Codon usage bias in phylum Actinobacteria : relevance to environmental adaptation and host pathogenicity

Microalgae growth-promoting bacteria for cultivation strategies: Recent updates and progress

Microalgae growth-promoting bacteria (MGPB), both actinobacteria and non-actinobacteria, have received considerable attention recently because of their potential to develop microalgae-bacteria co-culture strategies for improved efficiency and sustainability of the water-energy-environment nexus. Owing to their diverse metabolic pathways and ability to adapt to diverse conditions, microalgal-MGPB co-cultures could be promising biological systems under uncertain environmental and nutrient conditions. This review proposes the recent updates and progress on MGPB for microalgae cultivation through co-culture strategies. Firstly, potential MGPB strains for microalgae cultivation are introduced. Following, microalgal-MGPB interaction mechanisms and applications of their co-cultures for biomass production and wastewater treatment are reviewed. Moreover, state-of-the-art studies on synthetic biology and metabolic network analysis, along with the challenges and prospects of opting these approaches for microalgal-MGPB co-cultures are presented. It is anticipated that these strategies may significantly improve the sustainability of microalgal-MGPB co-cultures for wastewater treatment, biomass valorization, and bioproducts synthesis in a circular bioeconomy paradigm.

The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea

We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome  and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.

A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.

The evolutionary characterization of Gamasida based on mitochondrial genes codon usage pattern

Mites belonging to the suborder Gamasida are species-rich and habitat-diverse, with a worldwide distribution. To adapt to the environment and obtain better living conditions, all species of the suborder Gamasida have been undergoing constant evolution. The complete mitochondrial genome (mitogenome) is an invaluable molecular marker for studying the origin of species, genetic differentiation between closely related species, and between intraspecific groups. In some species of the suborder Gamasida, mitochondrial tRNA genes are truncated and carried unstable genetic information. This study presents a comparative analysis of codon usage pattern and preference of 13 protein-coding genes of 24 species in 17 genera and 10 families of the suborder Gamasida. Results showed that have an obvious AT preference (0.664-0.829) for codon usage in the suborder Gamasida. Most of the optimal and high-frequency codons also end in A/T. The degree of natural selection varies between the same protein-coding genes of different gamasid mites or among different protein-coding genes within the same gamasid mites. Base and codon usage pattern and preference are very similar between the same species and genus, namely the closer species, the more similar their bases and codons usage patterns and preference are. T bases and C bases were the preference bases for codon usage of 24 species in the suborder Gamasida. Evolution of the suborder Gamasida was dominated by natural selection (64.1%). This study provides the first comprehensive analysis of codon usage in the suborder Gamasida, which will greatly improve our understanding of codon usage patterns and preference, genetics, and evolution of the suborder Gamasida. It will help to evaluate the degree of molecular adaptation in the suborder Gamasida and to further explore evolutionary features of the suborder Gamasida.

Antimicrobial peptides in Dendrobium officinale: Genomic parameters, peptide structures, and gene expression patterns

A weak codon usage bias was found in Dendrobium catenatum (D. officiale) antimicrobial peptides (AMPs), after the analysis of relative synonymous codon usage, GC contents, and the effective number of codons. The codon usage preference was mainly influenced by natural selection pressure. The self-optimized prediction method and SWISS-MODEL were applied for peptide structural and domain analyses, and some typical antimicrobial domains were found in D. officinale AMP amino sequences, such as knot1 domain, gibberellins-stimulated domain, cupin_1 domain, defensin_like domain, and SLR1-BP (S locus-related glycoprotein 1 binding pollen coat protein) domain. To investigate the AMPs gene expression pattern, abiotic stresses, such as salt stress, drought stress, salicylic acid (SA), and methyl jasmonate (JA), were applied and the gene expression levels were detected by the real-time fluorescent quantitative polymerase chain reaction. Results showed that, even though the basic AMPs gene expressions were low, some AMPs can still be induced by salt dress, while the drought dress did not show the same impact. The SA and JA signaling pathways might be involved in most of the AMPs expressions. The natural selection of the D. officinale AMPs and thus forming diverse types of AMPs enhanced the plant's innate immunity and disease resistance capability, which would lead to a better understanding of the molecular mechanism for D. officinale adapting to the environment. The finding that salt stress, SA, and JA signaling pathways can induce AMP expression lays a foundation for the further development and functional verification of D. officinale AMPs.

Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Introduction

Codon basis is a common and complex natural phenomenon observed in many kinds of organisms.

Methods

In the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.

Results

The results showed that the codons of all Amanita species tended to end in A/T, demonstrating the preference of mitochondrial codons of Amanita species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of Amanita is 30.81, which is <35, demonstrating the strong codon preference of mitochondrial core PCGs of Amanita. The neutrality plot analysis and PR2-Bias plot analysis further demonstrated that natural selection plays an important role in Amanita codon bias. In addition, we obtained 5–10 optimal codons (ΔRSCU > 0.08 and RSCU > 1) in nine Amanita species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different Amanita species and found large variations between them.

Discussion

This study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Introduction

Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.

Methods

In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.

Results

The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species.

Discussion

This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain

Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNA^Thr, tRNA^Arg, tRNA^Gly and tRNA^Asn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.

Codon usage divergence of important functional genes in Mycobacterium tuberculosis

Sequence characteristics are usually used to explain the adaptive ability to hosts, metabolism, genetic diversity, drug resistance, and infectivity of Mycobacterium tuberculosis. Exploring the codon usage pattern of coding sequences in Mycobacterium tuberculosis is of great significance. In the present study, two hundred random complete genomes of Mycobacterium tuberculosis were downloaded from the National Center for Biotechnology Information database. The important codon usage pattern, such as the codon bias index, the effective number of codons, the relative synonymous codon usage as well as the base component, of twenty one specific functional genes were counted or calculated. The differences of the relative synonymous codon usage values among those functional genes, and the summation of the standard deviations of codon usage parameters were used to evaluate the divergence degree of the concerned genes. The results show that among the concerned genes, 1) all genes are high GC sequences, the codon usage frequency corresponding to each amino acid of these functional genes had a significant bias; 2) the genes of those with high effective number of codons, such as the coding sequences of Myco-bacterial membrane protein large family, usually have higher divergences; and 3) genes with lower divergences, such as the ag85A and the sigH, are usually highly conserved and are often used as drug target genes. The findings of the present work would improve new understandings on the evolution of Mycobacterium tuberculosis and on the measures to prevent and control tuberculosis from the gene engineering.

The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction of Stylonychia lemnae

Ciliates represent higher unicellular animals, and several species are also important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome in ciliates can not only promote a better understanding of the genetic mode and evolution history of these organisms but also help optimize codons to improve the gene editing efficiency of model ciliates. In this study, macronuclear genome sequences of nine free-living ciliates were analyzed with CodonW software to calculate the following indices: the guanine-cytosine content (GC); the frequency of the nucleotides U, C, A, and G at the third position of codons (U3s, C3s, A3s, G3s); the effective number of codons (ENC); the correlation between GC at the first and second positions (GC12); the frequency of the nucleotides G + C at the third position of synonymous codons (GC3s); the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, neutrality plot analysis, and correlation analysis were performed to explore the factors that influence codon preference. The results showed that the GC contents in nine ciliates' MAC genomes were lower than 50% and appeared AT-rich. The base compositions of GC12 and GC3s are markedly distinct and the codon usage pattern and evolution of ciliates are affected by genetic mutation and natural selection. According to the synonymous codon analysis, the codons of most ciliates ended with A or U and eight codons were the general optimal codons of nine ciliates. A clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) expression vector of Stylonychia lemnae was constructed by optimizing the macronuclear genome codon and was successfully used to knock out the Adss gene. This is the first such extensive investigation of the MAC genome CUB of ciliates and the initial successful application of the CRISPR/Cas9 technique in free-living ciliates.

Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis

Streptococcus suis (S. suis) is a gram-positive coccus that causes disease in humans and animals. The codon usage pattern of bacteria reveals a range of evolutionary changes that assist them to enhance tolerance to environments. To better understand the genetic features during the evolution of S. suis, we performed codon usage analysis. Nine pathogenic strains of different serotypes and different geographical distribution were analyzed to better understand the differences in their evolutionary process. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A/T-ending codons are dominant in S. suis. Neutrality analysis, correspondence analysis and ENC-plot results revealed that natural selection is the predominant element prompting codon usage. Cluster analysis based on RSCU was roughly consistent with the dendrogram rooted genomic BLAST analysis. Comparison of synonymous codon usage pattern between S. suis and susceptible hosts (H. sapiens and S. scrofa) revealed that the codon usage of S. suis is separated from the synonymous codon usage of susceptible hosts. The CAI values implied that S. suis includes a series of predicted highly expressed coding sequences contained in metabolism and transcriptional regulation, revealing the necessity of this pathogen to deal with various environmental conditions. The study of codon usage in S. suis may provide evidence involving the molecular evolution of bacteria and a better understanding of evolutionary relationships between S. suis and its corresponding hosts.

Comparative genome-wide analysis of codon usage of different bacterial species infecting Oryza sativa

Oryza sativa is vastly affected by microbial pathogen, causing blight-related diseases, which in turn deplete the growth and productivity of rice. In this study, we analyzed four bacterial rice pathogen genomes and reported on their codon usage that might have greater implication in mutation-related research. Differential codon usage indices, such as codon adaptation index (CAI), codon bias index (CBI), effective number of codons (ENc), relative synonymous codon usage (RSCU), correspondence analysis (COA), and parity plots, were applied on coding sequences of Pseudomonas fuscovaginae, Pseudomonas syringae, Xanthomonas oryzae, and Pseudomonas avenae speices. The RSCU results proposed a high-frequency usage of CUG and CGC that codes for leucine and arginine in all of the species. The CBI and CAI values between the genomes range from 0.17 to 0.3 and from 0.26 to 0.35, respectively, indicating a direct proportionality between these indexes. The mean ENc value of P. avenae coding sequence showed high codon bias compared with other genomes. The axis I variation from COA analysis shows a mean value of 42.28% codon variations in these bacterial species. Correlation studies between axis I and ENc-GC3, along with CAI and CBI, suggested the presence of nucleotide bias and mutational pressure as major forces for codon bias within these species. Hence, certain genes with high CAI-CBI have been correlated for better gene expression. Our study highlights the importance of nucleotide biasness, mutation pressure, and natural selection in shaping protein-coding genes in these four rice-affecting bacteria. This would further help in investigating the evolution of pathogenic gene families, which may direct research toward synthetic genes that could be suppressed or overrepresented based on their codon usage pattern toward pathogenicity.

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G₃, GC₁₂, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A₃/(A₃ + T₃) and G₃/(G₃ + C₃), GC₁₂ versus GC₃ plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC₃ and GC₁₂) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times

Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, suggests that the average codon translation-rate per gene can vary widely. Yet, ribosome run-off experiments have found that the average codon translation rate for different groups of transcripts in mouse stem cells is constant at 5.6 AA/s. How these seemingly contradictory results can be reconciled is the focus of this study. Here, we combine knowledge of the molecular factors shown to influence translation speed with genomic information from Escherichia coli, Saccharomyces cerevisiae and Homo sapiens to simulate the synthesis of cytosolic proteins in these organisms. The model recapitulates a near constant average translation rate, which we demonstrate arises because the molecular determinants of translation speed are distributed nearly randomly amongst most of the transcripts. Consequently, codon translation rates are also randomly distributed and fast-translating segments of a transcript are likely to be offset by equally probable slow-translating segments, resulting in similar average elongation rates for most transcripts. We also show that the codon usage bias does not significantly affect the near random distribution of codon translation rates because only about 10% of the total transcripts in an organism have high codon usage bias while the rest have little to no bias. Analysis of Ribo-Seq data and an in vivo fluorescent assay supports these conclusions.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

Nucleotide and amino acid compositions were studied to determine the genomic and structural relationship of photolyase gene in freshwater, marine and hot spring cyanobacteria. Among three habitats, photolyase encoding genes from hot spring cyanobacteria were found to have highest GC content. The genomic GC content was found to influence the codon usage and amino acid variability in photolyases. The third position of codon was found to have more effect on amino acid variability in photolyases than the first and second positions of codon. The variation of amino acids Ala, Asp, Glu, Gly, His, Leu, Pro, Gln, Arg and Val in photolyases of three different habitats was found to be controlled by first position of codon (G1C1). However, second position (G2C2) of codon regulates variation of Ala, Cys, Gly, Pro, Arg, Ser, Thr and Tyr contents in photolyases. Third position (G3C3) of codon controls incorporation of amino acids such as Ala, Phe, Gly, Leu, Gln, Pro, Arg, Ser, Thr and Tyr in photolyases from three habitats. Photolyase encoding genes of hot spring cyanobacteria have 85% codons with G or C at third position, whereas marine and freshwater cyanobacteria showed 82 and 60% codons, respectively, with G or C at third position. Principal component analysis (PCA) showed that GC content has a profound effect in separating the genes along the first major axis according to their RSCU (relative synonymous codon usage) values, and neutrality analysis indicated that mutational pressure has resulted in codon bias in photolyase genes of cyanobacteria.