The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1

Identification and Expression Profile of NCED Genes in Arachis hypogaea L. during Drought Stress

Peanut (Arachis hypogaea L.) is an important crop that provides essential proteins and oils for human and animal consumption. 9-cis-epoxycarotenoid dioxygenase (NCED) have been found can play a vital role in abscisic acid (ABA) biosynthesis and may be a response to drought stress. Until now, in Arachis hypogaea, no information about the NCED gene family has been reported and the importance of NCED-related drought tolerance is unclear. In this study, eight NCED genes in Arachis hypogaea, referred to as AhNCEDs, are distributed across eight chromosomes, with duplication events in AhNCED1 and AhNCED2, AhNCED3 and AhNCED4, and AhNCED6 and AhNCED7. Comparative analysis revealed that NCED genes are highly conserved among plant species, including Pisum sativum, Phaseolus vulgaris, Glycine max, Arabidopsis thaliana, Gossypium hirsutum, and Oryza sativa. Further promoter analysis showed AhNCEDs have ABA-related and drought-inducible elements. The phenotyping of Arachis hypogaea cultivars NH5 and FH18 demonstrated that NH5 is drought-tolerant and FH18 is drought-sensitive. Transcriptome expression analysis revealed the differential regulation of AhNCEDs expression in both NH5 and FH18 cultivars under drought stress. Furthermore, compared to the Arachis hypogaea cultivar FH18, the NH5 exhibited a significant upregulation of AhNCED1/2 expression under drought. To sum up, this study provides an insight into the drought-related AhNCED genes, screened out the potential candidates to regulate drought tolerance and ABA biosynthesis in Arachis hypogaea.

Using Machine Learning to Predict Genes Underlying Differentiation of Multipartite and Unipartite Traits in Bacteria

Since the discovery of the second chromosome in the Rhodobacter sphaeroides 2.4.1 by Suwanto and Kaplan in 1989 and the revelation of gene sequences, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This phenomenon shattered the dogma of a unipartite genome (a single circular chromosome) in bacteria. Recently, Artificial Intelligence (AI), machine learning (ML), and Deep Learning (DL) have emerged as powerful tools in the investigation of big data in a plethora of disciplines to decipher complex patterns in these data, including the large-scale analysis and interpretation of genomic data. An important inquiry in bacteriology pertains to the genetic factors that underlie the structural evolution of multipartite and unipartite bacterial species. Towards this goal, here we have attempted to leverage machine learning as a means to identify the genetic factors that underlie the differentiation of, in general, bacteria with multipartite genomes and bacteria with unipartite genomes. In this study, deploying ML algorithms yielded two gene lists of interest: one that contains 46 discriminatory genes obtained following an assessment on all gene sets, and another that contains 35 discriminatory genes obtained based on an investigation of genes that are differentially present (or absent) in the genomes of the multipartite bacteria and their respective close relatives. Our study revealed a small pool of genes that discriminate bacteria with multipartite genomes and their close relatives with single-chromosome genomes. Machine learning thus aided in uncovering the genetic factors that underlie the differentiation of bacterial multipartite and unipartite traits.

Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines

Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.

Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats

Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.

Replicate Once Per Cell Cycle: Replication Control of Secondary Chromosomes

Faithful vertical transmission of genetic information, especially of essential core genes, is a prerequisite for bacterial survival. Hence, replication of all the replicons is tightly controlled to ensure that all daughter cells get the same genome copy as their mother cell. Essential core genes are very often carried by the main chromosome. However they can occasionally be found on secondary chromosomes, recently renamed chromids. Chromids have evolved from non-essential megaplasmids, and further acquired essential core genes and a genomic signature closed to that of the main chromosome. All chromids carry a plasmidic replication origin, belonging so far to either the iterons or repABC type. Based on these differences, two categories of chromids have been distinguished. In this review, we focus on the replication initiation controls of these two types of chromids. We show that the sophisticated mechanisms controlling their replication evolved from their plasmid counterparts to allow a timely controlled replication, occurring once per cell cycle.

The Divided Bacterial Genome: Structure, Function, and Evolution

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.

Distribution and diversity of ribosome binding sites in prokaryotic genomes

BACKGROUND

Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction between Shine-Dalgarno (SD) sequence and its complementary sequence in the 16S rRNA is important in initiation, some genes lacking an SD ribosome binding site (RBS) are still well expressed. The objective of this study is to examine the pattern of distribution and diversity of RBS in fully sequenced bacterial genomes. The following three hypotheses were tested: SD motifs are prevalent in bacterial genomes; all previously identified SD motifs are uniformly distributed across prokaryotes; and genes with specific cluster of orthologous gene (COG) functions differ in their use of SD motifs.

RESULTS

Data for 2,458 bacterial genomes, previously generated by Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm) and currently available at the National Center for Biotechnology Information (NCBI), were analyzed. Of the total genes examined, ~77.0% use an SD RBS, while ~23.0% have no RBS. Majority of the genes with the most common SD motifs are distributed in a manner that is representative of their abundance for each COG functional category, while motifs 13 (5'-GGA-3'/5'-GAG-3'/5'-AGG-3') and 27 (5'-AGGAGG-3') appear to be predominantly used by genes for information storage and processing, and translation and ribosome biogenesis, respectively.

CONCLUSION

These findings suggest that an SD sequence is not obligatory for translation initiation; instead, other signals, such as the RBS spacer, may have an overarching influence on translation of mRNAs. Subsequent analyses of the 5' secondary structure of these mRNAs may provide further insight into the translation initiation mechanism.

Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1

Background

Gene duplication is a major force that contributes to the evolution of new metabolic functions in all organisms. Rhodobacter sphaeroides 2.4.1 is a bacterium that displays a wide degree of metabolic versatility and genome complexity and therefore is a fitting model for the study of gene duplications in bacteria. A comprehensive analysis of 234 duplicate gene-pairs in R. sphaeroides was performed using structural constraint and expression analysis.

Results

The results revealed that most gene-pairs in in-paralogs are maintained under negative selection (ω ≤ 0.3), but the strength of selection differed among in-paralog gene-pairs. Although in-paralogs located on different replicons are maintained under purifying selection, the duplicated genes distributed between the primary chromosome (CI) and the second chromosome (CII) are relatively less selectively constrained than the gene-pairs located within each chromosome. The mRNA expression patterns of duplicate gene-pairs were examined through microarray analysis of this organism grown under seven different growth conditions. Results revealed that ~62% of paralogs have similar expression patterns (cosine ≥ 0.90) over all of these growth conditions, while only ~7% of paralogs are very different in their expression patterns (cosine < 0.50).

Conclusions

The overall findings of the study suggest that only a small proportion of paralogs contribute to the metabolic diversity and the evolution of novel metabolic functions in R. sphaeroides. In addition, the lack of relationships between structural constraints and gene-pair expression suggests that patterns of gene-pair expression are likely associated with conservation or divergence of gene-pair promoter regions and other coregulation mechanisms.