analysis always resulted in the identification of a single protein, suggesting sufficient spot resolution, although the same protein may be detected in two or more neighboring spots, possibly indicating posttranslational modifications. Comparison to the theoretical proteome revealed an underrepresentation of membrane proteins, though the identified proteins cover all predicted subcellular localizations and all functional classes. These data provide a basis for subsequent comparative studies of the biology and metabolism of P. aeruginosa, aimed at unraveling global regulatory networks.

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke "design creationism" to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective "pore" for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the "jackprot," which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the "jackprot," or highest-fitness complete-peptide sequence, required cumulative smaller "wins" (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons ("jackdons" that led to "jackacids" that led to the "jackprot"). The "jackprot" is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide "edition" and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.